has_not_completed
type: ObjectProperty

lacks_part
type: ObjectProperty
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y

lacks_plasma_membrane_part
type: ObjectProperty
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)

cell
type: Class
subclass of: UBERON_0000061
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_131567
disjoint with: GO_0031012
disjoint with: GO_0032991
disjoint with: GO_0043226
disjoint with: GO_0044423
IAO_0000115: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has db xref: CALOHA:TS-2035
has db xref: FBbt:00007002
has db xref: FMA:68646
has db xref: GO:0005623
has db xref: KUPO:0000002
has db xref: MESH:D002477
has db xref: VHOG:0001533
has db xref: WBbt:0004017
has db xref: XAO:0003012
has db xref: ZFA:0009000
in subset: cellxgene subset
in subset: upper level
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

Axiom
annotated source: cell
annotated property: IAO_0000115
annotated target: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has db xref: CARO:mah

Axiom
annotated source: cell
annotated property: hasDbXref
annotated target: FBbt:00007002
mapping justification: ManualMappingCuration

Axiom
annotated source: cell
annotated property: hasDbXref
annotated target: ZFA:0009000
mapping justification: UnspecifiedMatching

neural crest derived fibroblast
type: Class
equivalent class: Class
  intersection of: fibroblast
  intersection of: Restriction
    on property: RO_0002202
    some values from: migratory neural crest cell
subclass of: fibroblast
subclass of: Restriction
  on property: RO_0002202
  some values from: migratory cranial neural crest cell
IAO_0000115: Any fibroblast that is derived from the neural crest.
has exact synonym: fibroblast neural crest derived

Axiom
annotated source: neural crest derived fibroblast
annotated property: IAO_0000115
annotated target: Any fibroblast that is derived from the neural crest.
has db xref: https://orcid.org/0000-0001-5208-3432

neuronal receptor cell
type: Class
equivalent class: Class
  intersection of: sensory receptor cell
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050906
subclass of: sensory neuron
subclass of: sensory receptor cell
IAO_0000115: Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.
has db xref: ZFA:0009001
has exact synonym: neuronal receptor cell (sensu Animalia)
in subset: cellxgene subset

Axiom
annotated source: neuronal receptor cell
annotated property: IAO_0000115
annotated target: Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.
has db xref: FBC:Autogenerated

Axiom
annotated source: neuronal receptor cell
annotated property: hasDbXref
annotated target: ZFA:0009001
mapping justification: UnspecifiedMatching

early embryonic cell (metazoa)
type: Class
subclass of: CL_0002321
IAO_0000115: A cell found in the embryo before the formation of all the germ layers is complete.
has db xref: ZFA:0009002

Axiom
annotated source: early embryonic cell (metazoa)
annotated property: IAO_0000115
annotated target: A cell found in the embryo before the formation of all the germ layers is complete.
has db xref: GOC:tfm

Axiom
annotated source: early embryonic cell (metazoa)
annotated property: hasDbXref
annotated target: ZFA:0009002
mapping justification: UnspecifiedMatching

migratory cranial neural crest cell
type: Class
subclass of: migratory neural crest cell
IAO_0000115: Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
has db xref: ZFA:0007091

Axiom
annotated source: migratory cranial neural crest cell
annotated property: IAO_0000115
annotated target: Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
has db xref: ZFA:0007091
has db xref: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: migratory cranial neural crest cell
annotated property: hasDbXref
annotated target: ZFA:0007091
mapping justification: UnspecifiedMatching

migratory trunk neural crest cell
type: Class
subclass of: migratory neural crest cell
IAO_0000115: Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
has db xref: ZFA:0007095

Axiom
annotated source: migratory trunk neural crest cell
annotated property: IAO_0000115
annotated target: Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
has db xref: ZFA:0007095
has db xref: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: migratory trunk neural crest cell
annotated property: hasDbXref
annotated target: ZFA:0007095
mapping justification: UnspecifiedMatching

germ line stem cell
type: Class
equivalent class: Class
  intersection of: germ line cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0017145
subclass of: stem cell
subclass of: germ line cell
IAO_0000115: A stem cell that is the precursor of gametes.
has db xref: FBbt:00004861
has db xref: ZFA:0005956
has exact synonym: germline stem cell

Axiom
annotated source: germ line stem cell
annotated property: subClassOf
annotated target: stem cell
is inferred: true

Axiom
annotated source: germ line stem cell
annotated property: IAO_0000115
annotated target: A stem cell that is the precursor of gametes.
has db xref: doi:10.1016/j.stem.2012.05.016

Axiom
annotated source: germ line stem cell
annotated property: hasDbXref
annotated target: FBbt:00004861
mapping justification: ManualMappingCuration

Axiom
annotated source: germ line stem cell
annotated property: hasDbXref
annotated target: ZFA:0005956
mapping justification: UnspecifiedMatching

male germ cell
type: Class
subclass of: germ cell
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0007283
IAO_0000115: A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis.
description: Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:72290
has db xref: MA:0002765
has db xref: VHOG:0001531
has db xref: ncithesaurus:Spermatogenic_Cell
in subset: cellxgene subset

Axiom
annotated source: male germ cell
annotated property: subClassOf
annotated target: germ cell
is inferred: true

Axiom
annotated source: male germ cell
annotated property: IAO_0000115
annotated target: A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis.
has db xref: PMID:29462262
has db xref: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: male germ cell
annotated property: description
annotated target: Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/S0092-8674(00)81834-6
has db xref: DOI:10.1016/S1534-5807(02)00173-9
has db xref: DOI:10.1242/dev.202046
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK553142/

male germ cell on CELLxGENE CellGuide
type: Axiom
annotated source: male germ cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000015

male germ line stem cell
type: Class
subclass of: germ line stem cell
subclass of: male germ cell
IAO_0000115: A stem cell that is the precursor of male gametes.
has db xref: FBbt:00004929

Axiom
annotated source: male germ line stem cell
annotated property: IAO_0000115
annotated target: A stem cell that is the precursor of male gametes.
has db xref: doi:10.1016/j.stem.2012.05.016

Axiom
annotated source: male germ line stem cell
annotated property: hasDbXref
annotated target: FBbt:00004929
mapping justification: ManualMappingCuration

spermatocyte
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048137
subclass of: BFO_0000002
subclass of: male germ cell
subclass of: Restriction
  on property: RO_0002202
  some values from: spermatogonium
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048137
IAO_0000115: A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
has db xref: BTO:0001275
has db xref: CALOHA:TS-0951
has db xref: EMAPA:31484
has db xref: FBbt:00004936
has db xref: FMA:84049
has db xref: WBbt:0006799
has db xref: ZFA:0009005
in subset: cellxgene subset

Axiom
annotated source: spermatocyte
annotated property: IAO_0000115
annotated target: A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
has db xref: GOC:tfm
has db xref: MESH:D013090

Axiom
annotated source: spermatocyte
annotated property: hasDbXref
annotated target: FBbt:00004936
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatocyte
annotated property: hasDbXref
annotated target: ZFA:0009005
mapping justification: UnspecifiedMatching

spermatid
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001375
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001675
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007288
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007289
subclass of: BFO_0000002
subclass of: male germ cell
subclass of: eukaryotic cell
subclass of: haploid cell
subclass of: Restriction
  on property: RO_0002202
  some values from: secondary spermatocyte
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001675
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007288
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007289
IAO_0000115: A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
has db xref: BTO:0001274
has db xref: CALOHA:TS-0950
has db xref: EMAPA:31486
has db xref: FBbt:00004942
has db xref: FMA:72294
has db xref: WBbt:0006800
has db xref: ZFA:0005769
has exact synonym: nematoblast
in subset: cellxgene subset

Axiom
annotated source: spermatid
annotated property: IAO_0000115
annotated target: A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
has db xref: MESH:D013087

Axiom
annotated source: spermatid
annotated property: hasDbXref
annotated target: FBbt:00004942
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatid
annotated property: hasDbXref
annotated target: ZFA:0005769
mapping justification: UnspecifiedMatching

sperm
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: male gamete
subclass of: Restriction
  on property: RO_0002202
  some values from: spermatid
IAO_0000115: A mature male germ cell that develops from a spermatid.
description: Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001277
has db xref: BTO:0002046
has db xref: CALOHA:TS-0949
has db xref: FBbt:00004954
has db xref: FMA:67338
has db xref: WBbt:0006798
has db xref: ZFA:0009006
has exact synonym: sperm cell
has exact synonym: spermatozoid
has exact synonym: spermatozoon

Axiom
annotated source: sperm
annotated property: subClassOf
annotated target: male gamete
is inferred: true

Axiom
annotated source: sperm
annotated property: IAO_0000115
annotated target: A mature male germ cell that develops from a spermatid.
has db xref: GOC:tfm
has db xref: MESH:D013094

Axiom
annotated source: sperm
annotated property: description
annotated target: Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1080/19420889.2015.1017156
has db xref: DOI:10.1152/physrev.00009.2020
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK26914/

Axiom
annotated source: sperm
annotated property: hasDbXref
annotated target: FBbt:00004954
mapping justification: ManualMappingCuration

Axiom
annotated source: sperm
annotated property: hasDbXref
annotated target: ZFA:0009006
mapping justification: UnspecifiedMatching

sperm on CELLxGENE CellGuide
type: Axiom
annotated source: sperm
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000019

spermatogonium
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001394
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001501
subclass of: male germ cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001394
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001501
IAO_0000115: An euploid male germ cell of an early stage of spermatogenesis.
has db xref: BTO:0000958
has db xref: CALOHA:TS-2193
has db xref: EMAPA:31482
has db xref: FBbt:00004934
has db xref: FBbt:00004935
has db xref: FMA:72291
has db xref: ZFA:0009007
has exact synonym: spermatogonial cell
in subset: cellxgene subset

Axiom
annotated source: spermatogonium
annotated property: IAO_0000115
annotated target: An euploid male germ cell of an early stage of spermatogenesis.
has db xref: MESH:D013093

Axiom
annotated source: spermatogonium
annotated property: hasDbXref
annotated target: FBbt:00004934
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatogonium
annotated property: hasDbXref
annotated target: FBbt:00004935
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatogonium
annotated property: hasDbXref
annotated target: ZFA:0009007
mapping justification: UnspecifiedMatching

female germ cell
type: Class
equivalent class: Class
  intersection of: germ cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048477
subclass of: eukaryotic cell
subclass of: germ cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048477
IAO_0000115: Female germ cell is a germ cell that supports female gamete production.
has db xref: MA:0000388
has db xref: VHOG:0001530
has db xref: ncithesaurus:Egg
in subset: cellxgene subset

Axiom
annotated source: female germ cell
annotated property: subClassOf
annotated target: germ cell
is inferred: true

Axiom
annotated source: female germ cell
annotated property: IAO_0000115
annotated target: Female germ cell is a germ cell that supports female gamete production.
has db xref: GOC:tfm
has db xref: PMID:11023867
has db xref: PMID:20454446

female germ line stem cell
type: Class
equivalent class: Class
  intersection of: female germ cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0017145
subclass of: germ line stem cell
subclass of: female germ cell
IAO_0000115: A stem cell that is the precursor of female gametes.
has db xref: FBbt:00004873

Axiom
annotated source: female germ line stem cell
annotated property: subClassOf
annotated target: germ line stem cell
is inferred: true

Axiom
annotated source: female germ line stem cell
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

Axiom
annotated source: female germ line stem cell
annotated property: IAO_0000115
annotated target: A stem cell that is the precursor of female gametes.
has db xref: doi:10.1016/j.stem.2012.05.016

Axiom
annotated source: female germ line stem cell
annotated property: hasDbXref
annotated target: FBbt:00004873
mapping justification: ManualMappingCuration

oocyte
type: Class
subclass of: BFO_0000002
subclass of: female germ cell
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0007143
IAO_0000115: A female germ cell that has entered meiosis.
has db xref: BTO:0000964
has db xref: CALOHA:TS-0711
has db xref: FBbt:00004886
has db xref: FMA:18644
has db xref: MESH:D009865
has db xref: WBbt:0006797
has db xref: ZFA:0001109
has related synonym: oogonium
in subset: cellxgene subset

Axiom
annotated source: oocyte
annotated property: IAO_0000115
annotated target: A female germ cell that has entered meiosis.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: oocyte
annotated property: hasDbXref
annotated target: FBbt:00004886
mapping justification: ManualMappingCuration

Axiom
annotated source: oocyte
annotated property: hasDbXref
annotated target: ZFA:0001109
mapping justification: UnspecifiedMatching

Axiom
annotated source: oocyte
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

oogonial cell
type: Class
equivalent class: Class
  intersection of: female germ cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0000278
subclass of: BFO_0000002
subclass of: female germ cell
subclass of: Restriction
  on property: RO_0002202
  some values from: primordial germ cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0000278
IAO_0000115: An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
has db xref: FMA:83673
has db xref: ZFA:0005878
in subset: cellxgene subset

Axiom
annotated source: oogonial cell
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

Axiom
annotated source: oogonial cell
annotated property: IAO_0000115
annotated target: An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: oogonial cell
annotated property: hasDbXref
annotated target: ZFA:0005878
mapping justification: UnspecifiedMatching

egg cell
type: Class
subclass of: BFO_0000002
subclass of: female gamete
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0007143
subclass of: Restriction
  on property: RO_0002202
  some values from: oocyte
IAO_0000115: A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization.
has db xref: BTO:0000369
has db xref: BTO:0003801
has db xref: CALOHA:TS-2191
has db xref: FBbt:00057012
has db xref: FMA:67343
has db xref: MESH:D010063
has db xref: ZFA:0001570
has exact synonym: mature oocyte
has exact synonym: ovum

Axiom
annotated source: egg cell
annotated property: subClassOf
annotated target: female gamete
is inferred: true

Axiom
annotated source: egg cell
annotated property: IAO_0000115
annotated target: A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: egg cell
annotated property: hasDbXref
annotated target: FBbt:00057012
mapping justification: ManualMappingCuration

Axiom
annotated source: egg cell
annotated property: hasDbXref
annotated target: ZFA:0001570
mapping justification: UnspecifiedMatching

invertebrate nurse cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: polyploid cell
subclass of: CL_4029002
subclass of: Restriction
  on property: RO_0002202
  some values from: cystoblast
IAO_0000115: A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte.
has db xref: BTO:0000953
has db xref: FBbt:00004878
has related synonym: nurse cell

Axiom
annotated source: invertebrate nurse cell
annotated property: IAO_0000115
annotated target: A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte.
has db xref: GOC:tfm
has db xref: PMID:15848391

Axiom
annotated source: invertebrate nurse cell
annotated property: hasDbXref
annotated target: FBbt:00004878
mapping justification: ManualMappingCuration

smooth muscle cell neural crest derived
type: Class
equivalent class: Class
  intersection of: smooth muscle cell
  intersection of: Restriction
    on property: RO_0002202
    some values from: migratory neural crest cell
subclass of: smooth muscle cell
subclass of: Restriction
  on property: RO_0002202
  some values from: migratory cranial neural crest cell
IAO_0000115: A smooth muscle cell derived from the neural crest.

Axiom
annotated source: smooth muscle cell neural crest derived
annotated property: subClassOf
annotated target: smooth muscle cell
is inferred: true

Axiom
annotated source: smooth muscle cell neural crest derived
annotated property: IAO_0000115
annotated target: A smooth muscle cell derived from the neural crest.
has db xref: https://orcid.org/0000-0001-5208-3432

neural crest derived neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002202
    some values from: migratory neural crest cell
subclass of: BFO_0000002
subclass of: neuron
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002676
IAO_0000115: Any neuron that develops from some migratory neural crest cell.
has db xref: ZFA:0009009
has exact synonym: neuron neural crest derived
in subset: cellxgene subset

Axiom
annotated source: neural crest derived neuron
annotated property: subClassOf
annotated target: neuron
is inferred: true

Axiom
annotated source: neural crest derived neuron
annotated property: IAO_0000115
annotated target: Any neuron that develops from some migratory neural crest cell.
has db xref: FBC:Autogenerated

Axiom
annotated source: neural crest derived neuron
annotated property: hasDbXref
annotated target: ZFA:0009009
mapping justification: UnspecifiedMatching

glioblast
type: Class
subclass of: eukaryotic cell
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002202
  some values from: neurectodermal cell
IAO_0000115: A non-terminally differentiated cell that develops from the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes.
description: Glioblasts are primarily found in the central nervous system and are an integral part of the developing and mature brain tissue. They are primitive progenitor cells with the ability to self-renew and can differentiate into neuroglia, including astrocytes and oligodendrocytes, two primary cells involved in neurotransmission and protection of brain tissue. When glioblast multiplication is dysregulated, it can lead to harmful manifestations, most notably in the form of an aggressive brain tumor known as Glioblastoma multiforme, one of the most malignant types of neural cancers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009010
in subset: cellxgene subset

Axiom
annotated source: glioblast
annotated property: IAO_0000115
annotated target: A non-terminally differentiated cell that develops from the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes.
has db xref: PMID:37824650
has db xref: Wikipedia:Glioblast

Axiom
annotated source: glioblast
annotated property: description
annotated target: Glioblasts are primarily found in the central nervous system and are an integral part of the developing and mature brain tissue. They are primitive progenitor cells with the ability to self-renew and can differentiate into neuroglia, including astrocytes and oligodendrocytes, two primary cells involved in neurotransmission and protection of brain tissue. When glioblast multiplication is dysregulated, it can lead to harmful manifestations, most notably in the form of an aggressive brain tumor known as Glioblastoma multiforme, one of the most malignant types of neural cancers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1073/pnas.97.12.6242
has db xref: DOI:10.1186/s13064-016-0075-9
has db xref: DOI:10.12688/f1000research.22405.1
has db xref: DOI:10.4252/wjsc.v6.i2.230

Axiom
annotated source: glioblast
annotated property: hasDbXref
annotated target: ZFA:0009010
mapping justification: UnspecifiedMatching

glioblast on CELLxGENE CellGuide
type: Axiom
annotated source: glioblast
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000030

neuroblast (sensu Vertebrata)
type: Class
subclass of: eukaryotic cell
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
IAO_0000115: A cell that will develop into a neuron often after a migration phase.
has db xref: BTO:0000930
has db xref: FMA:70563
has db xref: ZFA:0009011
has exact synonym: neuroblast
in subset: cellxgene subset

Axiom
annotated source: neuroblast (sensu Vertebrata)
annotated property: IAO_0000115
annotated target: A cell that will develop into a neuron often after a migration phase.
has db xref: GOC:NV
has db xref: http://en.wikipedia.org/wiki/Neuroblast

Axiom
annotated source: neuroblast (sensu Vertebrata)
annotated property: hasDbXref
annotated target: ZFA:0009011
mapping justification: UnspecifiedMatching

stem cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0017145
subclass of: CL_0011115
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0017145
IAO_0000115: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
description: Stem cells are a unique type of cell that has the remarkable ability to divide and develop into many different types of cells in the body. These cells are undifferentiated, meaning they haven't yet developed into a specific cell type, and they can renew themselves through cell division. As a result, stem cells have the potential to replace damaged or diseased cells in the body, making them a valuable tool in medicine and research. There are two main types of stem cells: embryonic stem cells and adult stem cells. Embryonic stem cells are derived from embryos and can develop into any type of cell in the body. Adult stem cells, on the other hand, are found in various tissues and organs throughout the body and can only develop into certain types of cells. Stem cells have numerous potential applications in medicine, including the treatment of various diseases and the repair of damaged tissues. For example, they could be used to replace damaged heart tissue after a heart attack or to repair spinal cord injuries. Stem cells also have potential uses in drug development and disease research, as they can be used to model diseases and test potential therapies in vitro. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: CALOHA:TS-2086
has db xref: FMA:63368
has db xref: ZFA:0005957
has narrow synonym: animal stem cell
in subset: cellxgene subset
in subset: general cell types upper slim
in subset: human reference atlas

Axiom
annotated source: stem cell
annotated property: IAO_0000115
annotated target: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
has db xref: GOC:tfm
has db xref: MESH:D013234

Axiom
annotated source: stem cell
annotated property: description
annotated target: Stem cells are a unique type of cell that has the remarkable ability to divide and develop into many different types of cells in the body. These cells are undifferentiated, meaning they haven't yet developed into a specific cell type, and they can renew themselves through cell division. As a result, stem cells have the potential to replace damaged or diseased cells in the body, making them a valuable tool in medicine and research. There are two main types of stem cells: embryonic stem cells and adult stem cells. Embryonic stem cells are derived from embryos and can develop into any type of cell in the body. Adult stem cells, on the other hand, are found in various tissues and organs throughout the body and can only develop into certain types of cells. Stem cells have numerous potential applications in medicine, including the treatment of various diseases and the repair of damaged tissues. For example, they could be used to replace damaged heart tissue after a heart attack or to repair spinal cord injuries. Stem cells also have potential uses in drug development and disease research, as they can be used to model diseases and test potential therapies in vitro. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.cell.2016.05.043
has db xref: DOI:10.1016/j.cell.2018.09.010
has db xref: DOI:10.1016/j.stem.2023.05.015
has db xref: DOI:10.1038/nm.4502
has db xref: https://www.mayoclinic.org/tests-procedures/bone-marrow-transplant/in-depth/stem-cells/art-20048117#:~:text=These%20stem%20cells%20are%20manipulated,injected%20into%20the%20heart%20muscle.

Axiom
annotated source: stem cell
annotated property: hasDbXref
annotated target: ZFA:0005957
mapping justification: UnspecifiedMatching

stem cell on CELLxGENE CellGuide
type: Axiom
annotated source: stem cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000034

single fate stem cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001400
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0017145
subclass of: somatic stem cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001400
IAO_0000115: A stem cell that self-renews as well as give rise to a single mature cell type.
description: Single fate stem cells, or unipotent stem cells, constitute a distinctive subtype among the diverse range of stem cells, exhibiting significant biological roles and applications. These cells possess the inherent ability to self-renew and generate a single, specialized cell lineage exclusive to their nature, reflecting their unipotent or single fate characteristic. Engaged in the maintenance and regeneration of specific tissues or organs, these stem cells play a crucial role as pivotal contributors to the body's self-maintenance and repair mechanisms. Single fate stem cells play a crucial role in the body's diverse tissues by ensuring the appropriate renewal and repair mechanisms specific to their respective tissues. For example, the human skin, where basal cells located at the base layer of the epidermis act as single fate stem cells. These basal cells continuously generate new keratinocytes, replacing the older ones shed from the skin surface. This perpetual cycle of renewal exemplifies the fundamental function of single fate stem cells—specialized cellular regeneration to uphold tissue homeostasis and function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:70569
has db xref: ZFA:0009013
has exact synonym: unipotent stem cell
has exact synonym: unipotential stem cell

Axiom
annotated source: single fate stem cell
annotated property: IAO_0000115
annotated target: A stem cell that self-renews as well as give rise to a single mature cell type.
has db xref: GOC:tfm

Axiom
annotated source: single fate stem cell
annotated property: description
annotated target: Single fate stem cells, or unipotent stem cells, constitute a distinctive subtype among the diverse range of stem cells, exhibiting significant biological roles and applications. These cells possess the inherent ability to self-renew and generate a single, specialized cell lineage exclusive to their nature, reflecting their unipotent or single fate characteristic. Engaged in the maintenance and regeneration of specific tissues or organs, these stem cells play a crucial role as pivotal contributors to the body's self-maintenance and repair mechanisms. Single fate stem cells play a crucial role in the body's diverse tissues by ensuring the appropriate renewal and repair mechanisms specific to their respective tissues. For example, the human skin, where basal cells located at the base layer of the epidermis act as single fate stem cells. These basal cells continuously generate new keratinocytes, replacing the older ones shed from the skin surface. This perpetual cycle of renewal exemplifies the fundamental function of single fate stem cells—specialized cellular regeneration to uphold tissue homeostasis and function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.cps.2017.02.020
has db xref: DOI:10.52965/001c.37498
has db xref: https://training.seer.cancer.gov/melanoma/anatomy/layers.html
has db xref: https://www.sciencedirect.com/topics/immunology-and-microbiology/stem-cell

Axiom
annotated source: single fate stem cell
annotated property: hasDbXref
annotated target: ZFA:0009013
mapping justification: UnspecifiedMatching

single fate stem cell on CELLxGENE CellGuide
type: Axiom
annotated source: single fate stem cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000035

epithelial fate stem cell
type: Class
equivalent class: Class
  intersection of: somatic stem cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030855
subclass of: eukaryotic cell
subclass of: somatic stem cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030855
IAO_0000115: A somatic stem cell that is committed to an epithelial fate, possessing the capacity for self-renewal and the ability to differentiate into one or more distinct mature cell types of the epithelial lineage. This cell is crucial for the development, homeostasis, repair, and regeneration of epithelial tissues.
description: Epithelial fate stem cells, also known as epithelial stem cells, possess remarkable abilities for self-renewal and the generation of diverse cell types constituting epithelial tissues. The epithelium, derived from these cells, acts as the body's frontline defense against external threats and facilitates the exchange of nutrients, gases, and waste materials within the internal environment. Epithelial fate stem cells contribute to tissue development, homeostasis, and repair, maintaining the structural and functional stability of epithelial tissues throughout the human body, including the skin, organs, and glands. Through a delicate balance of quiescence, proliferation, and differentiation, these cells ensure the continuous turnover of epithelial cells. Furthermore, these cells serve a critical role in cellular differentiation, where initially unspecialized stem cells mature into specialized entities that perpetuate the functionality of epithelial tissues. This process is intricately regulated by a network of gene expression patterns and external signaling cues to guarantee a coordinated and balanced cellular turnover. Hence, epithelial fate stem cells, with their unique attributes of self-renewal and differentiation, are central to the physiological and reparative functions performed by epithelial tissues in the human body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: epithelial stem cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: epithelial fate stem cell
annotated property: IAO_0000115
annotated target: A somatic stem cell that is committed to an epithelial fate, possessing the capacity for self-renewal and the ability to differentiate into one or more distinct mature cell types of the epithelial lineage. This cell is crucial for the development, homeostasis, repair, and regeneration of epithelial tissues.
has db xref: PMID:17289566
has db xref: doi:/10.1038/sj.eye.6700575

Axiom
annotated source: epithelial fate stem cell
annotated property: description
annotated target: Epithelial fate stem cells, also known as epithelial stem cells, possess remarkable abilities for self-renewal and the generation of diverse cell types constituting epithelial tissues. The epithelium, derived from these cells, acts as the body's frontline defense against external threats and facilitates the exchange of nutrients, gases, and waste materials within the internal environment. Epithelial fate stem cells contribute to tissue development, homeostasis, and repair, maintaining the structural and functional stability of epithelial tissues throughout the human body, including the skin, organs, and glands. Through a delicate balance of quiescence, proliferation, and differentiation, these cells ensure the continuous turnover of epithelial cells. Furthermore, these cells serve a critical role in cellular differentiation, where initially unspecialized stem cells mature into specialized entities that perpetuate the functionality of epithelial tissues. This process is intricately regulated by a network of gene expression patterns and external signaling cues to guarantee a coordinated and balanced cellular turnover. Hence, epithelial fate stem cells, with their unique attributes of self-renewal and differentiation, are central to the physiological and reparative functions performed by epithelial tissues in the human body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.cell.2007.01.014
has db xref: DOI:10.1016/j.celrep.2022.111451
has db xref: DOI:10.1016/j.stem.2020.09.011
has db xref: DOI:10.1038/nrm2766

epithelial fate stem cell on CELLxGENE CellGuide
type: Axiom
annotated source: epithelial fate stem cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000036

hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002244
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048103
subclass of: eukaryotic cell
subclass of: somatic stem cell
subclass of: CL_0008001
subclass of: CL_0011026
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: RO_0002202
  some values from: angioblastic mesenchymal cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002244
IAO_0000115: A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
description: Hematopoietic stem cells (HSCs) are multipotent cells, capable of differentiating into a wide variety of specialized blood cells. During embryonic development hematopoietic stem cells emerge from the hemogenic endothelium, a specialized subset of endothelial cells with hematopoietic potential. HSCs can be found in several organs, in particular in bone marrow, as well as peripheral blood and umbilical cord blood. These stem cells have a distinctive ability to self-renew, and to differentiate into all lymphoid and myeloid cell types that together form the blood and immune systems including erythrocytes (red blood cells), leukocytes (white blood cells), and platelets. Their primary function is to ensure the continuous replenishment of the blood and immune system throughout an individual's lifespan. In response to various signals, hematopoietic stem cells can either remain dormant or actively divide and differentiate. Under normal conditions, the majority of these stem cells exist in a quiescent (inactive) state, making them somewhat resistant to chemotherapy or radiation therapy in the treatment of various diseases such as leukemia. However, when the body encounters stress such as infection, bleeding, or disease, hematopoietic stem cells can rapidly become active in order to replenish the affected cells and maintain homeostasis. Furthermore, hematopoietic stem cells are extremely important in the field of regenerative medicine and transplantation. Regarded as lifesaving in the field of oncology, they are often extracted, purified, and reinfused back into the same (autologous transplantation) or different (allogeneic transplantation) individuals to reestablish a healthy, functioning hematopoietic and immune system after high-dose chemotherapy or to replace dysfunctional bone marrow. Understanding and manipulating the behavior of these stem cells has immense potential in treating various blood disorders, autoimmune diseases, and cancers. (This extended description was ge…
has db xref: BTO:0000725
has db xref: CALOHA:TS-0448
has db xref: FMA:86475
has db xref: MESH:D006412
has db xref: VHOG:0001485
has db xref: ZFA:0009014
has exact synonym: blood forming stem cell
has exact synonym: hemopoietic stem cell
has related synonym: HSC
has related synonym: colony forming unit hematopoietic
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.

Axiom
annotated source: hematopoietic stem cell
annotated property: IAO_0000115
annotated target: A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: PMID:19022770
has db xref: http://en.wikipedia.org/wiki/Hematopoietic_stem_cell

Axiom
annotated source: hematopoietic stem cell
annotated property: description
annotated target: Hematopoietic stem cells (HSCs) are multipotent cells, capable of differentiating into a wide variety of specialized blood cells. During embryonic development hematopoietic stem cells emerge from the hemogenic endothelium, a specialized subset of endothelial cells with hematopoietic potential. HSCs can be found in several organs, in particular in bone marrow, as well as peripheral blood and umbilical cord blood. These stem cells have a distinctive ability to self-renew, and to differentiate into all lymphoid and myeloid cell types that together form the blood and immune systems including erythrocytes (red blood cells), leukocytes (white blood cells), and platelets. Their primary function is to ensure the continuous replenishment of the blood and immune system throughout an individual's lifespan. In response to various signals, hematopoietic stem cells can either remain dormant or actively divide and differentiate. Under normal conditions, the majority of these stem cells exist in a quiescent (inactive) state, making them somewhat resistant to chemotherapy or radiation therapy in the treatment of various diseases such as leukemia. However, when the body encounters stress such as infection, bleeding, or disease, hematopoietic stem cells can rapidly become active in order to replenish the affected cells and maintain homeostasis. Furthermore, hematopoietic stem cells are extremely important in the field of regenerative medicine and transplantation. Regarded as lifesaving in the field of oncology, they are often extracted, purified, and reinfused back into the same (autologous transplantation) or different (allogeneic transplantation) individuals to reestablish a healthy, functioning hematopoietic and immune system after high-dose chemotherapy or to replace dysfunctional bone marrow. Understanding and manipulating the behavior of these stem cells has immense potential in treating various blood disorders, autoimmune diseases, and cancers. (This extended description was ge…
has db xref: DOI:10.1038/s41580-019-0103-9
has db xref: DOI:10.1101/gr.192237.115
has db xref: DOI:10.1186/s12915-021-00955-z
has db xref: DOI:10.3389/fcell.2022.664261

Axiom
annotated source: hematopoietic stem cell
annotated property: hasDbXref
annotated target: ZFA:0009014
mapping justification: UnspecifiedMatching

Axiom
annotated source: hematopoietic stem cell
annotated property: hasRelatedSynonym
annotated target: HSC
has synonym type: OMO_0003000

hematopoietic stem cell on CELLxGENE CellGuide
type: Axiom
annotated source: hematopoietic stem cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000037

erythroid progenitor cell
type: Class
subclass of: erythroid lineage cell
subclass of: myeloid lineage restricted progenitor cell
subclass of: Restriction
  on property: RO_0002202
  some values from: megakaryocyte-erythroid progenitor cell
IAO_0000115: A progenitor cell committed to the erythroid lineage.
description: Erythroid progenitor cells play a key role in the hematopoietic system, specifically in the process of erythropoiesis – the production of red blood cells (erythrocytes). Found within the bone marrow, these cells are dedicated precursors to erythrocytes, and ensue in the hematopoietic lineage from multipotent progenitors. They represent a transitional cell type that bridges the gap between the early-stage erythroid precursors and the maturing red blood cell population. The earliest committed erythroid progenitor cell is thought to be the burst-forming unit-erythroid (BFU-E) cell, which after several cell divisions gives rise to another erythroid progenitor, the colony-forming unit-erythroid (CFU-E) cell. Erythroid progenitor cells are primarily responsible for responding to the demand for new red blood cells during conditions of physiological stress like infection, blood loss, or illness. This responsive behavior is regulated by a glycoprotein hormone known as erythropoietin, which is produced by the kidneys. Erythropoietin interacts with the receptors on the erythroid progenitor cells, prompting them to proliferate and differentiate into erythroblasts. The erythroblasts then further mature, eventually producing new, functional red cells. The role of erythroid progenitor cells extends beyond their main function of erythrocyte production, as they also participate in maintaining the balance of iron in the body. Upon erythroid differentiation, they increase their uptake of transferrin-bound iron for hemoglobin synthesis, a vital component of red blood cells which allows them to transport oxygen. A deficiency or excess of erythroid progenitor cells can lead to extensive health issues such as anemia or polycythemia respectively, emphasizing their crucial role in human health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information th…
has db xref: BTO:0004911
has db xref: ZFA:0009015
has related synonym: BFU-E
has related synonym: CFU-E
has related synonym: blast forming unit erythroid
has related synonym: burst forming unit erythroid
has related synonym: colony forming unit erythroid
has related synonym: erythroid stem cell
in subset: blood and immune upper slim
in subset: cellxgene subset

Axiom
annotated source: erythroid progenitor cell
annotated property: subClassOf
annotated target: myeloid lineage restricted progenitor cell
is inferred: true

Axiom
annotated source: erythroid progenitor cell
annotated property: IAO_0000115
annotated target: A progenitor cell committed to the erythroid lineage.
has db xref: GOC:add
has db xref: ISBN:0721601464

Axiom
annotated source: erythroid progenitor cell
annotated property: description
annotated target: Erythroid progenitor cells play a key role in the hematopoietic system, specifically in the process of erythropoiesis – the production of red blood cells (erythrocytes). Found within the bone marrow, these cells are dedicated precursors to erythrocytes, and ensue in the hematopoietic lineage from multipotent progenitors. They represent a transitional cell type that bridges the gap between the early-stage erythroid precursors and the maturing red blood cell population. The earliest committed erythroid progenitor cell is thought to be the burst-forming unit-erythroid (BFU-E) cell, which after several cell divisions gives rise to another erythroid progenitor, the colony-forming unit-erythroid (CFU-E) cell. Erythroid progenitor cells are primarily responsible for responding to the demand for new red blood cells during conditions of physiological stress like infection, blood loss, or illness. This responsive behavior is regulated by a glycoprotein hormone known as erythropoietin, which is produced by the kidneys. Erythropoietin interacts with the receptors on the erythroid progenitor cells, prompting them to proliferate and differentiate into erythroblasts. The erythroblasts then further mature, eventually producing new, functional red cells. The role of erythroid progenitor cells extends beyond their main function of erythrocyte production, as they also participate in maintaining the balance of iron in the body. Upon erythroid differentiation, they increase their uptake of transferrin-bound iron for hemoglobin synthesis, a vital component of red blood cells which allows them to transport oxygen. A deficiency or excess of erythroid progenitor cells can lead to extensive health issues such as anemia or polycythemia respectively, emphasizing their crucial role in human health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information th…
has db xref: DOI:10.1016/j.exphem.2015.10.007
has db xref: DOI:10.1097/MOH.0000000000000328
has db xref: DOI:10.1111/bjh.13938
has db xref: DOI:10.1182/blood-2014-07-588806
has db xref: DOI:10.3389/fphys.2019.00304

Axiom
annotated source: erythroid progenitor cell
annotated property: hasDbXref
annotated target: ZFA:0009015
mapping justification: UnspecifiedMatching

Axiom
annotated source: erythroid progenitor cell
annotated property: hasRelatedSynonym
annotated target: BFU-E
has synonym type: OMO_0003000

Axiom
annotated source: erythroid progenitor cell
annotated property: hasRelatedSynonym
annotated target: CFU-E
has synonym type: OMO_0003000

erythroid progenitor cell on CELLxGENE CellGuide
type: Axiom
annotated source: erythroid progenitor cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000038

germ line cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0022414
IAO_0000115: A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
has db xref: ZFA:0009016
in subset: general cell types upper slim
in subset: upper level
comment: Originally this term had some plant germ line cell children.

Axiom
annotated source: germ line cell
annotated property: IAO_0000115
annotated target: A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: germ line cell
annotated property: hasDbXref
annotated target: ZFA:0009016
mapping justification: UnspecifiedMatching

monoblast
type: Class
equivalent class: Class
  intersection of: CL_0002194
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017503
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000791
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005730
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030224
subclass of: myeloid cell
subclass of: CL_0002194
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017503
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000791
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005730
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002009
IAO_0000115: A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.
has db xref: CALOHA:TS-1195
has db xref: FMA:83553
has db xref: ZFA:0009017
has related synonym: CFU-M
has related synonym: colony forming unit macrophage
has related synonym: colony forming unit monocyte
has related synonym: monocyte stem cell
comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.

Axiom
annotated source: monoblast
annotated property: subClassOf
annotated target: CL_0002194
is inferred: true

Axiom
annotated source: monoblast
annotated property: IAO_0000115
annotated target: A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.
has db xref: GOC:add
has db xref: PMID:1104740
has db xref: http://en.wikipedia.org/wiki/Monoblast
has db xref: http://www.copewithcytokines.de

Axiom
annotated source: monoblast
annotated property: hasDbXref
annotated target: ZFA:0009017
mapping justification: UnspecifiedMatching

Axiom
annotated source: monoblast
annotated property: hasRelatedSynonym
annotated target: CFU-M
has synonym type: OMO_0003000

neutrophilic myeloblast
type: Class
equivalent class: Class
  intersection of: myeloblast
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001944
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000005307
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007857
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000010799
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000014362
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030223
subclass of: neutrophil progenitor cell
subclass of: myeloblast
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001944
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000005307
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007857
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000010799
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000014362
subclass of: Restriction
  on property: RO_0002202
  some values from: neutrophil progenitor cell
IAO_0000115: A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor.
has db xref: ZFA:0009018
has related synonym: neutrophilic granuloblast
comment: These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction.

Axiom
annotated source: neutrophilic myeloblast
annotated property: subClassOf
annotated target: myeloblast
is inferred: true

Axiom
annotated source: neutrophilic myeloblast
annotated property: IAO_0000115
annotated target: A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor.
has db xref: GOC:add
has db xref: ISBN:0721601464
has db xref: PMID:12560239
has db xref: PMID:15514007

Axiom
annotated source: neutrophilic myeloblast
annotated property: hasDbXref
annotated target: ZFA:0009018
mapping justification: UnspecifiedMatching

mature basophil
type: Class
equivalent class: Class
  intersection of: basophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005634
      intersection of: Restriction
        on property: RO_0000053
        some values from: PATO_0001979
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002349
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002351
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002830
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0008015
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032616
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048295
subclass of: basophil
subclass of: CL_0002274
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: GO_0005634
    intersection of: Restriction
      on property: RO_0000053
      some values from: PATO_0001979
subclass of: Restriction
  on property: RO_0002202
  some values from: band form basophil
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002349
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002351
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002830
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032616
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048295
IAO_0000115: A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
has broad synonym: polymorphonuclear leucocyte
has broad synonym: polymorphonuclear leukocyte
has db xref: BTO:0001026
has db xref: CALOHA:TS-0688
has exact synonym: mature basophil leucocyte
has exact synonym: mature basophil leukocyte
comment: Mature basophils are also capable of producing IL-3, IL-5, IL-6, IL-8, IL-13, IL-25, CCL22, tslp, vegf, and LTC4.

Axiom
annotated source: mature basophil
annotated property: subClassOf
annotated target: basophil
is inferred: true

Axiom
annotated source: mature basophil
annotated property: IAO_0000115
annotated target: A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: PMID:18466030
has db xref: PMID:19231594
has db xref: PMID:20837449
has db xref: http://www.cap.org

neural stem cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0002319
subclass of: Restriction
  on property: RO_0002202
  some values from: neurectodermal cell
IAO_0000115: An undifferentiated neural cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple central nervous system neuronal and glial cell types.
has db xref: BTO:0002881
has db xref: CALOHA:TS-2360
has db xref: FMA:86684
has db xref: ZFA:0009019
has exact synonym: NSC
has exact synonym: neuronal stem cell
in subset: cellxgene subset

Axiom
annotated source: neural stem cell
annotated property: IAO_0000115
annotated target: An undifferentiated neural cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple central nervous system neuronal and glial cell types.
has db xref: PMID:30639325

Axiom
annotated source: neural stem cell
annotated property: hasDbXref
annotated target: ZFA:0009019
mapping justification: UnspecifiedMatching

Axiom
annotated source: neural stem cell
annotated property: hasExactSynonym
annotated target: neuronal stem cell
has db xref: PMID:16305818

multi fate stem cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001402
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0017145
subclass of: stem cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001402
IAO_0000115: A stem cell that can give rise to multiple lineages of cells.
has db xref: FMA:84789
has db xref: ZFA:0009020
has exact synonym: multi-fate stem cell
has exact synonym: multifate stem cell
has exact synonym: multipotent cell
has exact synonym: multipotent stem cell

Axiom
annotated source: multi fate stem cell
annotated property: IAO_0000115
annotated target: A stem cell that can give rise to multiple lineages of cells.
has db xref: GOC:add

Axiom
annotated source: multi fate stem cell
annotated property: hasDbXref
annotated target: ZFA:0009020
mapping justification: UnspecifiedMatching

common myeloid progenitor
type: Class
subclass of: CL_0002032
disjoint with: megakaryocyte-erythroid progenitor cell
disjoint with: common lymphoid progenitor
disjoint with: granulocyte monocyte progenitor cell
IAO_0000115: A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
description: The common myeloid progenitor (CMP) is a multipotent cell that serves as a crucial intermediary within the overall framework of hematopoietic cell differentiation, which is the process of blood cell production. This part of the hematopoiesis process leads to the formation of myeloid lineage cells, which includes granulocytes (neutrophils, eosinophils, and basophils), monocytes, erythrocytes (red blood cells), and megakaryocytes (platelet-forming cells). The primary function of common myeloid progenitors is differentiation and proliferation into various types of mature blood cells, thereby providing a critical contribution to maintaining homeostasis within the body's immune and circulatory systems. Single-cell analyses have shown that the CMP cell population is heterogeneous with at least two distinct subpopulations, characterized by different cell surface markers and likely already committed to downstream differentiation into either the granulocyte/macrophage lineage or the megakaryocyte/erythrocyte lineage-restricted progenitor. The destiny of a CMP is influenced by numerous cytokines and growth factors in its environment that promote differentiation along specific lineages. For example, IL-3 and GM-CSF stimulate the production of eosinophils, which are essential for the body’s defense against allergens and help fight fungal and parasitic infections. By being able to differentiate into a wide range of different immune cells, common myeloid progenitors play a crucial role in the body's ability to respond to injuries, infections, and other physiological challenges. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0004730
has db xref: ZFA:0009021
has exact synonym: common myeloid precursor
has related synonym: CFU-GEMM
has related synonym: CFU-S
has related synonym: CMP
has related synonym: colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
has related synonym: multipotential myeloid stem cell
has related synonym: myeloid stem cell
has related synonym: pluripotent stem cell (bone marrow)
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).

Axiom
annotated source: common myeloid progenitor
annotated property: subClassOf
annotated target: CL_0002032
is inferred: true

Axiom
annotated source: common myeloid progenitor
annotated property: IAO_0000115
annotated target: A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
has db xref: GOC:add
has db xref: ISBN:0878932437
has db xref: MESH:D023461

Axiom
annotated source: common myeloid progenitor
annotated property: description
annotated target: The common myeloid progenitor (CMP) is a multipotent cell that serves as a crucial intermediary within the overall framework of hematopoietic cell differentiation, which is the process of blood cell production. This part of the hematopoiesis process leads to the formation of myeloid lineage cells, which includes granulocytes (neutrophils, eosinophils, and basophils), monocytes, erythrocytes (red blood cells), and megakaryocytes (platelet-forming cells). The primary function of common myeloid progenitors is differentiation and proliferation into various types of mature blood cells, thereby providing a critical contribution to maintaining homeostasis within the body's immune and circulatory systems. Single-cell analyses have shown that the CMP cell population is heterogeneous with at least two distinct subpopulations, characterized by different cell surface markers and likely already committed to downstream differentiation into either the granulocyte/macrophage lineage or the megakaryocyte/erythrocyte lineage-restricted progenitor. The destiny of a CMP is influenced by numerous cytokines and growth factors in its environment that promote differentiation along specific lineages. For example, IL-3 and GM-CSF stimulate the production of eosinophils, which are essential for the body’s defense against allergens and help fight fungal and parasitic infections. By being able to differentiate into a wide range of different immune cells, common myeloid progenitors play a crucial role in the body's ability to respond to injuries, infections, and other physiological challenges. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/35004599
has db xref: DOI:10.1038/ni.3412
has db xref: DOI:10.1111/j.1600-065X.2010.00963.x
has db xref: DOI:10.7554/eLife.60939
has db xref: https://www.sciencedirect.com/topics/engineering/myeloid-progenitor-cell

Axiom
annotated source: common myeloid progenitor
annotated property: hasDbXref
annotated target: ZFA:0009021
mapping justification: UnspecifiedMatching

Axiom
annotated source: common myeloid progenitor
annotated property: hasRelatedSynonym
annotated target: CFU-GEMM
has db xref: ISBN:0878932437
has synonym type: OMO_0003000

Axiom
annotated source: common myeloid progenitor
annotated property: hasRelatedSynonym
annotated target: CFU-S
has db xref: ISBN:0878932437
has synonym type: OMO_0003000

Axiom
annotated source: common myeloid progenitor
annotated property: hasRelatedSynonym
annotated target: CMP
has db xref: ISBN:0878932437
has synonym type: OMO_0003000

Axiom
annotated source: common myeloid progenitor
annotated property: hasRelatedSynonym
annotated target: colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
has db xref: ISBN:0878932437

Axiom
annotated source: common myeloid progenitor
annotated property: hasRelatedSynonym
annotated target: multipotential myeloid stem cell
has db xref: ISBN:0878932437

Axiom
annotated source: common myeloid progenitor
annotated property: hasRelatedSynonym
annotated target: myeloid stem cell
has db xref: ISBN:0878932437

Axiom
annotated source: common myeloid progenitor
annotated property: hasRelatedSynonym
annotated target: pluripotent stem cell (bone marrow)
has db xref: ISBN:0878932437

common myeloid progenitor on CELLxGENE CellGuide
type: Axiom
annotated source: common myeloid progenitor
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000049

megakaryocyte-erythroid progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002032
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030218
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030219
subclass of: myeloid cell
subclass of: CL_0002032
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030218
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030219
disjoint with: granulocyte monocyte progenitor cell
disjoint with: CL_0002009
IAO_0000115: A progenitor cell committed to the megakaryocyte and erythroid lineages.
description: The megakaryocyte-erythroid progenitor (MEP) cell belongs to the multipotent hematopoietic progenitor cells, which can give rise to multiple different cell types. They are found in the bone marrow, the primary organ where new blood cells are generated. MEPs are specially programmed to develop into two distinct blood cell lineages, namely megakaryocytes, which go on to produce platelets for blood clotting, and the erythroid lineage which consists of red blood cells responsible for oxygen transport in the body. The MEP cells are the result of a decision-making process within the hematopoietic stem cell population. Hematopoietic stem cell can differentiate into multiple types of progenitor cells, including myeloid progenitor cells. A further subdivision within this myeloid lineage generates the MEP cells. Therefore, these megakaryocyte-erythroid progenitors represent a key juncture between hematopoietic stem cells and mature blood cell types in the myeloid lineage. Megakaryocyte-erythroid progenitor cells play a crucial role in the homeostasis of some of the most crucial constituents of blood. The megakaryocytes produced from these bipotent progenitor cells contribute to hemostasis by producing platelets - small anucleated fragments that are pivotal for blood clotting and preventing bleeding. Similarly, the erythroid lineage from MEP cells gives rise to erythrocytes, which harbor hemoglobin, the molecule that transports oxygen from lungs to every nook and corner of the body. An imbalance or malfunction in MEP function thus can significantly impact human health, leading to diseases like thrombocytopenia or anemia. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009022
has exact synonym: CFU-EM
has exact synonym: CFU-MegE
has exact synonym: MEP
has exact synonym: Meg/E progenitor
has exact synonym: colony forming unit erythroid megakaryocyte
has exact synonym: megakaryocyte/erythrocyte progenitor
has exact synonym: megakaryocyte/erythroid progenitor cell
in subset: cellxgene subset
in subset: human reference atlas
comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.

Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: subClassOf
annotated target: CL_0002032
is inferred: true

Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: IAO_0000115
annotated target: A progenitor cell committed to the megakaryocyte and erythroid lineages.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: MESH:D055015
has db xref: PMID:16647566
has db xref: http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell

Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: description
annotated target: The megakaryocyte-erythroid progenitor (MEP) cell belongs to the multipotent hematopoietic progenitor cells, which can give rise to multiple different cell types. They are found in the bone marrow, the primary organ where new blood cells are generated. MEPs are specially programmed to develop into two distinct blood cell lineages, namely megakaryocytes, which go on to produce platelets for blood clotting, and the erythroid lineage which consists of red blood cells responsible for oxygen transport in the body. The MEP cells are the result of a decision-making process within the hematopoietic stem cell population. Hematopoietic stem cell can differentiate into multiple types of progenitor cells, including myeloid progenitor cells. A further subdivision within this myeloid lineage generates the MEP cells. Therefore, these megakaryocyte-erythroid progenitors represent a key juncture between hematopoietic stem cells and mature blood cell types in the myeloid lineage. Megakaryocyte-erythroid progenitor cells play a crucial role in the homeostasis of some of the most crucial constituents of blood. The megakaryocytes produced from these bipotent progenitor cells contribute to hemostasis by producing platelets - small anucleated fragments that are pivotal for blood clotting and preventing bleeding. Similarly, the erythroid lineage from MEP cells gives rise to erythrocytes, which harbor hemoglobin, the molecule that transports oxygen from lungs to every nook and corner of the body. An imbalance or malfunction in MEP function thus can significantly impact human health, leading to diseases like thrombocytopenia or anemia. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/stem.2834
has db xref: DOI:10.1016/j.celrep.2018.10.084
has db xref: DOI:10.1097/MOH.0000000000000625
has db xref: DOI:10.1161/ATVBAHA.119.312129
has db xref: DOI:10.1182/blood-2016-01-693705

Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: hasDbXref
annotated target: ZFA:0009022
mapping justification: UnspecifiedMatching

megakaryocyte-erythroid progenitor cell on CELLxGENE CellGuide
type: Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000050

common lymphoid progenitor
type: Class
equivalent class: Class
  intersection of: CL_0002032
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030098
subclass of: CL_0002032
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030098
IAO_0000115: A oligopotent progenitor cell committed to the lymphoid lineage.
description: The common lymphoid progenitor (CLP) arises from the multipotential hematopoietic stem cell in the bone marrow. Hematopoietic stem cells have the unique capability of developing into any type of blood cell depending on the body's requirements. In contrast, common lymphoid progenitors are already committed to the lymphoid lineage but are still oligopotent with the capability to further differentiate into various types of lymphoid cells. In mice, cells in the common lymphoid progenitor population in the bone marrow can be identified by their Lin- IL7rα+ c-Kit+ Sca-1+ cell surface phenotype. The IL-7 receptor is first expressed on common lymphoid progenitor cells and distinguishes them from primitive common myeloid progenitors, and IL-7 is thought to play a critical role in the downstream development and homeostasis of immune cells. CLPs give rise to B lymphocytes, T lymphocytes, dendritic cells, and natural killer cells, all of which play a crucial and distinct role in immune responses. B and T lymphocytes are responsible for adaptive immunity, allowing the body to recognize and remember specific pathogens to fight them off more effectively in the future. B lymphocytes are responsible for producing antibodies, while T lymphocytes either help regulate immune responses or directly kill infected cells. Natural Killer cells are part of the body’s innate immune response, providing immediate, nonspecific defense against pathogens. They are able to interact with infected or malignant cells and induce controlled cell death, or apoptosis, effectively eliminating the threat to bodily health. Dendritic cells link the innate and adaptive immune systems by presenting antigens to T cells, promoting an adaptive response. Thus, common lymphoid progenitors provide the basis for the body's strategic and layered defense against varied and evolving external threats, making them an essential part of the immune system. (This extended description was generated by ChatGPT and reviewed by the…
has db xref: ZFA:0009023
has exact synonym: common lymphocyte precursor
has exact synonym: common lymphocyte progenitor
has exact synonym: common lymphoid precursor
has related synonym: CLP
has related synonym: ELP
has related synonym: committed lymphopoietic stem cell
has related synonym: early lymphocyte progenitor
has related synonym: lymphoid stem cell
has related synonym: lymphopoietic stem cell
in subset: cellxgene subset
in subset: human reference atlas
comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative.

Axiom
annotated source: common lymphoid progenitor
annotated property: subClassOf
annotated target: CL_0002032
is inferred: true

Axiom
annotated source: common lymphoid progenitor
annotated property: IAO_0000115
annotated target: A oligopotent progenitor cell committed to the lymphoid lineage.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: PMID:10407577
has db xref: PMID:16551251

Axiom
annotated source: common lymphoid progenitor
annotated property: description
annotated target: The common lymphoid progenitor (CLP) arises from the multipotential hematopoietic stem cell in the bone marrow. Hematopoietic stem cells have the unique capability of developing into any type of blood cell depending on the body's requirements. In contrast, common lymphoid progenitors are already committed to the lymphoid lineage but are still oligopotent with the capability to further differentiate into various types of lymphoid cells. In mice, cells in the common lymphoid progenitor population in the bone marrow can be identified by their Lin- IL7rα+ c-Kit+ Sca-1+ cell surface phenotype. The IL-7 receptor is first expressed on common lymphoid progenitor cells and distinguishes them from primitive common myeloid progenitors, and IL-7 is thought to play a critical role in the downstream development and homeostasis of immune cells. CLPs give rise to B lymphocytes, T lymphocytes, dendritic cells, and natural killer cells, all of which play a crucial and distinct role in immune responses. B and T lymphocytes are responsible for adaptive immunity, allowing the body to recognize and remember specific pathogens to fight them off more effectively in the future. B lymphocytes are responsible for producing antibodies, while T lymphocytes either help regulate immune responses or directly kill infected cells. Natural Killer cells are part of the body’s innate immune response, providing immediate, nonspecific defense against pathogens. They are able to interact with infected or malignant cells and induce controlled cell death, or apoptosis, effectively eliminating the threat to bodily health. Dendritic cells link the innate and adaptive immune systems by presenting antigens to T cells, promoting an adaptive response. Thus, common lymphoid progenitors provide the basis for the body's strategic and layered defense against varied and evolving external threats, making them an essential part of the immune system. (This extended description was generated by ChatGPT and reviewed by the…
has db xref: DOI:10.1016/s0092-8674(00)80453-5
has db xref: DOI:10.1038/ni.3168
has db xref: DOI:10.1111/j.1600-065X.2010.00963.x
has db xref: DOI:10.1182/blood-2009-08-236398
has db xref: DOI:10.3389/fimmu.2021.747324

Axiom
annotated source: common lymphoid progenitor
annotated property: hasDbXref
annotated target: ZFA:0009023
mapping justification: UnspecifiedMatching

Axiom
annotated source: common lymphoid progenitor
annotated property: hasRelatedSynonym
annotated target: CLP
has synonym type: OMO_0003000

Axiom
annotated source: common lymphoid progenitor
annotated property: hasRelatedSynonym
annotated target: ELP
has synonym type: OMO_0003000

common lymphoid progenitor on CELLxGENE CellGuide
type: Axiom
annotated source: common lymphoid progenitor
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000051

myoblast
type: Class
subclass of: muscle precursor cell
IAO_0000115: A cell that is committed to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
has db xref: BTO:0000222
has db xref: CALOHA:TS-0650
has db xref: FBbt:00005083
has db xref: FMA:70335
has db xref: VHOG:0001529
has db xref: ZFA:0009025
in subset: cellxgene subset

Axiom
annotated source: myoblast
annotated property: IAO_0000115
annotated target: A cell that is committed to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
has db xref: GOC:tfm
has db xref: MESH:D032446
has db xref: PMID:21849021

Axiom
annotated source: myoblast
annotated property: hasDbXref
annotated target: FBbt:00005083
mapping justification: ManualMappingCuration

Axiom
annotated source: myoblast
annotated property: hasDbXref
annotated target: ZFA:0009025
mapping justification: UnspecifiedMatching

fibroblast
type: Class
subclass of: stromal cell
IAO_0000115: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
has db xref: BTO:0000452
has db xref: CALOHA:TS-0362
has db xref: FMA:63877
has db xref: NCIT:C12482
has db xref: VHOG:0001482
has db xref: ZFA:0009026
in subset: cellxgene subset
in subset: human reference atlas
comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.

Axiom
annotated source: fibroblast
annotated property: IAO_0000115
annotated target: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
has db xref: ISBN:0517223651
has db xref: MESH:D005347
has db xref: http://en.wikipedia.org/wiki/Fibroblast

Axiom
annotated source: fibroblast
annotated property: hasDbXref
annotated target: ZFA:0009026
mapping justification: UnspecifiedMatching

chondroblast
type: Class
subclass of: CL_0002320
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0007009
subclass of: Restriction
  on property: RO_0003000
  some values from: UBERON_0002418
IAO_0000115: Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.
has db xref: BTO:0003607
has db xref: FMA:66783
has db xref: ZFA:0009027
has exact synonym: chrondoplast
in subset: cellxgene subset

Axiom
annotated source: chondroblast
annotated property: IAO_0000115
annotated target: Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.
has db xref: GOC:tfm
has db xref: GO_REF:0000034
has db xref: ISBN:0618947256

Axiom
annotated source: chondroblast
annotated property: hasDbXref
annotated target: ZFA:0009027
mapping justification: UnspecifiedMatching

ameloblast
type: Class
subclass of: simple columnar epithelial cell
subclass of: CL_0002077
subclass of: CL_1100001
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005176
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0007000
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0097186
subclass of: Restriction
  on property: RO_0002220
  some values from: UBERON_0001763
subclass of: Restriction
  on property: RO_0003000
  some values from: UBERON_0001752
IAO_0000115: Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell.
has db xref: BTO:0001663
has db xref: FMA:70576
has exact synonym: amelocyte
has exact synonym: enamel secreting cell
comment: non-encoded relationship from VSAO produces VSAO:0000066

Axiom
annotated source: ameloblast
annotated property: IAO_0000115
annotated target: Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell.
has db xref: GOC:tfm
has db xref: GO_REF:0000034
has db xref: MESH:D000565

odontoblast
type: Class
subclass of: neurecto-epithelial cell
subclass of: CL_0002148
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005176
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0007003
subclass of: Restriction
  on property: RO_0003000
  some values from: UBERON_0001751
IAO_0000115: Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell.
has db xref: BTO:0001769
has db xref: CALOHA:TS-0696
has db xref: FMA:62999
has db xref: MESH:D009804
has db xref: ZFA:0009029
in subset: cellxgene subset
comment: legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin.

Axiom
annotated source: odontoblast
annotated property: IAO_0000115
annotated target: Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell.
has db xref: GO_REF:0000034
has db xref: ISBN:0618947256

Axiom
annotated source: odontoblast
annotated property: hasDbXref
annotated target: ZFA:0009029
mapping justification: UnspecifiedMatching

osteoblast
type: Class
subclass of: BFO_0000002
subclass of: CL_0002320
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0007010
subclass of: Restriction
  on property: RO_0003000
  some values from: UBERON_0008883
IAO_0000115: Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell.
description: Osteoblasts are a type of bone cell primarily responsible for bone formation. Osteoblasts are derived from mesenchymal stem cells, which differentiate into osteoblasts under the influence of various growth factors, including bone morphogenetic proteins (BMPs). These multipotent cells play a critical role in the bone formation process known as ossification. The primary function of osteoblasts is to synthesize and deposit bone matrix, a mixture of organic substances and inorganic materials. This included producing a mix of collagen and non-collagenous proteins, which they secrete to create the organic portion of the extracellular bone matrix. The osteoblasts also initiate the mineralization process by depositing calcium and phosphate ions onto this organic matrix, generating a material that is incredibly strong and resilient, which we recognize as bone. Furthermore, osteoblasts are intricately involved in bone remodeling. They communicate with other specialized bone cells, like osteoclasts (involved in bone resorption) and osteocytes (derived from osteoblasts and important for bone maintenance), helping to maintain skeletal health and homeostasis. Dysregulation of osteoblast function can lead to various bone diseases, illustrating the importance of these cells in skeletal health and development. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001593
has db xref: CALOHA:TS-0720
has db xref: FMA:66780
has db xref: ZFA:0009031
in subset: cellxgene subset
in subset: human reference atlas
comment: non-encoded relationships from VSAO - capable_of_producing VSAO:0000020

Axiom
annotated source: osteoblast
annotated property: IAO_0000115
annotated target: Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell.
has db xref: GO_REF:0000034
has db xref: MESH:D010006

Axiom
annotated source: osteoblast
annotated property: description
annotated target: Osteoblasts are a type of bone cell primarily responsible for bone formation. Osteoblasts are derived from mesenchymal stem cells, which differentiate into osteoblasts under the influence of various growth factors, including bone morphogenetic proteins (BMPs). These multipotent cells play a critical role in the bone formation process known as ossification. The primary function of osteoblasts is to synthesize and deposit bone matrix, a mixture of organic substances and inorganic materials. This included producing a mix of collagen and non-collagenous proteins, which they secrete to create the organic portion of the extracellular bone matrix. The osteoblasts also initiate the mineralization process by depositing calcium and phosphate ions onto this organic matrix, generating a material that is incredibly strong and resilient, which we recognize as bone. Furthermore, osteoblasts are intricately involved in bone remodeling. They communicate with other specialized bone cells, like osteoclasts (involved in bone resorption) and osteocytes (derived from osteoblasts and important for bone maintenance), helping to maintain skeletal health and homeostasis. Dysregulation of osteoblast function can lead to various bone diseases, illustrating the importance of these cells in skeletal health and development. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/nrm3254
has db xref: DOI:10.1038/s41574-019-0246-y
has db xref: DOI:10.1038/s41580-020-00279-w
has db xref: DOI:10.1089/ten.teb.2016.0454
has db xref: DOI:10.3390/ijms19020360

Axiom
annotated source: osteoblast
annotated property: hasDbXref
annotated target: ZFA:0009031
mapping justification: UnspecifiedMatching

osteoblast on CELLxGENE CellGuide
type: Axiom
annotated source: osteoblast
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000062

ciliated cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005929
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005929
IAO_0000115: A cell that has a filiform extrusion of the cell surface.
has db xref: VHOG:0001532
has db xref: XAO:0000031
has db xref: ZFA:0009032
in subset: cellxgene subset

Axiom
annotated source: ciliated cell
annotated property: IAO_0000115
annotated target: A cell that has a filiform extrusion of the cell surface.
has db xref: GOC:tfm

Axiom
annotated source: ciliated cell
annotated property: hasDbXref
annotated target: ZFA:0009032
mapping justification: UnspecifiedMatching

ependymal cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0004670
subclass of: ciliated epithelial cell
subclass of: glial cell
subclass of: neurecto-epithelial cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004670
subclass of: Restriction
  on property: RO_0002207
  some values from: radial glial cell
IAO_0000115: A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile.
description: Ependymal cells are ciliated neuroepithelial cells lining the ventricles of the brain and the central canal of the spinal cord, forming a single-layered epithelium, known as the ependyma. Together with astrocytes, microglial cells, and oligodendrocytes, they are one of the four main types of neuroglia found in the nervous system. Ependymal cells are equipped with multiple functions that support the brain and spinal cord. Key amongst these functions are the secretion, circulation, and absorption of cerebrospinal fluid, which cushions the brain, distributes neuroendocrine factors, and disposes of neural waste. The cilia on the apical surface of ependymal cells vigorously beat in a coordinated fashion to circulate the cerebrospinal fluid. Additionally, these cells may also function in aiding the migration of neuroblasts during brain development. Ependymal cells form a barrier between the cerebrospinal fluid and the adjacent nervous tissue in the central nervous system, which appears to be particularly important during development. In response to injury, ependymal cells have been observed to proliferate and have the potential to transform into astrocytes or oligodendrocytes, suggesting stem cell-like functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001724
has db xref: FMA:70550
has db xref: ZFA:0009033
has narrow synonym: ependymocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: ependymal cell
annotated property: IAO_0000115
annotated target: A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile.
has db xref: GOC:tfm
has db xref: JB:jb
has db xref: PMID:34335193
has db xref: PMID:37008045
has db xref: PMID:9550134
has db xref: doi:/10.3389/fncel.2021.703951
has db xref: https://www.britannica.com/science/ependymal-cell

Axiom
annotated source: ependymal cell
annotated property: description
annotated target: Ependymal cells are ciliated neuroepithelial cells lining the ventricles of the brain and the central canal of the spinal cord, forming a single-layered epithelium, known as the ependyma. Together with astrocytes, microglial cells, and oligodendrocytes, they are one of the four main types of neuroglia found in the nervous system. Ependymal cells are equipped with multiple functions that support the brain and spinal cord. Key amongst these functions are the secretion, circulation, and absorption of cerebrospinal fluid, which cushions the brain, distributes neuroendocrine factors, and disposes of neural waste. The cilia on the apical surface of ependymal cells vigorously beat in a coordinated fashion to circulate the cerebrospinal fluid. Additionally, these cells may also function in aiding the migration of neuroblasts during brain development. Ependymal cells form a barrier between the cerebrospinal fluid and the adjacent nervous tissue in the central nervous system, which appears to be particularly important during development. In response to injury, ependymal cells have been observed to proliferate and have the potential to transform into astrocytes or oligodendrocytes, suggesting stem cell-like functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/s00401-009-0624-y
has db xref: DOI:10.14336/AD.2022.0826-1
has db xref: DOI:10.4161/tisb.28426

Axiom
annotated source: ependymal cell
annotated property: hasDbXref
annotated target: ZFA:0009033
mapping justification: UnspecifiedMatching

Axiom
annotated source: ependymal cell
annotated property: hasNarrowSynonym
annotated target: ependymocyte
has db xref: doi:10.53347/rID-51713

ependymal cell on CELLxGENE CellGuide
type: Axiom
annotated source: ependymal cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000065

epithelial cell
type: Class
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000483
disjoint with: leukocyte
IAO_0000115: A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
has db xref: BTO:0000414
has db xref: CALOHA:TS-2026
has db xref: CARO:0000077
has db xref: FBbt:00000124
has db xref: FMA:66768
has db xref: WBbt:0003672
has db xref: ZFA:0009034
has exact synonym: epitheliocyte
in subset: cellxgene subset
in subset: general cell types upper slim
in subset: human reference atlas

Axiom
annotated source: epithelial cell
annotated property: IAO_0000115
annotated target: A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
has db xref: FB:ma
has db xref: GOC:tfm
has db xref: MESH:D004847

Axiom
annotated source: epithelial cell
annotated property: hasDbXref
annotated target: FBbt:00000124
mapping justification: ManualMappingCuration

Axiom
annotated source: epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009034
mapping justification: UnspecifiedMatching

ciliated epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005929
subclass of: ciliated cell
subclass of: epithelial cell
IAO_0000115: An epithelial cell that has a cilia.
has db xref: FMA:70605
has db xref: ZFA:0009035
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: ciliated epithelial cell
annotated property: IAO_0000115
annotated target: An epithelial cell that has a cilia.
has db xref: GOC:tfm

Axiom
annotated source: ciliated epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009035
mapping justification: UnspecifiedMatching

duct epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000058
subclass of: epithelial cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000058
IAO_0000115: An epithelial cell that is part of a duct.
description: Duct epithelial cells are distinctly specialized cells that predominantly form the lining of glandular ducts. These cells play a crucial role in the secretion, absorption, and transport of fluids depending on the organ they inhabit. They are typically organized in a tubular structure, forming collectively the conduit for the transport of substances. These cells exhibit tight junctions, enabling the careful regulation of the passage of substances and ensuring that no unwanted particles seep through. They are predominantly characterized by their polarized nature, having distinct apical and basolateral surfaces that support its functions of secretion and absorption. The apical surface, exposed to the duct lumen, is specialized for secretion and interaction with the luminal environment, while the basolateral surface is oriented towards the underlying tissue, facilitating interactions with neighboring cells and the extracellular matrix. The ducts serve as the bridge between the gland and the site of secretion, allowing the substances produced by the gland to exit into the body. Thus, duct epithelial cells have a sweeping role in various physiological functions, ranging from defense against pathogens in the respiratory and digestive tracts, to secretion of digestive enzymes, to milk production in mammary glands. As a result of their specialized function, any impairment in the function of duct epithelial cells to function properly often leads to certain diseases or disorders. Studies have identified potential correlation between malfunctioning duct epithelial cells and conditions such as cystic fibrosis, chronic obstructive pulmonary disease, and certain cancers, particularly breast and pancreatic. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered de…
has db xref: ZFA:0009372
in subset: cellxgene subset

Axiom
annotated source: duct epithelial cell
annotated property: IAO_0000115
annotated target: An epithelial cell that is part of a duct.
has db xref: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: duct epithelial cell
annotated property: description
annotated target: Duct epithelial cells are distinctly specialized cells that predominantly form the lining of glandular ducts. These cells play a crucial role in the secretion, absorption, and transport of fluids depending on the organ they inhabit. They are typically organized in a tubular structure, forming collectively the conduit for the transport of substances. These cells exhibit tight junctions, enabling the careful regulation of the passage of substances and ensuring that no unwanted particles seep through. They are predominantly characterized by their polarized nature, having distinct apical and basolateral surfaces that support its functions of secretion and absorption. The apical surface, exposed to the duct lumen, is specialized for secretion and interaction with the luminal environment, while the basolateral surface is oriented towards the underlying tissue, facilitating interactions with neighboring cells and the extracellular matrix. The ducts serve as the bridge between the gland and the site of secretion, allowing the substances produced by the gland to exit into the body. Thus, duct epithelial cells have a sweeping role in various physiological functions, ranging from defense against pathogens in the respiratory and digestive tracts, to secretion of digestive enzymes, to milk production in mammary glands. As a result of their specialized function, any impairment in the function of duct epithelial cells to function properly often leads to certain diseases or disorders. Studies have identified potential correlation between malfunctioning duct epithelial cells and conditions such as cystic fibrosis, chronic obstructive pulmonary disease, and certain cancers, particularly breast and pancreatic. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered de…
has db xref: DOI:10.1038/s41467-018-04334-1
has db xref: DOI:10.1513/AnnalsATS.201402-049AW
has db xref: DOI:10.3389/fphar.2019.00074
has db xref: DOI:10.4161/tisb.25718
has db xref: https://www.sciencedirect.com/topics/medicine-and-dentistry/mammary-epithelium

Axiom
annotated source: duct epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009372
mapping justification: UnspecifiedMatching

duct epithelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: duct epithelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000068

branched duct epithelial cell
type: Class
subclass of: duct epithelial cell

blood vessel endothelial cell
type: Class
equivalent class: Class
  intersection of: endothelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001981
subclass of: CL_0002139
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004638
IAO_0000115: An endothelial cell that lines the vasculature.
description: Blood vessel endothelial cells, also known as vascular endothelial cells, form the delicate inner lining of the complex circulatory system, including arteries and veins. These cells form a single, continuous monolayer inside every blood vessel, acting as a crucial biomolecular barrier between the blood, and the rest of the body tissues. They perform various fundamental biological functions, ranging from maintenance of vessel integrity to blood clotting regulation. Additionally, they control the transportation of fluids, molecules, and blood particulate matter from and into the bloodstream. One of the primary functions of blood vessel endothelial cells is to maintain vascular homeostasis - a stable environment within the blood vessels. They accomplish this through several methods: they control vasomotor tone, i.e. the degree of contraction and dilation of blood vessels, by secreting vasoactive substances such as nitric oxide and endothelin; mediate responses to inflammatory stimuli; and they also regulate angiogenesis, the process of new blood vessel formations. Blood vessel endothelial cells play a significant role in preventing blood clot formation by generating a slick, non-thrombogenic surface that disallows platelets or coagulant proteins from adhering to it. Blood vessel endothelial cells are sensitive to various stimuli, including shear stress caused by blood flow, and they can respond by altering their morphology, function, and gene expression. This ability to adapt enables blood vessels to remodel and ensure the adequate delivery of nutrients and oxygen to all tissues, regardless of physiological demand variations. Conversely, endothelial dysfunction, often associated with a reduction in the bioavailability of endothelium-derived nitric oxide, can lead to the development of pathological conditions such as atherosclerosis, hypertension, diabetes mellitus, and even aging-related diseases. (This extended description was generated by ChatGPT and reviewed by the …
has db xref: ZFA:0009036
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: blood vessel endothelial cell
annotated property: IAO_0000115
annotated target: An endothelial cell that lines the vasculature.
has db xref: GOC:tfm

Axiom
annotated source: blood vessel endothelial cell
annotated property: description
annotated target: Blood vessel endothelial cells, also known as vascular endothelial cells, form the delicate inner lining of the complex circulatory system, including arteries and veins. These cells form a single, continuous monolayer inside every blood vessel, acting as a crucial biomolecular barrier between the blood, and the rest of the body tissues. They perform various fundamental biological functions, ranging from maintenance of vessel integrity to blood clotting regulation. Additionally, they control the transportation of fluids, molecules, and blood particulate matter from and into the bloodstream. One of the primary functions of blood vessel endothelial cells is to maintain vascular homeostasis - a stable environment within the blood vessels. They accomplish this through several methods: they control vasomotor tone, i.e. the degree of contraction and dilation of blood vessels, by secreting vasoactive substances such as nitric oxide and endothelin; mediate responses to inflammatory stimuli; and they also regulate angiogenesis, the process of new blood vessel formations. Blood vessel endothelial cells play a significant role in preventing blood clot formation by generating a slick, non-thrombogenic surface that disallows platelets or coagulant proteins from adhering to it. Blood vessel endothelial cells are sensitive to various stimuli, including shear stress caused by blood flow, and they can respond by altering their morphology, function, and gene expression. This ability to adapt enables blood vessels to remodel and ensure the adequate delivery of nutrients and oxygen to all tissues, regardless of physiological demand variations. Conversely, endothelial dysfunction, often associated with a reduction in the bioavailability of endothelium-derived nitric oxide, can lead to the development of pathological conditions such as atherosclerosis, hypertension, diabetes mellitus, and even aging-related diseases. (This extended description was generated by ChatGPT and reviewed by the …
has db xref: DOI:10.1007/s00441-021-03471-2
has db xref: DOI:10.1016/j.biomaterials.2007.01.039
has db xref: DOI:10.1038/s41569-022-00770-1
has db xref: DOI:10.1152/physrev.00001.2017
has db xref: DOI:10.3390/ijms20184411

Axiom
annotated source: blood vessel endothelial cell
annotated property: hasDbXref
annotated target: ZFA:0009036
mapping justification: UnspecifiedMatching

blood vessel endothelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: blood vessel endothelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000071

non-branched duct epithelial cell
type: Class
subclass of: duct epithelial cell
subclass of: CL_0002078

columnar/cuboidal epithelial cell
type: Class
subclass of: epithelial cell
IAO_0000115: A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
has db xref: ZFA:0009038
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: columnar/cuboidal epithelial cell
annotated property: IAO_0000115
annotated target: A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
has db xref: GO:0002065
has db xref: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: columnar/cuboidal epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009038
mapping justification: UnspecifiedMatching

squamous epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002254
subclass of: epithelial cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0002254
IAO_0000115: An epithelial cell that has a flattened morphology.
date: 2025-12-16T15:56:39Z
has db xref: CALOHA:TS-1249
has db xref: ZFA:0009039
in subset: cellxgene subset

Axiom
annotated source: squamous epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009039
mapping justification: UnspecifiedMatching

mesothelial cell
type: Class
subclass of: squamous epithelial cell
subclass of: CL_0002078
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001136
IAO_0000115: A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.
description: Mesothelial cells are crucial components of the mesothelium, a protective layer that lines the body's internal cavities, including pleural cavity (around the lungs), the pericardial cavity (around the heart), and the peritoneal cavity (within the abdomen). Derived from the embryonic mesoderm layer, these cells exhibit a squamous-like epithelial morphology, usually appearing as a single layer of flat, pavement-like cells in their healthy state. Mesothelial cells play a vital role in various physiological processes, such as intraperitoneal immunity, fibrinolysis, tissue repair, and tumor suppression. Their primary function is to provide a slippery, non-adhesive and protective surface to reduce friction and eases the movements of the organs within the pleural, pericardial, and peritoneal cavities, and they participate in the transport and movement of fluid and various molecules across the so-called serosal cavities. These cells have adaptive capabilities that facilitate their role in many pathological processes. In response to injury or inflammation, mesothelial cells can undergo morphological and functional changes, such as mesothelial-mesenchymal transitions, aiding in wound healing and tissue repair. Dysfunctions of mesothelial cells, however, can lead to serious health conditions, including adhesions, fibrosis, and malignancies such as peritoneal and pleural mesotheliomas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:66773
has db xref: ZFA:0009040
has exact synonym: mesotheliocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport.

Axiom
annotated source: mesothelial cell
annotated property: IAO_0000115
annotated target: A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.
has db xref: GOC:tfm
has db xref: ISBN:0721662544
has db xref: PMID:26106328

Axiom
annotated source: mesothelial cell
annotated property: description
annotated target: Mesothelial cells are crucial components of the mesothelium, a protective layer that lines the body's internal cavities, including pleural cavity (around the lungs), the pericardial cavity (around the heart), and the peritoneal cavity (within the abdomen). Derived from the embryonic mesoderm layer, these cells exhibit a squamous-like epithelial morphology, usually appearing as a single layer of flat, pavement-like cells in their healthy state. Mesothelial cells play a vital role in various physiological processes, such as intraperitoneal immunity, fibrinolysis, tissue repair, and tumor suppression. Their primary function is to provide a slippery, non-adhesive and protective surface to reduce friction and eases the movements of the organs within the pleural, pericardial, and peritoneal cavities, and they participate in the transport and movement of fluid and various molecules across the so-called serosal cavities. These cells have adaptive capabilities that facilitate their role in many pathological processes. In response to injury or inflammation, mesothelial cells can undergo morphological and functional changes, such as mesothelial-mesenchymal transitions, aiding in wound healing and tissue repair. Dysfunctions of mesothelial cells, however, can lead to serious health conditions, including adhesions, fibrosis, and malignancies such as peritoneal and pleural mesotheliomas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/S1357-2725(03)00242-5
has db xref: DOI:10.1038/s41467-020-16893-3
has db xref: DOI:10.1046/j.1440-1843.2002.00404.x
has db xref: DOI:10.3389/fphar.2015.00113

Axiom
annotated source: mesothelial cell
annotated property: hasDbXref
annotated target: ZFA:0009040
mapping justification: UnspecifiedMatching

Axiom
annotated source: mesothelial cell
annotated property: comment
annotated target: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport.
has db xref: PMID:26106328

mesothelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: mesothelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000077

stratified epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000486
subclass of: BFO_0000002
subclass of: epithelial cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000486
subclass of: Restriction
  on property: RO_0002202
  some values from: stratified epithelial stem cell
IAO_0000115: An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane.
description: Stratified epithelial cells form layers of cells stacked on top of one another, and they primarily function as a protective barrier. Their appearance can be cuboidal, columnar or squamous, and they offer a layer of defense against foreign bodies, harmful substances, pathogens, and prevent water loss and electrolyte imbalance within the body. Depending on the organ and its specific function, the topmost layer of these cells may be specialized as keratinized or non-keratinized. The skin, being constantly exposed to external physical stress, is composed of keratinized stratified epithelial cells that prevent desiccation and provide additional protection. In contrast, non-keratinized stratified epithelial cells line internally exposed surfaces like the oral cavity, esophagus, and vagina, where lubrication is required. In addition to protection, stratified epithelial cells also contribute to tissue repair processes, referred to as epithelialization. Basal epithelial cells are capable of rapid division and migration to heal wounds and maintain the protective barrier function of the tissues they line. Despite having a limited lifespan, these cells ensure a constant replacement process, maintaining their population and the integrity of epithelial layers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009042
in subset: cellxgene subset

Axiom
annotated source: stratified epithelial cell
annotated property: IAO_0000115
annotated target: An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane.
has db xref: Wikipedia:Epithelium
has db xref: doi:/10.1016/B978-0-12-410424-2.00003-2
has db xref: https://www.biologyonline.com/dictionary/stratified-epithelium

Axiom
annotated source: stratified epithelial cell
annotated property: description
annotated target: Stratified epithelial cells form layers of cells stacked on top of one another, and they primarily function as a protective barrier. Their appearance can be cuboidal, columnar or squamous, and they offer a layer of defense against foreign bodies, harmful substances, pathogens, and prevent water loss and electrolyte imbalance within the body. Depending on the organ and its specific function, the topmost layer of these cells may be specialized as keratinized or non-keratinized. The skin, being constantly exposed to external physical stress, is composed of keratinized stratified epithelial cells that prevent desiccation and provide additional protection. In contrast, non-keratinized stratified epithelial cells line internally exposed surfaces like the oral cavity, esophagus, and vagina, where lubrication is required. In addition to protection, stratified epithelial cells also contribute to tissue repair processes, referred to as epithelialization. Basal epithelial cells are capable of rapid division and migration to heal wounds and maintain the protective barrier function of the tissues they line. Despite having a limited lifespan, these cells ensure a constant replacement process, maintaining their population and the integrity of epithelial layers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/wdev.146
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK534261/

Axiom
annotated source: stratified epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009042
mapping justification: UnspecifiedMatching

stratified epithelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: stratified epithelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000079

blood cell
type: Class
equivalent class: Class
  intersection of: hematopoietic cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0008015
subclass of: hematopoietic cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0008015
IAO_0000115: A cell found predominately in the blood.
has db xref: FMA:62844
has db xref: MESH:D001773
has db xref: ZFA:0009044
in subset: cellxgene subset

Axiom
annotated source: blood cell
annotated property: subClassOf
annotated target: hematopoietic cell
is inferred: true

Axiom
annotated source: blood cell
annotated property: IAO_0000115
annotated target: A cell found predominately in the blood.
has db xref: GOC:add
has db xref: GOC:tfm

Axiom
annotated source: blood cell
annotated property: hasDbXref
annotated target: ZFA:0009044
mapping justification: UnspecifiedMatching

epithelial cell of lung
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000115
subclass of: CL_0002632
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000115
IAO_0000115: An epithelial cell of the lung.
has db xref: BTO:0004299
has exact synonym: lung epithelial cell
in subset: cellxgene subset

Axiom
annotated source: epithelial cell of lung
annotated property: IAO_0000115
annotated target: An epithelial cell of the lung.
has db xref: https://orcid.org/0000-0001-5208-3432

epithelial cell of pancreas
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001264
subclass of: CL_0002076
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001264
IAO_0000115: An epithelial cell of the pancreas.
has db xref: BTO:0000028
has db xref: ZFA:0009045
has exact synonym: pancreas epithelial cell
has exact synonym: pancreatic epithelial cell
in subset: cellxgene subset

Axiom
annotated source: epithelial cell of pancreas
annotated property: IAO_0000115
annotated target: An epithelial cell of the pancreas.
has db xref: GOC:tfm

Axiom
annotated source: epithelial cell of pancreas
annotated property: hasDbXref
annotated target: ZFA:0009045
mapping justification: UnspecifiedMatching

T cell
type: Class
equivalent class: Class
  intersection of: lymphocyte
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002456
subclass of: lymphocyte
subclass of: Restriction
  on property: RO_0002202
  some values from: pro-T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002456
disjoint with: lymphocyte of B lineage
IAO_0000115: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
has db xref: BTO:0000782
has db xref: CALOHA:TS-1001
has db xref: FMA:62870
has db xref: MESH:D013601
has db xref: VHOG:0001479
has db xref: ZFA:0009046
has exact synonym: T lymphocyte
has exact synonym: T-cell
has exact synonym: T-lymphocyte
has related synonym: immature T cell
has related synonym: mature T cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: T cell
annotated property: subClassOf
annotated target: lymphocyte
is inferred: true

Axiom
annotated source: T cell
annotated property: IAO_0000115
annotated target: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: T cell
annotated property: hasDbXref
annotated target: ZFA:0009046
mapping justification: UnspecifiedMatching

osteoclast
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001474
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001850
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001937
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001944
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007597
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000011178
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001954
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002062
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045453
subclass of: phagocyte (sensu Vertebrata)
subclass of: myeloid leukocyte
subclass of: bone cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001850
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001937
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001944
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007597
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000011178
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001954
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002062
subclass of: Restriction
  on property: RO_0002202
  some values from: monocyte
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045453
IAO_0000115: A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive.
description: Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000968
has db xref: CALOHA:TS-0721
has db xref: FMA:66781
has db xref: MESH:D010010
has db xref: ZFA:0009047
has related synonym: chondroclast
in subset: cellxgene subset
comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid.

Axiom
annotated source: osteoclast
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: osteoclast
annotated property: subClassOf
annotated target: bone cell
is inferred: true

Axiom
annotated source: osteoclast
annotated property: IAO_0000115
annotated target: A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: PMID:10428500
has db xref: PMID:15055519
has db xref: PMID:17380158

Axiom
annotated source: osteoclast
annotated property: description
annotated target: Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.3389/fmed.2017.00234
has db xref: DOI:10.37175/stemedicine.v1i4.57
has db xref: https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast

Axiom
annotated source: osteoclast
annotated property: hasDbXref
annotated target: ZFA:0009047
mapping justification: UnspecifiedMatching

osteoclast on CELLxGENE CellGuide
type: Axiom
annotated source: osteoclast
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000092

granulocyte
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0030141
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001332
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001969
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0008015
subclass of: blood cell
subclass of: myeloid leukocyte
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0030141
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001332
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001969
IAO_0000115: A leukocyte with abundant granules in the cytoplasm.
has db xref: BTO:0000539
has db xref: BTO:0001026
has db xref: CALOHA:TS-0422
has db xref: FMA:62854
has db xref: ZFA:0009048
has exact synonym: granular leucocyte
has exact synonym: granular leukocyte
has exact synonym: polymorphonuclear leukocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: granulocyte
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: granulocyte
annotated property: IAO_0000115
annotated target: A leukocyte with abundant granules in the cytoplasm.
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: MESH:D006098
has db xref: http://en.wikipedia.org/wiki/Granulocyte

Axiom
annotated source: granulocyte
annotated property: hasDbXref
annotated target: ZFA:0009048
mapping justification: UnspecifiedMatching

neuron associated cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0002319
subclass of: Restriction
  on property: RO_0002202
  some values from: neurectodermal cell
in subset: cellxgene subset

mature neutrophil
type: Class
equivalent class: Class
  intersection of: neutrophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017500
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0070820
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: GO_0005634
      intersection of: Restriction
        on property: RO_0000053
        some values from: PATO_0001979
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000009978
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000010543
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000010799
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001256
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001257
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001456
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001483
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001879
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001944
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000007597
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002536
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002690
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0006909
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032637
subclass of: phagocyte
subclass of: neutrophil
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017500
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0070820
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    intersection of: GO_0005634
    intersection of: Restriction
      on property: RO_0000053
      some values from: PATO_0001979
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000009978
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000010543
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000010799
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001256
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001257
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001456
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001483
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001944
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000007597
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002536
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002690
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032637
IAO_0000115: A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive.
has broad synonym: poly
has broad synonym: polymorphonuclear leucocyte
has broad synonym: polymorphonuclear leukocyte
has db xref: BTO:0003473
has db xref: ZFA:0009049
has exact synonym: PMN
has exact synonym: mature neutrocyte
has exact synonym: mature neutrophil leucocyte
has exact synonym: mature neutrophil leukocyte
has exact synonym: mature neutrophilic leucocyte
has exact synonym: mature neutrophilic leukocyte
has exact synonym: polymorphonuclear neutrophil
has exact synonym: polynuclear neutrophilic leucocyte
has exact synonym: polynuclear neutrophilic leukocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)).

Axiom
annotated source: mature neutrophil
annotated property: subClassOf
annotated target: neutrophil
is inferred: true

Axiom
annotated source: mature neutrophil
annotated property: IAO_0000115
annotated target: A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: MESH:D009504
has db xref: PMID:11138776
has db xref: PMID:12560239
has db xref: PMID:15514007
has db xref: PMID:7880385
has db xref: http://www.cap.org

Axiom
annotated source: mature neutrophil
annotated property: hasDbXref
annotated target: ZFA:0009049
mapping justification: UnspecifiedMatching

mast cell
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0030141
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001865
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001255
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000006169
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002349
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002539
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002660
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002690
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002830
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030210
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000007431
subclass of: myeloid leukocyte
subclass of: CL_0002274
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0030141
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001865
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001255
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000006169
subclass of: Restriction
  on property: RO_0002202
  some values from: mast cell progenitor
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002349
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002539
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002660
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002690
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002830
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030210
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000007431
IAO_0000115: A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
description: Mast cells, also known as mastocytes, are a type of innate immune cell. They originate from multipotent hematopoietic progenitor cells within the bone marrow, after which they migrate into nearly all tissues throughout the body. In these tissues, mast cells undergo complete maturation, with the exception of the blood. They are most densely located in the interfaces between the internal and external environments, such as the skin, respiratory system, and gastrointestinal mucosa. Mast cells are crucial players against pathogens and serve as first-line defense components. They contain numerous granules rich in histamine and heparin and are known primarily for their role in allergy and anaphylaxis. Upon encountering an allergen, pathogen, or even certain drugs and toxins, mast cells release these mediators via degranulation. Histamine induces vasodilation and vascular permeability, allowing for immune cells to rapidly reach the site of infection, while heparin prevents clotting in these areas to facilitate immune cell recruitment. Mast cells may also selectively secrete mediators without degranulation. These cells also play other functions beyond immune defense. They are involved in wound healing processes and maintenance of tissue integrity, angiogenesis, and even regulation of physiological functions in the gut. Consequently, because of their wide-ranging impacts, abnormalities in mast cell function can result in various disorders, including those related to allergies, inflammation, and autoimmune conditions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000830
has db xref: CALOHA:TS-0603
has db xref: FMA:66784
has exact synonym: histaminocyte
has exact synonym: labrocyte
has exact synonym: mastocyte
has related synonym: tissue basophil
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5.

Axiom
annotated source: mast cell
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: mast cell
annotated property: IAO_0000115
annotated target: A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:068340007X
has db xref: MESH:D008407
has db xref: PMCID:PMC1312421
has db xref: PMCID:PMC2855166
has db xref: PMID:15153310
has db xref: PMID:16455980
has db xref: PMID:19671378
has db xref: PMID:212366338
has db xref: PMID:9354811

Axiom
annotated source: mast cell
annotated property: description
annotated target: Mast cells, also known as mastocytes, are a type of innate immune cell. They originate from multipotent hematopoietic progenitor cells within the bone marrow, after which they migrate into nearly all tissues throughout the body. In these tissues, mast cells undergo complete maturation, with the exception of the blood. They are most densely located in the interfaces between the internal and external environments, such as the skin, respiratory system, and gastrointestinal mucosa. Mast cells are crucial players against pathogens and serve as first-line defense components. They contain numerous granules rich in histamine and heparin and are known primarily for their role in allergy and anaphylaxis. Upon encountering an allergen, pathogen, or even certain drugs and toxins, mast cells release these mediators via degranulation. Histamine induces vasodilation and vascular permeability, allowing for immune cells to rapidly reach the site of infection, while heparin prevents clotting in these areas to facilitate immune cell recruitment. Mast cells may also selectively secrete mediators without degranulation. These cells also play other functions beyond immune defense. They are involved in wound healing processes and maintenance of tissue integrity, angiogenesis, and even regulation of physiological functions in the gut. Consequently, because of their wide-ranging impacts, abnormalities in mast cell function can result in various disorders, including those related to allergies, inflammation, and autoimmune conditions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/s11894-010-0132-1
has db xref: DOI:10.1007/s12016-019-08729-w
has db xref: DOI:10.1016/j.bbadis.2010.12.014
has db xref: DOI:10.1056/NEJMra1409760
has db xref: DOI:10.1146/annurev-immunol-071719-094903

Axiom
annotated source: mast cell
annotated property: hasExactSynonym
annotated target: labrocyte
has db xref: ISBN:0721601464

Axiom
annotated source: mast cell
annotated property: hasExactSynonym
annotated target: mastocyte
has db xref: ISBN:0721601464

Axiom
annotated source: mast cell
annotated property: hasRelatedSynonym
annotated target: tissue basophil
has db xref: ISBN:068340007X

mast cell on CELLxGENE CellGuide
type: Axiom
annotated source: mast cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000097

sensory epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050906
subclass of: epithelial cell
subclass of: sensory receptor cell
IAO_0000115: A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.
has broad synonym: neuroepithelial cell
has db xref: BTO:0004301
has db xref: ZFA:0009050
comment: The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).

Axiom
annotated source: sensory epithelial cell
annotated property: IAO_0000115
annotated target: A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.
has db xref: GOC:tfm
has db xref: ISBN:0517223651
has db xref: ISBN:0721662544

Axiom
annotated source: sensory epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009050
mapping justification: UnspecifiedMatching

interneuron
type: Class
subclass of: CL_2000029
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001017
IAO_0000115: Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
has db xref: BTO:0003811
has db xref: FBbt:00005125
has db xref: FMA:67313
has db xref: WBbt:0005113
has db xref: ZFA:0009051
has related synonym: CNS interneuron
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: interneuron
annotated property: IAO_0000115
annotated target: Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
has db xref: GOC:tfm
has db xref: MESH:D007395

Axiom
annotated source: interneuron
annotated property: hasDbXref
annotated target: FBbt:00005125
mapping justification: ManualMappingCuration

Axiom
annotated source: interneuron
annotated property: hasDbXref
annotated target: ZFA:0009051
mapping justification: UnspecifiedMatching

motor neuron
type: Class
subclass of: efferent neuron
IAO_0000115: An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
description: Motor neurons, also known as motoneurons, are a type of neural cell that is fundamental to voluntary movement of muscles. Located within the central nervous system (CNS), motor neurons in the motor cortex travel to the brainstem and spinal cord. Motor neurons in the brainstem and spinal cord extend their lengthy axons out to muscles throughout the body. These specialized neurons are an inherent part of the so-called somatic division of the nervous system which mediates conscious control of skeletal muscles. The primary function of motor neurons is to relay signals from the CNS to the body's many muscles, controlling both their contraction and relaxation. In response to impulses transmitted from the brain or spinal cord, it creates an electrical signal (action potential), which travels along its axon to cause the controlled movement of specific muscles. Motor neurons can connect with skeletal muscles, cardiac muscles, or glands, leading to three respective types: somatic motor neurons, autonomic motor neurons, and the neurons of the enteric nervous system. Key components of motor neurons include the cell body (soma), dendrites, and axons. The cell body houses the nucleus and is the site of the neuron's intrinsic functions. Dendrites are thin structures that branch from the cell body and receive messages (electrical signals) from other neurons. The axon, a long, single tail-like extension, carries these signals away from the cell body towards the targeted muscle. If a motor neuron is damaged or dies, the muscle or gland it controls can lose function, which can result in conditions like motor neuron disease, leading to muscle weakness and atrophy. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000312
has db xref: FBbt:00005123
has db xref: FMA:83617
has db xref: WBbt:0005409
has db xref: ZFA:0009052
has exact synonym: motoneuron
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: motor neuron
annotated property: IAO_0000115
annotated target: An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
has db xref: MESH:D009046
has db xref: PMID:16875686

Axiom
annotated source: motor neuron
annotated property: description
annotated target: Motor neurons, also known as motoneurons, are a type of neural cell that is fundamental to voluntary movement of muscles. Located within the central nervous system (CNS), motor neurons in the motor cortex travel to the brainstem and spinal cord. Motor neurons in the brainstem and spinal cord extend their lengthy axons out to muscles throughout the body. These specialized neurons are an inherent part of the so-called somatic division of the nervous system which mediates conscious control of skeletal muscles. The primary function of motor neurons is to relay signals from the CNS to the body's many muscles, controlling both their contraction and relaxation. In response to impulses transmitted from the brain or spinal cord, it creates an electrical signal (action potential), which travels along its axon to cause the controlled movement of specific muscles. Motor neurons can connect with skeletal muscles, cardiac muscles, or glands, leading to three respective types: somatic motor neurons, autonomic motor neurons, and the neurons of the enteric nervous system. Key components of motor neurons include the cell body (soma), dendrites, and axons. The cell body houses the nucleus and is the site of the neuron's intrinsic functions. Dendrites are thin structures that branch from the cell body and receive messages (electrical signals) from other neurons. The axon, a long, single tail-like extension, carries these signals away from the cell body towards the targeted muscle. If a motor neuron is damaged or dies, the muscle or gland it controls can lose function, which can result in conditions like motor neuron disease, leading to muscle weakness and atrophy. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.semcdb.2017.11.016
has db xref: DOI:10.1146/annurev.neuro.051508.135722
has db xref: DOI:10.1249/JES.0000000000000032
has db xref: DOI:10.3389/fncel.2014.00293

Axiom
annotated source: motor neuron
annotated property: hasDbXref
annotated target: FBbt:00005123
mapping justification: ManualMappingCuration

Axiom
annotated source: motor neuron
annotated property: hasDbXref
annotated target: ZFA:0009052
mapping justification: UnspecifiedMatching

motor neuron on CELLxGENE CellGuide
type: Axiom
annotated source: motor neuron
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000100

sensory neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050906
subclass of: afferent neuron
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050906
IAO_0000115: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
has db xref: BTO:0001037
has db xref: FBbt:00005124
has db xref: FMA:84649
has db xref: MESH:D011984
has db xref: WBbt:0005759
has db xref: ZFA:0009053
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: sensory neuron
annotated property: IAO_0000115
annotated target: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
has db xref: ISBN:0721662544

Axiom
annotated source: sensory neuron
annotated property: hasDbXref
annotated target: FBbt:00005124
mapping justification: ManualMappingCuration

Axiom
annotated source: sensory neuron
annotated property: hasDbXref
annotated target: ZFA:0009053
mapping justification: UnspecifiedMatching

bipolar neuron
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0070006
subclass of: interneuron
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0070006
IAO_0000115: A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
description: The bipolar neuron is a type of nerve cell primarily found mainly in the sensory systems of the human body. These specialized cells possess two distinctive extensions or processes - one axon and one dendrite, emerging from the cell body on opposite ends, which gives them their bipolar appearance. These two extensions serve as conduits for electrical signals, with the dendrite primarily playing the role of receiving signals, and the axon transmitting them further. Functionally, bipolar neurons are crucial in facilitating the transmission of special senses, particularly in the senses of sight, smell, hearing, and balance. For example, the bipolar neurons in the retina convey information about light intensity, color, and movement from the photoreceptors to the ganglion cells, forming part of the pathway for visual input to travel towards the brain. Similarly, in the olfactory system, the olfactory cells are bipolar neurons characterized by a peripheral process, called the olfactory rod, which projects fine cilia. These cilia are the sites of olfactory receptors which play a critical role in recognizing thousands of odorant molecules and transmit information about smell from the nose to the brain. Bipolar neurons are also involved in hearing. The vestibular ganglion contains thousands of bipolar neurons that receive sensory signals from hair cells in the inner ear. The nerve signals pass through the bipolar neurons and leave along the vestibular nerve. The morphology of bipolar neurons with their single dendrite and axon also subtly boosts their efficiency, maintaining a streamlined path for signal conduction. Their distinctive structuring allows for faster and more targeted relay of sensory information from the body's peripheries to the central nervous system. Loss or damage of these neurons would directly impact sensory reception and could lead to disorders related to vision, hearing, smell, or balance, underlining the significance of this cell type in the body's sens…
has db xref: FMA:67282
has db xref: ZFA:0009055
in subset: BDS subset
in subset: cellxgene subset

Axiom
annotated source: bipolar neuron
annotated property: IAO_0000115
annotated target: A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
has db xref: GOC:tfm
has db xref: ISBN:0444009442

Axiom
annotated source: bipolar neuron
annotated property: description
annotated target: The bipolar neuron is a type of nerve cell primarily found mainly in the sensory systems of the human body. These specialized cells possess two distinctive extensions or processes - one axon and one dendrite, emerging from the cell body on opposite ends, which gives them their bipolar appearance. These two extensions serve as conduits for electrical signals, with the dendrite primarily playing the role of receiving signals, and the axon transmitting them further. Functionally, bipolar neurons are crucial in facilitating the transmission of special senses, particularly in the senses of sight, smell, hearing, and balance. For example, the bipolar neurons in the retina convey information about light intensity, color, and movement from the photoreceptors to the ganglion cells, forming part of the pathway for visual input to travel towards the brain. Similarly, in the olfactory system, the olfactory cells are bipolar neurons characterized by a peripheral process, called the olfactory rod, which projects fine cilia. These cilia are the sites of olfactory receptors which play a critical role in recognizing thousands of odorant molecules and transmit information about smell from the nose to the brain. Bipolar neurons are also involved in hearing. The vestibular ganglion contains thousands of bipolar neurons that receive sensory signals from hair cells in the inner ear. The nerve signals pass through the bipolar neurons and leave along the vestibular nerve. The morphology of bipolar neurons with their single dendrite and axon also subtly boosts their efficiency, maintaining a streamlined path for signal conduction. Their distinctive structuring allows for faster and more targeted relay of sensory information from the body's peripheries to the central nervous system. Loss or damage of these neurons would directly impact sensory reception and could lead to disorders related to vision, hearing, smell, or balance, underlining the significance of this cell type in the body's sens…
has db xref: DOI:10.1016/j.cell.2016.07.054
has db xref: DOI:10.1016/j.yexcr.2006.10.010
has db xref: DOI:10.1038/nrn3783
has db xref: DOI:10.1152/physrev.1986.66.3.772
has db xref: https://www.sciencedirect.com/topics/neuroscience/bipolar-neuron

Axiom
annotated source: bipolar neuron
annotated property: hasDbXref
annotated target: ZFA:0009055
mapping justification: UnspecifiedMatching

bipolar neuron on CELLxGENE CellGuide
type: Axiom
annotated source: bipolar neuron
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000103

unipolar neuron
type: Class
subclass of: CL_2000032
IAO_0000115: Neuron with one neurite that extends from the cell body.
has db xref: FMA:67278
has db xref: ZFA:0009058
in subset: BDS subset

Axiom
annotated source: unipolar neuron
annotated property: IAO_0000115
annotated target: Neuron with one neurite that extends from the cell body.
has db xref: FMA:67278
has db xref: GOC:nv

Axiom
annotated source: unipolar neuron
annotated property: hasDbXref
annotated target: ZFA:0009058
mapping justification: UnspecifiedMatching

autonomic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002100
    some values from: UBERON_0002410
subclass of: BFO_0000002
subclass of: CL_2000032
subclass of: Restriction
  on property: RO_0002100
  some values from: UBERON_0002410
IAO_0000115: A neuron whose cell body is within an autonomic ganglion.
has db xref: FMA:80121
has db xref: ZFA:0009059

Axiom
annotated source: autonomic neuron
annotated property: IAO_0000115
annotated target: A neuron whose cell body is within an autonomic ganglion.
has db xref: GOC:tfm

Axiom
annotated source: autonomic neuron
annotated property: hasDbXref
annotated target: ZFA:0009059
mapping justification: UnspecifiedMatching

cholinergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0014055
subclass of: secretory cell
subclass of: neuron
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0014055
IAO_0000115: A neuron that uses acetylcholine as a vesicular neurotransmitter.
has db xref: BTO:0004902
has db xref: FBbt:00007173
has db xref: FMA:84796
has db xref: MESH:D059329
has db xref: WBbt:0006840
has db xref: ZFA:0009060
in subset: human reference atlas

Axiom
annotated source: cholinergic neuron
annotated property: IAO_0000115
annotated target: A neuron that uses acetylcholine as a vesicular neurotransmitter.
has db xref: GOC:tfm

Axiom
annotated source: cholinergic neuron
annotated property: hasDbXref
annotated target: FBbt:00007173
mapping justification: ManualMappingCuration

Axiom
annotated source: cholinergic neuron
annotated property: hasDbXref
annotated target: ZFA:0009060
mapping justification: UnspecifiedMatching

mononuclear phagocyte
type: Class
equivalent class: Class
  intersection of: phagocyte (sensu Vertebrata)
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
subclass of: phagocyte (sensu Vertebrata)
subclass of: mononuclear leukocyte
IAO_0000115: A vertebrate phagocyte with a single nucleus.
description: Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it …
has db xref: BTO:0001433
has db xref: ZFA:0009064
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: mononuclear phagocyte
annotated property: subClassOf
annotated target: phagocyte (sensu Vertebrata)
is inferred: true

Axiom
annotated source: mononuclear phagocyte
annotated property: IAO_0000115
annotated target: A vertebrate phagocyte with a single nucleus.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: mononuclear phagocyte
annotated property: description
annotated target: Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it …
has db xref: DOI:10.1016/j.coi.2005.11.008
has db xref: DOI:10.1038/nri3087
has db xref: DOI:10.3389/fimmu.2019.01893

Axiom
annotated source: mononuclear phagocyte
annotated property: hasDbXref
annotated target: ZFA:0009064
mapping justification: UnspecifiedMatching

mononuclear phagocyte on CELLxGENE CellGuide
type: Axiom
annotated source: mononuclear phagocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000113

surface ectodermal cell
type: Class
equivalent class: Class
  intersection of: ectodermal cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000076
subclass of: ectodermal cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000076
IAO_0000115: An ectodermal cell that is part of the external ectoderm, forming the outermost layer of the developing embryo. It is characterized by its polarized nature, with distinct apical and basal surfaces (Ferrante Jr., Reinke, & Stanley, 1995). Surface ectodermal cell gives rise to the epidermis, hair follicles, nails, sensory organs, and specialized structures like the apical ectodermal ridge crucial for limb development (Skoufa et al., 2024).
description: Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:72552
has exact synonym: cell of surface ectoderm
has exact synonym: surface ectoderm cell

Axiom
annotated source: surface ectodermal cell
annotated property: IAO_0000115
annotated target: An ectodermal cell that is part of the external ectoderm, forming the outermost layer of the developing embryo. It is characterized by its polarized nature, with distinct apical and basal surfaces (Ferrante Jr., Reinke, & Stanley, 1995). Surface ectodermal cell gives rise to the epidermis, hair follicles, nails, sensory organs, and specialized structures like the apical ectodermal ridge crucial for limb development (Skoufa et al., 2024).
has db xref: PMID:7892198
has db xref: Wikipedia:Surface_ectoderm
has db xref: doi:/10.1101/2024.07.02.601324

Axiom
annotated source: surface ectodermal cell
annotated property: description
annotated target: Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/srep32007
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK539836/
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK563130

Axiom
annotated source: surface ectodermal cell
annotated property: hasExactSynonym
annotated target: surface ectoderm cell
has db xref: doi:/10.1101/2024.07.02.601324

surface ectodermal cell on CELLxGENE CellGuide
type: Axiom
annotated source: surface ectodermal cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000114

endothelial cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: mesodermal cell
IAO_0000115: An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
has db xref: BTO:0001176
has db xref: CALOHA:TS-0278
has db xref: FMA:66772
has db xref: ZFA:0009065
has exact synonym: endotheliocyte
in subset: cellxgene subset
in subset: general cell types upper slim
in subset: human reference atlas
comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].

Axiom
annotated source: endothelial cell
annotated property: IAO_0000115
annotated target: An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
has db xref: GOC:tfm
has db xref: MESH:D042783
has db xref: PMID:21275341
has db xref: http://en.wikipedia.org/wiki/Endothelial_cell
has db xref: https://sourceforge.net/tracker/

Axiom
annotated source: endothelial cell
annotated property: hasDbXref
annotated target: ZFA:0009065
mapping justification: UnspecifiedMatching

cerebellar Golgi cell
type: Class
subclass of: CL_4023057
subclass of: Restriction
  on property: RO_0002100
  some values from: UBERON_0002956
subclass of: Restriction
  on property: RO_0002113
  some values from: UBERON_0002956
subclass of: Restriction
  on property: RO_0002360
  some values from: UBERON_0002974
IAO_0000115: Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.
description: Cerebellar Golgi cells are a specific type of inhibitory interneuron found within the granular layer of the cerebellum, a major part of the vertebrate brain responsible for motor control, learning, and cognitive functions. Named after the Italian scientist Camillo Golgi, these cells play a unique and important role in modulating electrical signals in the complex cerebellar neural network. The distinctive feature of the cerebellar Golgi cells is their dendritic arbor that extends throughout the molecular layer of the cerebellum, in line with the axons of the granule cells. The axons of Golgi cells primarily synapse with the dendrites of granule cells, generating a synaptic feedback loop that plays a vital role in regulating the intensity and timing of signal transmission. They also form synapses with mossy fiber terminals, which provide primary input to the cerebellar cortex. Functionally, cerebellar Golgi cells serve as "gatekeepers" of the cerebellar cortex. They have a strong inhibitory influence on granule cells, modulating the information flow to the Purkinje cells, the main output neurons of the cerebellar cortex. Thus, Golgi cells play a critical role in controlling the input-output relationship within the cerebellum, shaping the timing and strength of signals originating from various sensory and motor areas of the cerebral cortex. This regulatory function is instrumental for the fine-tuning of motor coordination, timing and learning. Thus, alterations in Golgi cell functions can contribute to a range of neurological and neuropsychiatric disorders such as ataxias and cognitive deficits. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: MESH:D000080906
has db xref: ZFA:0009069
has exact synonym: Golgi cell
has exact synonym: Golgi neuron
has exact synonym: cerebellar Golgi neuron
has exact synonym: cerebellum Golgi cell
in subset: cellxgene subset

Axiom
annotated source: cerebellar Golgi cell
annotated property: IAO_0000115
annotated target: Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.
has db xref: NIFSTD:sao1415726815

Axiom
annotated source: cerebellar Golgi cell
annotated property: description
annotated target: Cerebellar Golgi cells are a specific type of inhibitory interneuron found within the granular layer of the cerebellum, a major part of the vertebrate brain responsible for motor control, learning, and cognitive functions. Named after the Italian scientist Camillo Golgi, these cells play a unique and important role in modulating electrical signals in the complex cerebellar neural network. The distinctive feature of the cerebellar Golgi cells is their dendritic arbor that extends throughout the molecular layer of the cerebellum, in line with the axons of the granule cells. The axons of Golgi cells primarily synapse with the dendrites of granule cells, generating a synaptic feedback loop that plays a vital role in regulating the intensity and timing of signal transmission. They also form synapses with mossy fiber terminals, which provide primary input to the cerebellar cortex. Functionally, cerebellar Golgi cells serve as "gatekeepers" of the cerebellar cortex. They have a strong inhibitory influence on granule cells, modulating the information flow to the Purkinje cells, the main output neurons of the cerebellar cortex. Thus, Golgi cells play a critical role in controlling the input-output relationship within the cerebellum, shaping the timing and strength of signals originating from various sensory and motor areas of the cerebral cortex. This regulatory function is instrumental for the fine-tuning of motor coordination, timing and learning. Thus, alterations in Golgi cell functions can contribute to a range of neurological and neuropsychiatric disorders such as ataxias and cognitive deficits. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/S0896-6273(00)81126-5
has db xref: DOI:10.1016/j.neuron.2011.10.030
has db xref: DOI:10.1113/jphysiol.2010.189605
has db xref: DOI:10.1126/science.1215101
has db xref: DOI:10.3389/fncir.2013.00093

Axiom
annotated source: cerebellar Golgi cell
annotated property: hasDbXref
annotated target: ZFA:0009069
mapping justification: UnspecifiedMatching

cerebellar Golgi cell on CELLxGENE CellGuide
type: Axiom
annotated source: cerebellar Golgi cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000119

Axiom
annotated source: cerebellar Golgi cell
annotated property: depiction
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
has db xref: doi:10.1016/j.cnp.2022.11.002

Axiom
annotated source: cerebellar Golgi cell
annotated property: depiction
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
has db xref: doi:10.3389/fnins.2020.00293

granule cell
type: Class
subclass of: CL_2000029
IAO_0000115: A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb.
description: Granule cells are a class of small neurons found significantly in the cerebellum, olfactory bulb, and the dentate gyrus of the hippocampus in the human central nervous system. Their name derives from the presence of internal granular structures and they are one of the most abundant cell types in the entire brain, with estimates suggesting they likely comprise over half of all neurons. Due to their location, these cells play a vital role in the modulation of motor coordination, the olfactory system, and some aspects of memory and learning. Structurally, granule cells differ depending on their location. They have unmyelinated, very thin, T-shaped axons and a few short dendrites in the cerebellum. These dendrites receive information from a variety of sources, while their axons transmit the information to other parts of the brain. In granule cells of the cerebellum, the axons form parallel fibers that run into the molecular layer and synapse onto Purkinje cells, stellate, and basket cells, setting up a neuronal circuit critical for generating precise and fluid movements. Functionally, granule cells receive excitatory input from mossy fibers, which deliver sensory and motor information to the cerebellum, and this interaction is fundamental for the timing and coordination of body movements. In the olfactory bulb, granule cells process and modify olfactory information before passing it to the cerebral cortex, thereby aiding smell perception. Meanwhile, in the hippocampus, these cells participate in the formation and sorting of memories, particularly episodic memories. Due to their number, location, and function, the granule cells have a significant influence on cognition and behavior. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0003393
has db xref: ZFA:0009070
in subset: cellxgene subset

Axiom
annotated source: granule cell
annotated property: IAO_0000115
annotated target: A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb.
has db xref: granule+cell

Axiom
annotated source: granule cell
annotated property: description
annotated target: Granule cells are a class of small neurons found significantly in the cerebellum, olfactory bulb, and the dentate gyrus of the hippocampus in the human central nervous system. Their name derives from the presence of internal granular structures and they are one of the most abundant cell types in the entire brain, with estimates suggesting they likely comprise over half of all neurons. Due to their location, these cells play a vital role in the modulation of motor coordination, the olfactory system, and some aspects of memory and learning. Structurally, granule cells differ depending on their location. They have unmyelinated, very thin, T-shaped axons and a few short dendrites in the cerebellum. These dendrites receive information from a variety of sources, while their axons transmit the information to other parts of the brain. In granule cells of the cerebellum, the axons form parallel fibers that run into the molecular layer and synapse onto Purkinje cells, stellate, and basket cells, setting up a neuronal circuit critical for generating precise and fluid movements. Functionally, granule cells receive excitatory input from mossy fibers, which deliver sensory and motor information to the cerebellum, and this interaction is fundamental for the timing and coordination of body movements. In the olfactory bulb, granule cells process and modify olfactory information before passing it to the cerebral cortex, thereby aiding smell perception. Meanwhile, in the hippocampus, these cells participate in the formation and sorting of memories, particularly episodic memories. Due to their number, location, and function, the granule cells have a significant influence on cognition and behavior. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/S0168-0102(97)00099-0
has db xref: DOI:10.1016/j.brainresrev.2007.03.005
has db xref: DOI:10.1016/j.neubiorev.2016.02.021
has db xref: DOI:10.12688/f1000research.15021.1
has db xref: DOI:10.3389/fncir.2020.611841

Axiom
annotated source: granule cell
annotated property: hasDbXref
annotated target: ZFA:0009070
mapping justification: UnspecifiedMatching

granule cell on CELLxGENE CellGuide
type: Axiom
annotated source: granule cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000120

Purkinje cell
type: Class
subclass of: GABAergic neuron
subclass of: CL_1001611
subclass of: Restriction
  on property: RO_0002100
  some values from: UBERON_0002979
IAO_0000115: An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress.
description: Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction …
has db xref: BTO:0001011
has db xref: CALOHA:TS-0845
has db xref: FMA:67969
has db xref: ZFA:0009071
has exact synonym: Purkinje neuron
has exact synonym: cerebellar Purkinje cell
has related synonym: PC
has related synonym: PN
in subset: cellxgene subset
comment: Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024).

Axiom
annotated source: Purkinje cell
annotated property: IAO_0000115
annotated target: An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress.
has db xref: MESH:D011689
has db xref: PMID:12907269
has db xref: PMID:14568361
has db xref: PMID:31424738
has db xref: PMID:33288911
has db xref: PMID:38168772

Axiom
annotated source: Purkinje cell
annotated property: description
annotated target: Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction …
has db xref: DOI:10.1007/s12311-018-0985-7
has db xref: DOI:10.1038/nrn3886
has db xref: DOI:10.7554/eLife.63668
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK545154/
has db xref: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell

Axiom
annotated source: Purkinje cell
annotated property: hasDbXref
annotated target: ZFA:0009071
mapping justification: UnspecifiedMatching

Axiom
annotated source: Purkinje cell
annotated property: hasExactSynonym
annotated target: Purkinje neuron
has db xref: PMID:28821816

Axiom
annotated source: Purkinje cell
annotated property: hasExactSynonym
annotated target: cerebellar Purkinje cell
has db xref: https://doi.org/10.1016/j.proghi.2004.07.002

Axiom
annotated source: Purkinje cell
annotated property: hasRelatedSynonym
annotated target: PC
has db xref: PMID:38168772
has synonym type: OMO_0003000

Axiom
annotated source: Purkinje cell
annotated property: hasRelatedSynonym
annotated target: PN
has db xref: PMID:28821816
has synonym type: OMO_0003000

Axiom
annotated source: Purkinje cell
annotated property: comment
annotated target: Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024).
has db xref: PMID:17535929
has db xref: PMID:27215193
has db xref: PMID:37426070
has db xref: https://doi.org/10.1016/j.stem.2023.11.013

Purkinje cell on CELLxGENE CellGuide
type: Axiom
annotated source: Purkinje cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000121

Axiom
annotated source: Purkinje cell
annotated property: depiction
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
has db xref: doi:10.1016/j.cnp.2022.11.002

Axiom
annotated source: Purkinje cell
annotated property: depiction
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
has db xref: doi:10.3389/fnins.2020.00293

stellate neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0070010
subclass of: CL_2000029
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0070010
IAO_0000115: A neuron that has dendritic processes radiating from the cell body forming a star-like shape.
description: Stellate neurons are a specialized type of interneurons found predominantly in the cerebral cortex and the cerebellum, two major components of the brain's central nervous system. These neurons are named for their distinct star-like shape, characterized by short dendrites that radiate from the cell body in multiple directions. They are a key component of the mammalian neural circuit due to their unique morphology and crucial functions in neural communication. Stellate neurons play a pivotal role in the processing and transmission of information within the brain. In the cerebellum, these neurons are predominantly inhibitory and release the neurotransmitter gamma-aminobutyric acid (GABA), effectively regulating the excitability of other neurons within the network and thus fine-tuning the neuron-to-neuron communication. Their extensive dendritic network allows for connections with multiple neurons allowing for the integration of synaptic inputs from various sources in the brain. This widespread connectivity places stellate neurons at the heart of information processing in the central nervous system. In addition to their important inhibitory role in regulating and processing information, the role of stellate neurons in the cerebellum differs slightly from their cortical counterparts. The cortical spiny stellate neurons are excitatory and release the neurotransmitter glutamate. They are involved in motor control and responsible for coordinating precise, voluntary movements and maintaining posture and balance. Any dysfunction in these cerebellar neurons can lead to movement disorders, highlighting their significance in our daily activities. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0002316
has db xref: ZFA:0009072
in subset: BDS subset
in subset: cellxgene subset

Axiom
annotated source: stellate neuron
annotated property: IAO_0000115
annotated target: A neuron that has dendritic processes radiating from the cell body forming a star-like shape.
has db xref: ISBN:9780123973481

Axiom
annotated source: stellate neuron
annotated property: description
annotated target: Stellate neurons are a specialized type of interneurons found predominantly in the cerebral cortex and the cerebellum, two major components of the brain's central nervous system. These neurons are named for their distinct star-like shape, characterized by short dendrites that radiate from the cell body in multiple directions. They are a key component of the mammalian neural circuit due to their unique morphology and crucial functions in neural communication. Stellate neurons play a pivotal role in the processing and transmission of information within the brain. In the cerebellum, these neurons are predominantly inhibitory and release the neurotransmitter gamma-aminobutyric acid (GABA), effectively regulating the excitability of other neurons within the network and thus fine-tuning the neuron-to-neuron communication. Their extensive dendritic network allows for connections with multiple neurons allowing for the integration of synaptic inputs from various sources in the brain. This widespread connectivity places stellate neurons at the heart of information processing in the central nervous system. In addition to their important inhibitory role in regulating and processing information, the role of stellate neurons in the cerebellum differs slightly from their cortical counterparts. The cortical spiny stellate neurons are excitatory and release the neurotransmitter glutamate. They are involved in motor control and responsible for coordinating precise, voluntary movements and maintaining posture and balance. Any dysfunction in these cerebellar neurons can lead to movement disorders, highlighting their significance in our daily activities. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/cne.901460304
has db xref: DOI:10.1007/s11055-006-0093-x
has db xref: DOI:10.1038/nn1698
has db xref: DOI:10.1126/science.aai8178
has db xref: DOI:10.1523/JNEUROSCI.2929-06.2006

Axiom
annotated source: stellate neuron
annotated property: hasDbXref
annotated target: ZFA:0009072
mapping justification: UnspecifiedMatching

stellate neuron on CELLxGENE CellGuide
type: Axiom
annotated source: stellate neuron
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000122

neuron associated cell (sensu Vertebrata)
type: Class
subclass of: neuron associated cell
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
in subset: cellxgene subset

glial cell
type: Class
subclass of: neuron associated cell
IAO_0000115: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
description: Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease a…
has db xref: BTO:0002606
has db xref: CALOHA:TS-0415
has db xref: FBbt:00005144
has db xref: FMA:54536
has db xref: ZFA:0009073
has exact synonym: neuroglial cell
has related synonym: neuroglia
in subset: cellxgene subset
in subset: human reference atlas
comment: Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571

Axiom
annotated source: glial cell
annotated property: IAO_0000115
annotated target: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
has db xref: MESH:D009457

Axiom
annotated source: glial cell
annotated property: description
annotated target: Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease a…
has db xref: DOI:10.1002/glia.24343
has db xref: DOI:10.1038/nn1988
has db xref: DOI:10.1101/cshperspect.a020602
has db xref: DOI:10.1126/science.aat0473
has db xref: DOI:10.3389/fncel.2017.00024

Axiom
annotated source: glial cell
annotated property: hasDbXref
annotated target: FBbt:00005144
mapping justification: ManualMappingCuration

Axiom
annotated source: glial cell
annotated property: hasDbXref
annotated target: ZFA:0009073
mapping justification: UnspecifiedMatching

glial cell on CELLxGENE CellGuide
type: Axiom
annotated source: glial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000125

macroglial cell
type: Class
subclass of: glial cell
subclass of: Restriction
  on property: RO_0002202
  some values from: glioblast (sensu Vertebrata)
IAO_0000115: A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together.
has db xref: BTO:0000771
has db xref: CALOHA:TS-2027
has db xref: FMA:54538
has db xref: ZFA:0009074
has exact synonym: macrogliocyte
has related synonym: macroglia
in subset: cellxgene subset

Axiom
annotated source: macroglial cell
annotated property: IAO_0000115
annotated target: A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: macroglial cell
annotated property: hasDbXref
annotated target: ZFA:0009074
mapping justification: UnspecifiedMatching

Axiom
annotated source: macroglial cell
annotated property: hasRelatedSynonym
annotated target: macroglia
has db xref: doi:10.1152/physrev.2001.81.2.871
has synonym type: OMO_0003004

astrocyte
type: Class
subclass of: macroglial cell
IAO_0000115: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury.
has db xref: BTO:0000099
has db xref: CALOHA:TS-0060
has db xref: FMA:54537
has db xref: ZFA:0009075
has exact synonym: astrocytic glia
in subset: cellxgene subset
in subset: human reference atlas
comment: Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive.

Axiom
annotated source: astrocyte
annotated property: IAO_0000115
annotated target: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury.
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: MESH:D001253
has db xref: PMID:11746784
has db xref: PMID:12162730
has db xref: PMID:12898703
has db xref: PMID:20942978
has db xref: http://en.wikipedia.org/wiki/Astrocyte

Axiom
annotated source: astrocyte
annotated property: hasDbXref
annotated target: ZFA:0009075
mapping justification: UnspecifiedMatching

oligodendrocyte
type: Class
subclass of: macroglial cell
subclass of: CL_4023154
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001017
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002453
IAO_0000115: A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.
has db xref: BTO:0000962
has db xref: CALOHA:TS-0709
has db xref: FMA:54540
has db xref: ZFA:0009076
has exact synonym: OLs
has related synonym: oligodendroglia
in subset: cellxgene subset
in subset: human reference atlas
comment: Oligodendrocytes are reportedly MDP-positive and CD4-negative.

Axiom
annotated source: oligodendrocyte
annotated property: subClassOf
annotated target: macroglial cell
is inferred: true

Axiom
annotated source: oligodendrocyte
annotated property: IAO_0000115
annotated target: A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.
has db xref: MESH:D009836
has db xref: http://en.wikipedia.org/wiki/Oligodendrocyte

Axiom
annotated source: oligodendrocyte
annotated property: hasDbXref
annotated target: ZFA:0009076
mapping justification: UnspecifiedMatching

Axiom
annotated source: oligodendrocyte
annotated property: hasExactSynonym
annotated target: OLs
has db xref: PMID:8734446

microglial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001017
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001813
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002064
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045087
subclass of: glial cell
subclass of: central nervous system macrophage
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001813
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002064
subclass of: Restriction
  on property: RO_0002202
  some values from: mesodermal cell
subclass of: Restriction
  on property: RO_0002202
  some values from: Class
    intersection of: stem cell
    intersection of: Restriction
      on property: BFO_0000050
      some values from: UBERON_0001040
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045087
IAO_0000115: A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.
description: Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. (This extended description was generated by ChatGPT and revi…
has broad synonym: brain macrophage
has db xref: BTO:0000078
has db xref: BTO:0000962
has db xref: FMA:54539
has db xref: ZFA:0009077
has exact synonym: brain-resident macrophage
has exact synonym: hortega cells
has exact synonym: microgliocyte
has related synonym: MF.microglia.CNS
has related synonym: microglia
in subset: cellxgene subset
in subset: human reference atlas
comment: Unlike macroglial cells, microglial cells arise from hematopoietic stem cells in the yolk sac during early embryogenesis that populate the central nervous system. They derive from embryonic mesoderm and are not from neuroectoderm where glioblast develops from. Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive.

Axiom
annotated source: microglial cell
annotated property: IAO_0000115
annotated target: A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: MESH:D017628
has db xref: PMID:11517395
has db xref: PMID:12430718
has db xref: PMID:14561199
has db xref: PMID:14612429
has db xref: PMID:16177057
has db xref: PMID:19461673
has db xref: PMID:2089275
has db xref: http://en.wikipedia.org/wiki/Microglia

Axiom
annotated source: microglial cell
annotated property: description
annotated target: Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. (This extended description was generated by ChatGPT and revi…
has db xref: DOI:10.1016/j.cell.2019.08.053
has db xref: DOI:10.1016/j.conb.2022.102674
has db xref: DOI:10.1016/j.tins.2021.11.001
has db xref: DOI:10.1038/nri3086
has db xref: DOI:10.3389/fnins.2021.742065

Axiom
annotated source: microglial cell
annotated property: hasDbXref
annotated target: ZFA:0009077
mapping justification: UnspecifiedMatching

Axiom
annotated source: microglial cell
annotated property: hasExactSynonym
annotated target: hortega cells
has db xref: http://www.copewithcytokines.de/

Axiom
annotated source: microglial cell
annotated property: hasExactSynonym
annotated target: microgliocyte
has db xref: http://www.copewithcytokines.de/

Axiom
annotated source: microglial cell
annotated property: hasRelatedSynonym
annotated target: microglia
has db xref: doi:10.1038/s41598-020-66092-9
has synonym type: OMO_0003004

Axiom
annotated source: microglial cell
annotated property: comment
annotated target: Unlike macroglial cells, microglial cells arise from hematopoietic stem cells in the yolk sac during early embryogenesis that populate the central nervous system. They derive from embryonic mesoderm and are not from neuroectoderm where glioblast develops from. Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive.
has db xref: PMID:23616747

microglial cell on CELLxGENE CellGuide
type: Axiom
annotated source: microglial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000129

gut endothelial cell
type: Class
equivalent class: Class
  intersection of: endothelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001555
subclass of: endothelial cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001555
subclass of: Restriction
  on property: RO_0002202
  some values from: endodermal cell
IAO_0000115: An endothelial cell that lines the blood and lymphatic vessels of the digestive tract. This cell forms the gut–vascular barrier (GVB) through tight junctions and crosstalk with pericytes and enteric glial cells, regulating the passage of nutrients and immune cells while restricting microbial translocation into the bloodstream.
description: Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or "gut". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009078
in subset: cellxgene subset

Axiom
annotated source: gut endothelial cell
annotated property: IAO_0000115
annotated target: An endothelial cell that lines the blood and lymphatic vessels of the digestive tract. This cell forms the gut–vascular barrier (GVB) through tight junctions and crosstalk with pericytes and enteric glial cells, regulating the passage of nutrients and immune cells while restricting microbial translocation into the bloodstream.
has db xref: PMID:26564856

Axiom
annotated source: gut endothelial cell
annotated property: description
annotated target: Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or "gut". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/nri2171
has db xref: DOI:10.1111/bph.14527
has db xref: DOI:10.3390/ijms23073698
has db xref: DOI:10.3748/wjg.v17.i5.578
has db xref: DOI:full/10.15252/emmm.202114121

Axiom
annotated source: gut endothelial cell
annotated property: hasDbXref
annotated target: ZFA:0009078
mapping justification: UnspecifiedMatching

gut endothelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: gut endothelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000131

neurectodermal cell
type: Class
subclass of: ectodermal cell
IAO_0000115: Ectoderm destined to be nervous tissue.
has db xref: ZFA:0009080
has exact synonym: neurectoderm cell
in subset: cellxgene subset

Axiom
annotated source: neurectodermal cell
annotated property: IAO_0000115
annotated target: Ectoderm destined to be nervous tissue.
has db xref: GOC:tfm
has db xref: ISBN:068340007X

Axiom
annotated source: neurectodermal cell
annotated property: hasDbXref
annotated target: ZFA:0009080
mapping justification: UnspecifiedMatching

mesenchymal stem cell
type: Class
subclass of: multi fate stem cell
subclass of: CL_0002320
IAO_0000115: A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
description: Mesenchymal stem cells (MSCs) are multipotent stromal cells that can differentiate into a variety of cell types, including osteoblasts, chondrocytes, myocytes, and adipocytes. These cells originate mainly from the mesoderm of the embryo, which forms connective tissues, muscle, and the circulatory and urinary systems. However, in adults, MSCs are found in multiple tissues, including bone marrow, adipose tissue, the umbilical cord, and dental tissues. The primary function of MSCs is to maintain and repair the tissues in which they are found. When damage occurs, the MSCs are able to migrate to the site of injury, where they aid in regenerating the damaged tissue by differentiating into the required cell type and by secreting growth factors that enhance tissue repair and reduce inflammation. Furthermore, MSCs can also act as immunomodulators, suppressing immune reactions and reducing inflammation, both locally and systemically. Apart from their role in tissue maintenance and repair, MSCs are integral to the field of regenerative medicine and are being investigated for their therapeutic potential in various clinical settings. Owing to their multipotent nature, immunomodulatory activity, and the relative ease of isolation, these cells can be engineered and translated into therapies to treat a variety of diseases, including bone and cartilage defects, liver diseases, heart disorders, and autoimmune diseases, amongst others. They have also been used as vectors for anticancer agents and in cell and gene therapy applications. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0002625
has db xref: BTO:0003298
has db xref: FMA:70546
has db xref: ZFA:0009081
has narrow synonym: bone marrow stromal cells
has narrow synonym: colony-forming unit-fibroblast
has narrow synonym: marrow stromal cells
has related synonym: BMSC
has related synonym: CFU-F
has related synonym: MSC
has related synonym: mesenchymal precursor cell
has related synonym: mesenchymal progenitor cells
has related synonym: mesenchymal stem cell
has related synonym: mesenchymal stromal cell
has related synonym: mesenchymal stromal cells
has related synonym: stem cells, mesenchymal
in subset: cellxgene subset
in subset: human reference atlas
comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.

Axiom
annotated source: mesenchymal stem cell
annotated property: subClassOf
annotated target: CL_0002320
is inferred: true

Axiom
annotated source: mesenchymal stem cell
annotated property: IAO_0000115
annotated target: A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
has db xref: FB:ma
has db xref: GOC:dsd
has db xref: PMCID:PMC2613570
has db xref: PMID:10102814
has db xref: PMID:16923606
has db xref: PMID:17986482
has db xref: PMID:19960544
has db xref: http://en.wikipedia.org/wiki/Mesenchymal_stem_cell
has db xref: http://www.copewithcytokines.de/cope.cgi

Axiom
annotated source: mesenchymal stem cell
annotated property: description
annotated target: Mesenchymal stem cells (MSCs) are multipotent stromal cells that can differentiate into a variety of cell types, including osteoblasts, chondrocytes, myocytes, and adipocytes. These cells originate mainly from the mesoderm of the embryo, which forms connective tissues, muscle, and the circulatory and urinary systems. However, in adults, MSCs are found in multiple tissues, including bone marrow, adipose tissue, the umbilical cord, and dental tissues. The primary function of MSCs is to maintain and repair the tissues in which they are found. When damage occurs, the MSCs are able to migrate to the site of injury, where they aid in regenerating the damaged tissue by differentiating into the required cell type and by secreting growth factors that enhance tissue repair and reduce inflammation. Furthermore, MSCs can also act as immunomodulators, suppressing immune reactions and reducing inflammation, both locally and systemically. Apart from their role in tissue maintenance and repair, MSCs are integral to the field of regenerative medicine and are being investigated for their therapeutic potential in various clinical settings. Owing to their multipotent nature, immunomodulatory activity, and the relative ease of isolation, these cells can be engineered and translated into therapies to treat a variety of diseases, including bone and cartilage defects, liver diseases, heart disorders, and autoimmune diseases, amongst others. They have also been used as vectors for anticancer agents and in cell and gene therapy applications. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/cdd.2013.158
has db xref: DOI:10.1038/nri2395
has db xref: DOI:10.1038/s41536-019-0083-6
has db xref: DOI:10.3727/096368910X

Axiom
annotated source: mesenchymal stem cell
annotated property: hasDbXref
annotated target: ZFA:0009081
mapping justification: UnspecifiedMatching

Axiom
annotated source: mesenchymal stem cell
annotated property: hasNarrowSynonym
annotated target: marrow stromal cells
has db xref: PMID:11378515

Axiom
annotated source: mesenchymal stem cell
annotated property: hasRelatedSynonym
annotated target: BMSC
has synonym type: OMO_0003000

Axiom
annotated source: mesenchymal stem cell
annotated property: hasRelatedSynonym
annotated target: CFU-F
has synonym type: OMO_0003000

Axiom
annotated source: mesenchymal stem cell
annotated property: hasRelatedSynonym
annotated target: MSC
has db xref: PMID:11378515
has synonym type: OMO_0003000

Axiom
annotated source: mesenchymal stem cell
annotated property: hasRelatedSynonym
annotated target: mesenchymal progenitor cells
has db xref: MESH:D044982
has synonym type: OMO_0003004

Axiom
annotated source: mesenchymal stem cell
annotated property: hasRelatedSynonym
annotated target: mesenchymal stromal cells
has synonym type: OMO_0003004

Axiom
annotated source: mesenchymal stem cell
annotated property: hasRelatedSynonym
annotated target: stem cells, mesenchymal
has db xref: MESH:D044982
has synonym type: OMO_0003004

mesenchymal stem cell on CELLxGENE CellGuide
type: Axiom
annotated source: mesenchymal stem cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000134

adipocyte
type: Class
subclass of: BFO_0000002
subclass of: stuff accumulating cell
subclass of: CL_0002320
subclass of: Restriction
  on property: RO_0002202
  some values from: mesenchymal stem cell
IAO_0000115: A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
description: A fat cell, also known as an adipocyte, is a specialized type of connective tissue cell responsible for the storage of fat in the body. These cells can be found throughout the body, but are most densely located in adipose tissue, such as the subcutaneous tissue beneath the skin and around organs, and act as the body’s energy storage units. The primary function of fat cells is to store energy in the form of fat, also known as triglycerides, for use during periods of caloric deficit. When we consume more calories than we use for energy, our bodies convert the excess energy into fat and store it in adipose tissue. Fat cells also play a role in regulating energy balance by secreting hormones, such as leptin and adiponectin, which help to regulate appetite and metabolism. Fat calls have also been implicated in the development of obesity-related diseases, such as insulin resistance and type 2 diabetes. Finally, fat cells have been found to play a role in the immune system by secreting cytokines, which can either promote or inhibit inflammation depending on the type of cytokine produced. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000443
has db xref: CALOHA:TS-0012
has db xref: FMA:63880
has db xref: ZFA:0009082
has exact synonym: adipose cell
has exact synonym: fat cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: adipocyte
annotated property: IAO_0000115
annotated target: A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
has db xref: MESH:D017667

Axiom
annotated source: adipocyte
annotated property: description
annotated target: A fat cell, also known as an adipocyte, is a specialized type of connective tissue cell responsible for the storage of fat in the body. These cells can be found throughout the body, but are most densely located in adipose tissue, such as the subcutaneous tissue beneath the skin and around organs, and act as the body’s energy storage units. The primary function of fat cells is to store energy in the form of fat, also known as triglycerides, for use during periods of caloric deficit. When we consume more calories than we use for energy, our bodies convert the excess energy into fat and store it in adipose tissue. Fat cells also play a role in regulating energy balance by secreting hormones, such as leptin and adiponectin, which help to regulate appetite and metabolism. Fat calls have also been implicated in the development of obesity-related diseases, such as insulin resistance and type 2 diabetes. Finally, fat cells have been found to play a role in the immune system by secreting cytokines, which can either promote or inhibit inflammation depending on the type of cytokine produced. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/s10753-021-01559-z
has db xref: DOI:10.1091/mbc.e15-10-0749
has db xref: DOI:10.1098/rstb.2006.1859

Axiom
annotated source: adipocyte
annotated property: hasDbXref
annotated target: ZFA:0009082
mapping justification: UnspecifiedMatching

adipocyte on CELLxGENE CellGuide
type: Axiom
annotated source: adipocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000136

chondrocyte
type: Class
subclass of: glycosaminoglycan secreting cell
subclass of: collagen secreting cell
subclass of: CL_0007001
subclass of: Restriction
  on property: RO_0001025
  some values from: UBERON_0002418
subclass of: Restriction
  on property: RO_0002202
  some values from: chondroblast
IAO_0000115: A skeletogenic cell that secretes a specialized, avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell.
description: Chondrocytes are specialized cells derived from the mesenchyme. They are the only cells found in healthy cartilage, and their primary function is the synthesis and maintenance of the extracellular matrix of cartilaginous tissues. They synthesize various molecules essential for biomechanical function, including collagen types II, IX, and XI, link proteins, and proteoglycans like aggrecan and decorin. Beyond structural integrity, chondrocytes also contribute significantly to the homeostasis of articular cartilage in joints. The chondrocyte lifecycle involves proliferation, maturation, and hypertrophy, catering to growing, mature, and aging cartilage. Despite their typically low metabolic activity, conditions like osteoarthritis and rheumatoid arthritis can induce chondrocyte proliferation, leading to increased matrix production and the development of musculoskeletal issues. The unique extracellular matrix, rich in aggrecan, provides compression resistance, crucial for cartilage function in the musculoskeletal system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000249
has db xref: CALOHA:TS-0138
has db xref: FMA:66782
has db xref: ZFA:0009084
has exact synonym: cartilage cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: chondrocyte
annotated property: IAO_0000115
annotated target: A skeletogenic cell that secretes a specialized, avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell.
has db xref: GO_REF:0000034
has db xref: MESH:D019902
has db xref: PMID:32491508

Axiom
annotated source: chondrocyte
annotated property: description
annotated target: Chondrocytes are specialized cells derived from the mesenchyme. They are the only cells found in healthy cartilage, and their primary function is the synthesis and maintenance of the extracellular matrix of cartilaginous tissues. They synthesize various molecules essential for biomechanical function, including collagen types II, IX, and XI, link proteins, and proteoglycans like aggrecan and decorin. Beyond structural integrity, chondrocytes also contribute significantly to the homeostasis of articular cartilage in joints. The chondrocyte lifecycle involves proliferation, maturation, and hypertrophy, catering to growing, mature, and aging cartilage. Despite their typically low metabolic activity, conditions like osteoarthritis and rheumatoid arthritis can induce chondrocyte proliferation, leading to increased matrix production and the development of musculoskeletal issues. The unique extracellular matrix, rich in aggrecan, provides compression resistance, crucial for cartilage function in the musculoskeletal system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/art.34453
has db xref: DOI:10.1177/19417381093504
has db xref: DOI:10.1186/ar396
has db xref: DOI:10.3390/jdb3040177

Axiom
annotated source: chondrocyte
annotated property: hasDbXref
annotated target: ZFA:0009084
mapping justification: UnspecifiedMatching

chondrocyte on CELLxGENE CellGuide
type: Axiom
annotated source: chondrocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000138

professional antigen presenting cell
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002504
subclass of: leukocyte
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002504
IAO_0000115: A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response.
description: Professional antigen presenting cells, also known as APCs, are essential orchestrators of adaptive immunity. These cells possess the abilities to capture and process antigens and constitutively express MHC class II molecules to facilitate antigen presentation. These cells are able to deliver the three signals to activate naïve T cells, thereby initiating adaptive immunity. Professional APCs include dendritic cells, macrophages, and B cells. Among these, dendritic cells are often considered the predominant APC as they have been demonstrated to activate naïve T cells. Macrophages and B cells also possess antigen-processing machinery and constitutively express MHC class II molecules. Dendritic cells and macrophages obtain antigens via phagocytosis of cells and cell debris, while B cells obtain antigens via the B cell receptor. APCs are responsible for stimulating an appropriate immune response. Following antigen presentation (signal 1), they deliver costimulatory signals (signal 2) and secrete mediators such as cytokines (signal 3) that shape the subsequent immune response. APCs can also induce tolerogenic responses to self-antigens. APCs play important roles in diseases such as cancer and autoimmune diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009088
has related synonym: APC
in subset: blood and immune upper slim
in subset: cellxgene subset
comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells.

Axiom
annotated source: professional antigen presenting cell
annotated property: IAO_0000115
annotated target: A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response.
has db xref: GOC:add
has db xref: ISBN:0781735149

Axiom
annotated source: professional antigen presenting cell
annotated property: description
annotated target: Professional antigen presenting cells, also known as APCs, are essential orchestrators of adaptive immunity. These cells possess the abilities to capture and process antigens and constitutively express MHC class II molecules to facilitate antigen presentation. These cells are able to deliver the three signals to activate naïve T cells, thereby initiating adaptive immunity. Professional APCs include dendritic cells, macrophages, and B cells. Among these, dendritic cells are often considered the predominant APC as they have been demonstrated to activate naïve T cells. Macrophages and B cells also possess antigen-processing machinery and constitutively express MHC class II molecules. Dendritic cells and macrophages obtain antigens via phagocytosis of cells and cell debris, while B cells obtain antigens via the B cell receptor. APCs are responsible for stimulating an appropriate immune response. Following antigen presentation (signal 1), they deliver costimulatory signals (signal 2) and secrete mediators such as cytokines (signal 3) that shape the subsequent immune response. APCs can also induce tolerogenic responses to self-antigens. APCs play important roles in diseases such as cancer and autoimmune diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/B978-0-12-394447-4.30111-0
has db xref: DOI:10.1038/nri3754
has db xref: DOI:10.1159/000512729
has db xref: DOI:10.3389/fimmu.2022.954936

Axiom
annotated source: professional antigen presenting cell
annotated property: hasDbXref
annotated target: ZFA:0009088
mapping justification: UnspecifiedMatching

Axiom
annotated source: professional antigen presenting cell
annotated property: hasRelatedSynonym
annotated target: APC
has synonym type: OMO_0003000

professional antigen presenting cell on CELLxGENE CellGuide
type: Axiom
annotated source: professional antigen presenting cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000145

simple columnar epithelial cell
type: Class
subclass of: columnar/cuboidal epithelial cell
has db xref: ZFA:0009089
in subset: human reference atlas

Axiom
annotated source: simple columnar epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009089
mapping justification: UnspecifiedMatching

pigment cell
type: Class
subclass of: stuff accumulating cell
IAO_0000115: A pigment cell is a cell that contains pigment granules.
has db xref: VHOG:0001678
has db xref: ZFA:0009090
has exact synonym: chromatocyte
has exact synonym: chromatophore

Axiom
annotated source: pigment cell
annotated property: IAO_0000115
annotated target: A pigment cell is a cell that contains pigment granules.
has db xref: GOC:tfm

Axiom
annotated source: pigment cell
annotated property: hasDbXref
annotated target: ZFA:0009090
mapping justification: UnspecifiedMatching

melanocyte
type: Class
equivalent class: Class
  intersection of: pigment cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042470
  intersection of: Restriction
    on property: RO_0002202
    some values from: melanoblast
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042470
subclass of: Restriction
  on property: RO_0002202
  some values from: melanoblast
IAO_0000115: A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
description: Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000847
has db xref: CALOHA:TS-0613
has db xref: FMA:70545
has db xref: MESH:D008544
has db xref: VHOG:0001679
has db xref: ZFA:0009091
has narrow synonym: melanophore
in subset: cellxgene subset
in subset: general cell types upper slim
in subset: human reference atlas

Axiom
annotated source: melanocyte
annotated property: IAO_0000115
annotated target: A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
has db xref: SANBI:mhl

Axiom
annotated source: melanocyte
annotated property: description
annotated target: Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/med.21754
has db xref: DOI:10.1038/nrc.2016.37
has db xref: DOI:10.1111/j.1751-1097.2007.00226.x
has db xref: DOI:10.3390/ijms21249769
has db xref: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte

Axiom
annotated source: melanocyte
annotated property: hasDbXref
annotated target: ZFA:0009091
mapping justification: UnspecifiedMatching

melanocyte on CELLxGENE CellGuide
type: Axiom
annotated source: melanocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000148

visual pigment cell
type: Class
subclass of: pigment cell
has broad synonym: pigment cell

glandular secretory epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: secretory cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002530
subclass of: CL_1100001
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002530
IAO_0000115: An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous.
has db xref: CALOHA:TS-2085
has db xref: FMA:86494
has exact synonym: glandular epithelial cell
in subset: cellxgene subset

Axiom
annotated source: glandular secretory epithelial cell
annotated property: IAO_0000115
annotated target: An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous.
has db xref: GOC:tfm
has db xref: ORCID:0000-0002-7073-9172

secretory cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032940
subclass of: cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032940
IAO_0000115: A cell that specializes in controlled release of one or more substances.
has db xref: BTO:0003659
has db xref: FMA:86916
in subset: cellxgene subset

Axiom
annotated source: secretory cell
annotated property: IAO_0000115
annotated target: A cell that specializes in controlled release of one or more substances.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

exocrine cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002365
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002365
IAO_0000115: A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
has db xref: FMA:16014
has db xref: ZFA:0009092
in subset: cellxgene subset

Axiom
annotated source: exocrine cell
annotated property: IAO_0000115
annotated target: A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
has db xref: ISBN:0198547684

Axiom
annotated source: exocrine cell
annotated property: hasDbXref
annotated target: ZFA:0009092
mapping justification: UnspecifiedMatching

glycosaminoglycan secreting cell
type: Class
subclass of: extracellular matrix secreting cell
subclass of: carbohydrate secreting cell
IAO_0000115: A cell that secretes glycosaminoglycans.
has db xref: ZFA:0009093
has exact synonym: GAG secreting cell
has narrow synonym: hyaluronic acid secreting cell

Axiom
annotated source: glycosaminoglycan secreting cell
annotated property: IAO_0000115
annotated target: A cell that secretes glycosaminoglycans.
has db xref: GOC:tfm

Axiom
annotated source: glycosaminoglycan secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009093
mapping justification: UnspecifiedMatching

protein secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0009306
subclass of: secretory cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0009306
IAO_0000115: Any secretory cell that is capable of some protein secretion.

Axiom
annotated source: protein secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some protein secretion.
has db xref: FBC:Autogenerated

surfactant secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0043129
subclass of: secretory cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0043129
IAO_0000115: A cell that specializes in secretion of surfactant in the alveoli of the lung.

Axiom
annotated source: surfactant secreting cell
annotated property: subClassOf
annotated target: secretory cell
is inferred: true

Axiom
annotated source: surfactant secreting cell
annotated property: IAO_0000115
annotated target: A cell that specializes in secretion of surfactant in the alveoli of the lung.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

club cell
type: Class
subclass of: surfactant secreting cell
subclass of: CL_0002202
subclass of: CL_0008055
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0005902
IAO_0000115: A non-mucous, epithelial secretory cell that is part of the tracheobronchial tree. A club cell has short microvilli but no cilia. A club cell is able to multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium and it also protects the tracheobronchial epithelium.
description: Club cells, originally termed Clara cells, are specialized nonciliated epithelial cells primarily located in the bronchioles, or small airways, of the lungs. Compared to other cells in the lung epithelium, they are distinguished by their characteristic dome shape often marked by short, microvilli-like projections (but no cilia). Underneath their dome-like apex, they possess a large amount of cytoplasm containing numerous granules, and they have a round, centrally located nucleus. Their name 'club' was adopted to signify their appearance, which resembles a club or goblet. Club cells perform various crucial roles in maintaining the homeostasis of the respiratory tract. Among their functions is the production and secretion of a variety of proteins, including the club cell secretory protein (CCSP), which plays a role in the immune response of the lungs, particularly, in mitigating inflammation. The secretion of surfactant proteins by these cells also contributes to reducing surface tension in the alveoli, thus facilitating the process of gas exchange. Besides helping to defend against oxidative stress and inflammatory response, surfactants also aid in preventing the air sacs in the lungs from collapsing. Another vital role of club cells is their capacity to self-proliferate and differentiate into ciliated cells or basal cells, highlighting their regenerative capacity. This quality is especially critical for maintaining the integrity of the epithelial layer in the lung following any injury or inflammation, aiding the lung tissue to recover and restore its function. Furthermore, it is speculated that club cells might minimize the adverse impact of harmful substances in the air we inhale, thanks to a range of cytochrome P450 enzymes present in them. These enzymes assist in detoxifying harmful substances, a protective mechanism that helps preserve the overall health of the lungs. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who add…
has db xref: BTO:0004811
has db xref: FMA:14119
has exact synonym: Clara cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: club cell
annotated property: IAO_0000115
annotated target: A non-mucous, epithelial secretory cell that is part of the tracheobronchial tree. A club cell has short microvilli but no cilia. A club cell is able to multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium and it also protects the tracheobronchial epithelium.
has db xref: DOI:10.1183/09031936.00146609
has db xref: DOI:10.1378/chest.12-2762
has db xref: GOC:tfm
has db xref: PMID:28128362
has db xref: PMID:29874100
has db xref: PMID:7905712

Axiom
annotated source: club cell
annotated property: description
annotated target: Club cells, originally termed Clara cells, are specialized nonciliated epithelial cells primarily located in the bronchioles, or small airways, of the lungs. Compared to other cells in the lung epithelium, they are distinguished by their characteristic dome shape often marked by short, microvilli-like projections (but no cilia). Underneath their dome-like apex, they possess a large amount of cytoplasm containing numerous granules, and they have a round, centrally located nucleus. Their name 'club' was adopted to signify their appearance, which resembles a club or goblet. Club cells perform various crucial roles in maintaining the homeostasis of the respiratory tract. Among their functions is the production and secretion of a variety of proteins, including the club cell secretory protein (CCSP), which plays a role in the immune response of the lungs, particularly, in mitigating inflammation. The secretion of surfactant proteins by these cells also contributes to reducing surface tension in the alveoli, thus facilitating the process of gas exchange. Besides helping to defend against oxidative stress and inflammatory response, surfactants also aid in preventing the air sacs in the lungs from collapsing. Another vital role of club cells is their capacity to self-proliferate and differentiate into ciliated cells or basal cells, highlighting their regenerative capacity. This quality is especially critical for maintaining the integrity of the epithelial layer in the lung following any injury or inflammation, aiding the lung tissue to recover and restore its function. Furthermore, it is speculated that club cells might minimize the adverse impact of harmful substances in the air we inhale, thanks to a range of cytochrome P450 enzymes present in them. These enzymes assist in detoxifying harmful substances, a protective mechanism that helps preserve the overall health of the lungs. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who add…
has db xref: DOI:10.1038/s41385-020-00370-7
has db xref: DOI:10.1038/s41467-022-32052-2
has db xref: DOI:10.1152/ajplung.00192.2022
has db xref: DOI:10.1378/chest.14-3171
has db xref: DOI:10.2147/JIR.S284800

club cell on CELLxGENE CellGuide
type: Axiom
annotated source: club cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000158

seromucus secreting cell
type: Class
subclass of: secretory cell
in subset: cellxgene subset

goblet cell
type: Class
subclass of: mucus secreting cell
subclass of: CL_1100001
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005902
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0098594
IAO_0000115: A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane.
description: Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some sub…
has db xref: BTO:0001540
has db xref: FMA:13148
has db xref: ZFA:0009094
has db xref: http://en.wikipedia.org/wiki/Goblet_cell
has exact synonym: chalice cell
in subset: cellxgene subset

Axiom
annotated source: goblet cell
annotated property: IAO_0000115
annotated target: A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane.
has db xref: MESH:D020397
has db xref: http://en.wikipedia.org/wiki/Goblet_cell

Axiom
annotated source: goblet cell
annotated property: description
annotated target: Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some sub…
has db xref: DOI:10.1016/S1357-2725(02)00083-3
has db xref: DOI:10.1038/s41575-022-00675-x
has db xref: DOI:10.1165/ajrcmb.25.5.f218
has db xref: DOI:10.1242/bio.20121701
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK553208/

Axiom
annotated source: goblet cell
annotated property: hasDbXref
annotated target: ZFA:0009094
mapping justification: UnspecifiedMatching

goblet cell on CELLxGENE CellGuide
type: Axiom
annotated source: goblet cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000160

endocrine cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: Class
      intersection of: GO_0046879
      intersection of: Restriction
        on property: RO_0002339
        some values from: UBERON_0001009
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000949
subclass of: Restriction
  on property: RO_0002215
  some values from: Class
    intersection of: GO_0046879
    intersection of: Restriction
      on property: RO_0002339
      some values from: UBERON_0001009
IAO_0000115: A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
has db xref: FMA:83809
has db xref: ZFA:0009096
has exact synonym: endocrinocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: endocrine cell
annotated property: IAO_0000115
annotated target: A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
has db xref: MESH:D055098

Axiom
annotated source: endocrine cell
annotated property: hasDbXref
annotated target: ZFA:0009096
mapping justification: UnspecifiedMatching

enteroendocrine cell
type: Class
subclass of: endocrine cell
subclass of: CL_1100001
IAO_0000115: An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
description: Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body. (This extended description was generated by Chat…
has db xref: BTO:0003865
has db xref: FMA:62930
has db xref: MESH:D019858
has db xref: ZFA:0009097
in subset: cellxgene subset

Axiom
annotated source: enteroendocrine cell
annotated property: IAO_0000115
annotated target: An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
has db xref: GOC:tfm
has db xref: SANBI:mhl

Axiom
annotated source: enteroendocrine cell
annotated property: description
annotated target: Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body. (This extended description was generated by Chat…
has db xref: DOI:10.1038/s41574-019-0168-8
has db xref: DOI:10.1111/j.1463-1326.2011.01438.x
has db xref: DOI:10.1196/annals.1294.001
has db xref: DOI:10.1210/endrev/bnaa018
has db xref: DOI:10.7554/elife.78512

Axiom
annotated source: enteroendocrine cell
annotated property: hasDbXref
annotated target: ZFA:0009097
mapping justification: UnspecifiedMatching

enteroendocrine cell on CELLxGENE CellGuide
type: Axiom
annotated source: enteroendocrine cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000164

neuroendocrine cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0046879
subclass of: endocrine cell
subclass of: efferent neuron
subclass of: neurecto-epithelial cell
subclass of: CL_1100001
IAO_0000115: A neuron that is capable of some hormone secretion in response to neuronal signals.
has db xref: BTO:0002691
has db xref: FBbt:00005130
has db xref: FMA:83810
has db xref: ZFA:0009098
has related synonym: neurosecretory cell
has related synonym: neurosecretory neuron
in subset: cellxgene subset
in subset: human reference atlas
comment: The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron.

Axiom
annotated source: neuroendocrine cell
annotated property: IAO_0000115
annotated target: A neuron that is capable of some hormone secretion in response to neuronal signals.
has db xref: MESH:D055099

Axiom
annotated source: neuroendocrine cell
annotated property: hasDbXref
annotated target: FBbt:00005130
mapping justification: ManualMappingCuration

Axiom
annotated source: neuroendocrine cell
annotated property: hasDbXref
annotated target: ZFA:0009098
mapping justification: UnspecifiedMatching

Axiom
annotated source: neuroendocrine cell
annotated property: comment
annotated target: The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron.
has db xref: PMID:5342440
has db xref: https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073

chromaffin cell
type: Class
subclass of: neural crest derived neuron
subclass of: amine precursor uptake and decarboxylation cell
IAO_0000115: A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system.
description: Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000259
has db xref: FMA:69263
has db xref: ZFA:0009099
has exact synonym: phaeochromocyte
in subset: cellxgene subset

Axiom
annotated source: chromaffin cell
annotated property: IAO_0000115
annotated target: A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system.
has db xref: MESH:D019439

Axiom
annotated source: chromaffin cell
annotated property: description
annotated target: Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/cphy.c190003
has db xref: DOI:10.1016/j.biocel.2016.02.003
has db xref: DOI:10.3389/fendo.2018.00711
has db xref: DOI:10.3389/fimmu.2022.977175
has db xref: DOI:10.3389/fimmu.2022.977175/full

Axiom
annotated source: chromaffin cell
annotated property: hasDbXref
annotated target: ZFA:0009099
mapping justification: UnspecifiedMatching

chromaffin cell on CELLxGENE CellGuide
type: Axiom
annotated source: chromaffin cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000166

peptide hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030072
subclass of: secretory cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030072
IAO_0000115: Any secretory cell that is capable of some peptide hormone secretion.
has db xref: ZFA:0009100

Axiom
annotated source: peptide hormone secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some peptide hormone secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: peptide hormone secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009100
mapping justification: UnspecifiedMatching

insulin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030073
subclass of: protein secreting cell
subclass of: peptide hormone secreting cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030073
IAO_0000115: Any secretory cell that is capable of some insulin secretion.
has db xref: BTO:0000783
has db xref: ZFA:0009101

Axiom
annotated source: insulin secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some insulin secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: insulin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009101
mapping justification: UnspecifiedMatching

type B pancreatic cell
type: Class
equivalent class: Class
  intersection of: enteroendocrine cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000006
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030073
subclass of: insulin secreting cell
subclass of: CL_0008024
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000006
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002351
IAO_0000115: A cell that secretes insulin and is located towards the center of the islets of Langerhans.
description: Type B pancreatic cells, also known as beta cells, are one of the endocrine cell types located in the pancreas. They represent 70-80% of the cells in the islets of Langerhans, the endocrine part of this organ. Unique to mammals, Type B pancreatic cells are the predominant cell type in the pancreatic islets (50–80% of all islet endocrine cells) and play a crucial role in the body's metabolic regulation and glucose homeostasis. The primary function of type B pancreatic cells is the production, storage, and release of insulin, accounting for almost all insulin production in the human body: each cell contains about 20 pg insulin. Insulin has a critical function in regulating blood sugar levels: whenever glucose levels in the blood are high, such as after a meal, type B pancreatic cells secrete insulin to promote glucose uptake into cells, transforming it into usable energy or storing it for later use. Additionally, insulin also inhibits glucose production by the liver, therefore lowering blood glucose levels. Impaired function of the type B cells is associated with type 1 and type 2 diabetes, metabolic diseases characterized by chronic hyperglycemia. In type 1 diabetes, an autoimmune response leads to the attack of the body’s own type B cells, resulting in the insufficient production and secretion of insulin. In type 2 diabetes, insulin resistance occurs, and type B cells are unable to compensate by producing more insulin. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has broad synonym: beta cell
has db xref: BTO:0000783
has db xref: EV:0200009
has db xref: FMA:70586
has db xref: MA:0002419
has db xref: ZFA:0009102
has db xref: ncithesaurus:Beta_Cell
has exact synonym: B-cell of pancreatic islet
has exact synonym: beta cell of pancreatic islet
has exact synonym: insulin-secreting cell
has exact synonym: pancreatic B cell
has exact synonym: pancreatic B-cell
has exact synonym: pancreatic beta cell
has exact synonym: pancreatic islet core
has exact synonym: type B enteroendocrine cell
has related synonym: beta cell islet
in subset: cellxgene subset
in subset: human reference atlas
comment: Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression.

Axiom
annotated source: type B pancreatic cell
annotated property: subClassOf
annotated target: insulin secreting cell
is inferred: true

Axiom
annotated source: type B pancreatic cell
annotated property: IAO_0000115
annotated target: A cell that secretes insulin and is located towards the center of the islets of Langerhans.
has db xref: GOC:tfm
has db xref: ISBN:0517223651
has db xref: http://en.wikipedia.org/wiki/Pancreatic_b_cell

Axiom
annotated source: type B pancreatic cell
annotated property: description
annotated target: Type B pancreatic cells, also known as beta cells, are one of the endocrine cell types located in the pancreas. They represent 70-80% of the cells in the islets of Langerhans, the endocrine part of this organ. Unique to mammals, Type B pancreatic cells are the predominant cell type in the pancreatic islets (50–80% of all islet endocrine cells) and play a crucial role in the body's metabolic regulation and glucose homeostasis. The primary function of type B pancreatic cells is the production, storage, and release of insulin, accounting for almost all insulin production in the human body: each cell contains about 20 pg insulin. Insulin has a critical function in regulating blood sugar levels: whenever glucose levels in the blood are high, such as after a meal, type B pancreatic cells secrete insulin to promote glucose uptake into cells, transforming it into usable energy or storing it for later use. Additionally, insulin also inhibits glucose production by the liver, therefore lowering blood glucose levels. Impaired function of the type B cells is associated with type 1 and type 2 diabetes, metabolic diseases characterized by chronic hyperglycemia. In type 1 diabetes, an autoimmune response leads to the attack of the body’s own type B cells, resulting in the insufficient production and secretion of insulin. In type 2 diabetes, insulin resistance occurs, and type B cells are unable to compensate by producing more insulin. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/s40828-021-00140-3
has db xref: DOI:10.1038/s41574-020-00443-4
has db xref: DOI:10.1155/2017/1478294
has db xref: DOI:10.3389/fcell.2017.00055
has db xref: DOI:10.3390/ijms22126403

Axiom
annotated source: type B pancreatic cell
annotated property: hasBroadSynonym
annotated target: beta cell
has db xref: ZFA:0009102

Axiom
annotated source: type B pancreatic cell
annotated property: hasDbXref
annotated target: ZFA:0009102
mapping justification: UnspecifiedMatching

Axiom
annotated source: type B pancreatic cell
annotated property: hasExactSynonym
annotated target: B-cell of pancreatic islet
has db xref: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: hasExactSynonym
annotated target: beta cell of pancreatic islet
has db xref: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: hasExactSynonym
annotated target: insulin-secreting cell
has db xref: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: hasExactSynonym
annotated target: pancreatic B-cell
has db xref: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: hasExactSynonym
annotated target: pancreatic beta cell
has db xref: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: hasExactSynonym
annotated target: pancreatic islet core
has db xref: MA:0002419

Axiom
annotated source: type B pancreatic cell
annotated property: hasExactSynonym
annotated target: type B enteroendocrine cell
has db xref: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: hasRelatedSynonym
annotated target: beta cell islet
has db xref: MA:0002419

type B pancreatic cell on CELLxGENE CellGuide
type: Axiom
annotated source: type B pancreatic cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000169

Axiom
annotated source: type B pancreatic cell
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM637.SFSW.654

glucagon secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0070091
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0070091
IAO_0000115: A cell that secretes glucagon.
has db xref: FMA:84045
has db xref: ZFA:0009103
has exact synonym: glucagon-secreting cell

Axiom
annotated source: glucagon secreting cell
annotated property: IAO_0000115
annotated target: A cell that secretes glucagon.
has db xref: GOC:tfm

Axiom
annotated source: glucagon secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009103
mapping justification: UnspecifiedMatching

pancreatic A cell
type: Class
equivalent class: Class
  intersection of: CL_0002067
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000006
subclass of: CL_0002067
subclass of: CL_0008024
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000006
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002351
IAO_0000115: A type A enteroendocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
description: Pancreatic A cells, also known as alpha cells, are one of the main endocrine cell types found within the islets of Langerhans in the pancreas. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the islets. Their primary role involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000990
has db xref: FMA:70585
has db xref: MESH:D050416
has db xref: ZFA:0009104
has exact synonym: alpha cell of islet of Langerhans
has exact synonym: pancreatic alpha cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: pancreatic A cell
annotated property: IAO_0000115
annotated target: A type A enteroendocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: pancreatic A cell
annotated property: description
annotated target: Pancreatic A cells, also known as alpha cells, are one of the main endocrine cell types found within the islets of Langerhans in the pancreas. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the islets. Their primary role involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.beem.2015.10.002
has db xref: DOI:10.1016/j.semcdb.2020.01.006
has db xref: DOI:10.1038/nature08894
has db xref: DOI:10.1210/er.2006-0007
has db xref: DOI:10.1677/JOE-08-0290

Axiom
annotated source: pancreatic A cell
annotated property: hasDbXref
annotated target: ZFA:0009104
mapping justification: UnspecifiedMatching

pancreatic A cell on CELLxGENE CellGuide
type: Axiom
annotated source: pancreatic A cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000171

Axiom
annotated source: pancreatic A cell
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM637.SFSW.654

somatostatin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0070253
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0070253
IAO_0000115: Any secretory cell that is capable of some somatostatin secretion.
has db xref: ZFA:0009105

Axiom
annotated source: somatostatin secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some somatostatin secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: somatostatin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009105
mapping justification: UnspecifiedMatching

pancreatic D cell
type: Class
equivalent class: Class
  intersection of: type D enteroendocrine cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001264
subclass of: type D enteroendocrine cell
subclass of: CL_0008024
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000006
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002351
IAO_0000115: A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
description: Pancreatic D cells, also known as delta cells, are one of the main cell types found in the islets of Langerhans within the pancreas. They represent a minor fraction of the islet cells, comprising about 5% to 10% of the total islet cell population. Their main function is to produce and secrete the peptide hormone somatostatin, an inhibitory hormone that regulates the endocrine system. Their complex morphology, coupled with their distinctive function, sets the pancreatic D cells apart from other cells in the islets of Langerhans. They have long, neurite-like processes which allow them to make contact with other pancreatic endocrine cells at some distance from the cell body and create an extensive paracrine network. The somatostatin secreted by the pancreatic D cells has a variety of inhibitory effects on the secretory activity of other cells within the pancreas and the gastrointestinal system. In the pancreas, one of the principal roles of somatostatin is to inhibit both insulin and glucagon secretion, thereby playing a potent role in the regulation of blood glucose levels. The processes of pancreatic D cells can be >20μm long and may make contact with multiple pancreatic A and B type cells, potentially explaining the secretion of both glucagon and insulin observed in the presence of somatostatin receptor antagonists. The dual inhibitory role makes somatostatin a key player in preventing the excessive action of these hormones and maintaining metabolic balance. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000803
has db xref: FMA:70587
has db xref: ZFA:0005743
has exact synonym: D-cell of pancreatic islet
has exact synonym: delta cell of islet
has exact synonym: delta cell of pancreatic islet
has exact synonym: pancreatic D-cell
has exact synonym: pancreatic delta cell
has exact synonym: somatostatin-secreting pancreatic cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: pancreatic D cell
annotated property: IAO_0000115
annotated target: A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
has db xref: FMA:0517223651
has db xref: GOC:tfm

Axiom
annotated source: pancreatic D cell
annotated property: description
annotated target: Pancreatic D cells, also known as delta cells, are one of the main cell types found in the islets of Langerhans within the pancreas. They represent a minor fraction of the islet cells, comprising about 5% to 10% of the total islet cell population. Their main function is to produce and secrete the peptide hormone somatostatin, an inhibitory hormone that regulates the endocrine system. Their complex morphology, coupled with their distinctive function, sets the pancreatic D cells apart from other cells in the islets of Langerhans. They have long, neurite-like processes which allow them to make contact with other pancreatic endocrine cells at some distance from the cell body and create an extensive paracrine network. The somatostatin secreted by the pancreatic D cells has a variety of inhibitory effects on the secretory activity of other cells within the pancreas and the gastrointestinal system. In the pancreas, one of the principal roles of somatostatin is to inhibit both insulin and glucagon secretion, thereby playing a potent role in the regulation of blood glucose levels. The processes of pancreatic D cells can be >20μm long and may make contact with multiple pancreatic A and B type cells, potentially explaining the secretion of both glucagon and insulin observed in the presence of somatostatin receptor antagonists. The dual inhibitory role makes somatostatin a key player in preventing the excessive action of these hormones and maintaining metabolic balance. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/s41467-019-11517-x
has db xref: DOI:10.1038/s41574-018-0020-6
has db xref: DOI:10.1369/0022155415583535
has db xref: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/delta-cell

Axiom
annotated source: pancreatic D cell
annotated property: hasDbXref
annotated target: ZFA:0005743
mapping justification: UnspecifiedMatching

pancreatic D cell on CELLxGENE CellGuide
type: Axiom
annotated source: pancreatic D cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000173

Axiom
annotated source: pancreatic D cell
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM637.SFSW.654

steroid hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0035929
subclass of: secretory cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035929
IAO_0000115: Any secretory cell that is capable of some steroid hormone secretion.
has db xref: ZFA:0009106

Axiom
annotated source: steroid hormone secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some steroid hormone secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: steroid hormone secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009106
mapping justification: UnspecifiedMatching

luteal cell
type: Class
subclass of: progesterone secreting cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002512
IAO_0000115: A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells.
has db xref: BTO:0003939
has db xref: FMA:18688
has exact synonym: corpus luteum cell
has exact synonym: lutein cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: luteal cell
annotated property: IAO_0000115
annotated target: A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells.
has db xref: MESH:D008184
has db xref: PMID:31849844

Axiom
annotated source: luteal cell
annotated property: hasExactSynonym
annotated target: corpus luteum cell
has db xref: PMID:16790079

ecdysteroid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045457
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045457
IAO_0000115: Any secretory cell that is capable of some ecdysteroid secretion.

Axiom
annotated source: ecdysteroid secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some ecdysteroid secretion.
has db xref: FBC:Autogenerated

testosterone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0035936
subclass of: secretory cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035936
IAO_0000115: Any secretory cell that is capable of some testosterone secretion.
has db xref: ZFA:0009107

Axiom
annotated source: testosterone secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some testosterone secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: testosterone secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009107
mapping justification: UnspecifiedMatching

Leydig cell
type: Class
subclass of: BFO_0000002
subclass of: testosterone secreting cell
subclass of: CL_4030031
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005212
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0009091
IAO_0000115: A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
description: Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biol…
has broad synonym: interstitial cell
has db xref: BTO:0000755
has db xref: CALOHA:TS-1150
has db xref: EMAPA:29655
has db xref: FMA:72297
has db xref: MESH:D007985
has db xref: ZFA:0009108
has exact synonym: interstitial cell of Leydig
in subset: cellxgene subset
comment: Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated

Axiom
annotated source: Leydig cell
annotated property: IAO_0000115
annotated target: A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
has db xref: GOC:tfm
has db xref: PMID:12050120

Axiom
annotated source: Leydig cell
annotated property: description
annotated target: Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biol…
has db xref: DOI:10.1016/j.coemr.2019.03.001
has db xref: DOI:10.1093/biolre/ioy059
has db xref: DOI:10.1210/clinem/dgaa603
has db xref: DOI:10.3389/fendo.2014.00006
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors.

Axiom
annotated source: Leydig cell
annotated property: hasDbXref
annotated target: ZFA:0009108
mapping justification: UnspecifiedMatching

Leydig cell on CELLxGENE CellGuide
type: Axiom
annotated source: Leydig cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000178

progesterone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0042701
subclass of: steroid hormone secreting cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042701
IAO_0000115: Any secretory cell that is capable of some progesterone secretion.
has db xref: ZFA:0009109

Axiom
annotated source: progesterone secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some progesterone secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: progesterone secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009109
mapping justification: UnspecifiedMatching

estradiol secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0035938
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035938
IAO_0000115: A steroid hormone secreting cell that secretes estradiol.
has db xref: ZFA:0009110

Axiom
annotated source: estradiol secreting cell
annotated property: IAO_0000115
annotated target: A steroid hormone secreting cell that secretes estradiol.
has db xref: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: estradiol secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009110
mapping justification: UnspecifiedMatching

hepatocyte
type: Class
subclass of: BFO_0000002
subclass of: epithelial cell
subclass of: endopolyploid cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002107
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0005026
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0006699
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0098754
IAO_0000115: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
description: Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform…
has db xref: BTO:0000575
has db xref: CALOHA:TS-0454
has db xref: FMA:14515
has db xref: ZFA:0009111
in subset: cellxgene subset
in subset: human reference atlas
comment: Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.

Axiom
annotated source: hepatocyte
annotated property: IAO_0000115
annotated target: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
has db xref: GOC:tfm
has db xref: ISBN:0412046911
has db xref: MESH:D022781
has db xref: PMID:19717280
has db xref: http://en.wikipedia.org/wiki/Hepatocyte

Axiom
annotated source: hepatocyte
annotated property: description
annotated target: Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform…
has db xref: DOI:10.1016/j.biocel.2011.11.011
has db xref: DOI:10.1055/s-2007-1007096
has db xref: DOI:10.1083/jcb.201903090
has db xref: DOI:10.1111/j.1439-0396.2007.00752.x

Axiom
annotated source: hepatocyte
annotated property: hasDbXref
annotated target: ZFA:0009111
mapping justification: UnspecifiedMatching

hepatocyte on CELLxGENE CellGuide
type: Axiom
annotated source: hepatocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000182

Axiom
annotated source: hepatocyte
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM889.CJPK.447

contractile cell
type: Class
subclass of: cell
IAO_0000115: A cell whose primary function is to shorten.
in subset: cellxgene subset

Axiom
annotated source: contractile cell
annotated property: IAO_0000115
annotated target: A cell whose primary function is to shorten.
has db xref: FB:ma

myofibroblast cell
type: Class
subclass of: contractile cell
subclass of: CL_0002320
IAO_0000115: An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell.
description: Myofibroblasts are specialized cells predominantly found within the connective tissues of the body, most notably in areas of injury or wound healing. They carry out a crucial role in many biological processes, including tissue repair and fibrosis, wound contraction, and organogenesis. Though similar to fibroblasts, myofibroblasts can be differentiated by their unique morphological features and the presence of specialized protein bundles called stress fibers. Myofibroblasts originate from several cell types based on the physiological condition or the injury context, including local fibroblasts, epithelial cells, and endothelial cells, shedding light onto their plasticity. Upon tissue injury or wound creation, myofibroblasts activate and undergo a transformation process whereby they develop contractile features. They express a type of protein called alpha-smooth muscle actin (α-SMA), allowing them to contract and aid in wound closure. These cells also produce extracellular matrix (ECM) components, primarily collagen, to support and provide structural integrity to the healing tissue. However, while myofibroblasts play a critical role in normal wound healing, their function can be detrimental in certain pathological conditions. For instance, in chronic diseases such as fibrosis or scarring, the extended presence or overactivity of myofibroblasts can lead to the excessive production of ECM and fibrous tissues, leading to hardened, rigid tissues and organ dysfunction. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: MFB
in subset: cellxgene subset
in subset: human reference atlas
comment: Myofibroblasts are alpha-SMA-positive, CD34-negative, CD45-negative. They are reportedly capable of secreting IL-1beta, IL-6, and TNF-alpha.

Axiom
annotated source: myofibroblast cell
annotated property: IAO_0000115
annotated target: An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell.
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: MESH:D058628
has db xref: PMID:19800625
has db xref: PMID:20630469
has db xref: PMID:22387320

Axiom
annotated source: myofibroblast cell
annotated property: description
annotated target: Myofibroblasts are specialized cells predominantly found within the connective tissues of the body, most notably in areas of injury or wound healing. They carry out a crucial role in many biological processes, including tissue repair and fibrosis, wound contraction, and organogenesis. Though similar to fibroblasts, myofibroblasts can be differentiated by their unique morphological features and the presence of specialized protein bundles called stress fibers. Myofibroblasts originate from several cell types based on the physiological condition or the injury context, including local fibroblasts, epithelial cells, and endothelial cells, shedding light onto their plasticity. Upon tissue injury or wound creation, myofibroblasts activate and undergo a transformation process whereby they develop contractile features. They express a type of protein called alpha-smooth muscle actin (α-SMA), allowing them to contract and aid in wound closure. These cells also produce extracellular matrix (ECM) components, primarily collagen, to support and provide structural integrity to the healing tissue. However, while myofibroblasts play a critical role in normal wound healing, their function can be detrimental in certain pathological conditions. For instance, in chronic diseases such as fibrosis or scarring, the extended presence or overactivity of myofibroblasts can lead to the excessive production of ECM and fibrous tissues, leading to hardened, rigid tissues and organ dysfunction. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/path.4104
has db xref: DOI:10.1038/nrm809
has db xref: DOI:10.2147/CCID.S50046
has db xref: DOI:10.3390/biom11081095
has db xref: DOI:10.7860/JCDR/2014/7820.4231

Axiom
annotated source: myofibroblast cell
annotated property: hasExactSynonym
annotated target: MFB
has db xref: PMID:8731193

myofibroblast cell on CELLxGENE CellGuide
type: Axiom
annotated source: myofibroblast cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000186

muscle cell
type: Class
subclass of: BFO_0000002
subclass of: contractile cell
subclass of: eukaryotic cell
subclass of: electrically responsive cell
subclass of: Restriction
  on property: RO_0002202
  some values from: myoblast
IAO_0000115: A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
has db xref: BTO:0000888
has db xref: BTO:0000902
has db xref: CALOHA:TS-2032
has db xref: FBbt:00005074
has db xref: FMA:67328
has db xref: WBbt:0003675
has db xref: ZFA:0009114
has exact synonym: muscle fiber
has exact synonym: myocyte
in subset: cellxgene subset
in subset: general cell types upper slim
in subset: human reference atlas

Axiom
annotated source: muscle cell
annotated property: IAO_0000115
annotated target: A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
has db xref: MESH:D032342

Axiom
annotated source: muscle cell
annotated property: hasDbXref
annotated target: FBbt:00005074
mapping justification: ManualMappingCuration

Axiom
annotated source: muscle cell
annotated property: hasDbXref
annotated target: ZFA:0009114
mapping justification: UnspecifiedMatching

cell of skeletal muscle
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001134
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001134
IAO_0000115: A somatic cell located in skeletal muscle.
description: Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0004392
has db xref: CALOHA:TS-2158
has db xref: FMA:9727
has db xref: ZFA:0009115
has exact synonym: skeletal muscle cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: cell of skeletal muscle
annotated property: IAO_0000115
annotated target: A somatic cell located in skeletal muscle.
has db xref: GOC:tfm

Axiom
annotated source: cell of skeletal muscle
annotated property: description
annotated target: Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/cphy.c160033
has db xref: DOI:10.3390/biology10101056
has db xref: https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK537139
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK9961/

Axiom
annotated source: cell of skeletal muscle
annotated property: hasDbXref
annotated target: ZFA:0009115
mapping justification: UnspecifiedMatching

cell of skeletal muscle on CELLxGENE CellGuide
type: Axiom
annotated source: cell of skeletal muscle
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000188

slow muscle cell
type: Class
subclass of: CL_0008046
subclass of: Restriction
  on property: RO_0002202
  some values from: slow muscle myoblast
IAO_0000115: A muscle cell that develops tension more slowly than a fast-twitch fiber.
description: Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009116
has related synonym: slow muscle fiber
in subset: cellxgene subset

Axiom
annotated source: slow muscle cell
annotated property: IAO_0000115
annotated target: A muscle cell that develops tension more slowly than a fast-twitch fiber.
has db xref: GOC:tfm
has db xref: ISBN:0323052908

Axiom
annotated source: slow muscle cell
annotated property: description
annotated target: Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1093/ptj/81.11.1810
has db xref: DOI:10.1186/s13578-015-0054-6
has db xref: DOI:10.3389/fphys.2021.747214
has db xref: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/slow-muscle-fiber

Axiom
annotated source: slow muscle cell
annotated property: hasDbXref
annotated target: ZFA:0009116
mapping justification: UnspecifiedMatching

Axiom
annotated source: slow muscle cell
annotated property: hasRelatedSynonym
annotated target: slow muscle fiber
has db xref: ISBN:0815316208

slow muscle cell on CELLxGENE CellGuide
type: Axiom
annotated source: slow muscle cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000189

smooth muscle cell
type: Class
subclass of: CL_0008000
subclass of: CL_0008007
subclass of: Restriction
  on property: RO_0002202
  some values from: smooth muscle myoblast
IAO_0000115: A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
description: Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has broad synonym: non-striated muscle cell
has db xref: BTO:0004576
has db xref: CALOHA:TS-2159
has db xref: FMA:14072
has db xref: ZFA:0009118
has exact synonym: SMCs
has exact synonym: myocytes, smooth muscle
has exact synonym: smooth muscle fiber
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: smooth muscle cell
annotated property: IAO_0000115
annotated target: A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
has db xref: MESH:D032389
has db xref: PMID:9315361
has db xref: http://en.wikipedia.org/wiki/Smooth_muscle_cell

Axiom
annotated source: smooth muscle cell
annotated property: description
annotated target: Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1093/ptj/81.11.1810
has db xref: https://training.seer.cancer.gov/anatomy/muscular/types.html
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK10854/
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK526125
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK556137/

Axiom
annotated source: smooth muscle cell
annotated property: hasDbXref
annotated target: ZFA:0009118
mapping justification: UnspecifiedMatching

Axiom
annotated source: smooth muscle cell
annotated property: hasExactSynonym
annotated target: SMCs
has db xref: PMID:9315361

Axiom
annotated source: smooth muscle cell
annotated property: hasExactSynonym
annotated target: myocytes, smooth muscle
has db xref: MESH:D032389

smooth muscle cell on CELLxGENE CellGuide
type: Axiom
annotated source: smooth muscle cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000192

sensory receptor cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001032
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050906
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001032
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050906
IAO_0000115: A cell that is capable of detection of a stimulus involved in sensory perception.
has db xref: MESH:D011984
has exact synonym: receptor cell

mechanoreceptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050974
subclass of: sensory neuron
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050974
IAO_0000115: A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
has db xref: ZFA:0009120
has related synonym: mechanoreceptor
in subset: cellxgene subset

Axiom
annotated source: mechanoreceptor cell
annotated property: IAO_0000115
annotated target: A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
has db xref: MESH:D008465

Axiom
annotated source: mechanoreceptor cell
annotated property: hasDbXref
annotated target: ZFA:0009120
mapping justification: UnspecifiedMatching

Axiom
annotated source: mechanoreceptor cell
annotated property: hasRelatedSynonym
annotated target: mechanoreceptor
has db xref: MP:0000972

touch receptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050976
subclass of: mechanoreceptor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050976
IAO_0000115: Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception of touch.

Axiom
annotated source: touch receptor cell
annotated property: IAO_0000115
annotated target: Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception of touch.
has db xref: FBC:Autogenerated

auditory hair cell
type: Class
subclass of: sensory hair cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050910
IAO_0000115: A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
has db xref: ZFA:0009121
has related synonym: auditory receptor cell
comment: In mammals these cells are located in the organ of Corti.

Axiom
annotated source: auditory hair cell
annotated property: IAO_0000115
annotated target: A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
has db xref: MESH:D006198
has db xref: WikipediaVersioned:Hair_cell&oldid=1045345915

Axiom
annotated source: auditory hair cell
annotated property: hasDbXref
annotated target: ZFA:0009121
mapping justification: UnspecifiedMatching

gravity sensitive cell
type: Class
equivalent class: Class
  intersection of: neuronal receptor cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050974
subclass of: neuronal receptor cell
subclass of: mechanoreceptor cell
IAO_0000115: Any neuronal receptor cell that is capable of some detection of mechanical stimulus involved in sensory perception.

Axiom
annotated source: gravity sensitive cell
annotated property: IAO_0000115
annotated target: Any neuronal receptor cell that is capable of some detection of mechanical stimulus involved in sensory perception.
has db xref: FBC:Autogenerated

thermoreceptor cell
type: Class
equivalent class: Class
  intersection of: neuronal receptor cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050960
subclass of: neuronal receptor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050960
IAO_0000115: A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain.
has db xref: ZFA:0009123

Axiom
annotated source: thermoreceptor cell
annotated property: IAO_0000115
annotated target: A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain.
has db xref: GOC:tfm
has db xref: MESH:D013823
has db xref: MP:0000971

Axiom
annotated source: thermoreceptor cell
annotated property: hasDbXref
annotated target: ZFA:0009123
mapping justification: UnspecifiedMatching

chemoreceptor cell
type: Class
equivalent class: Class
  intersection of: sensory receptor cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050907
subclass of: sensory receptor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050907
IAO_0000115: A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.
has db xref: ZFA:0009124

Axiom
annotated source: chemoreceptor cell
annotated property: IAO_0000115
annotated target: A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.
has db xref: MESH:D002628

Axiom
annotated source: chemoreceptor cell
annotated property: hasDbXref
annotated target: ZFA:0009124
mapping justification: UnspecifiedMatching

olfactory receptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050911
subclass of: neuronal receptor cell
subclass of: chemoreceptor cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005725
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050911
IAO_0000115: Any neuron that is capable of some detection of chemical stimulus involved in sensory perception of smell.
has db xref: BTO:0004185
has db xref: FMA:67860
has db xref: MESH:D018034
has db xref: Wikipedia:Olfactory_receptor_neuron
has db xref: ZFA:0009125
has exact synonym: Schultze's cell
has exact synonym: odorant receptor cell
has exact synonym: olfactory receptor neuron
has exact synonym: olfactory sensory neuron
in subset: cellxgene subset

Axiom
annotated source: olfactory receptor cell
annotated property: IAO_0000115
annotated target: Any neuron that is capable of some detection of chemical stimulus involved in sensory perception of smell.
has db xref: FBC:Autogenerated

Axiom
annotated source: olfactory receptor cell
annotated property: hasDbXref
annotated target: ZFA:0009125
mapping justification: UnspecifiedMatching

taste receptor cell
type: Class
equivalent class: Class
  intersection of: chemoreceptor cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050912
subclass of: sensory epithelial cell
subclass of: chemoreceptor cell
subclass of: CL_0002076
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050912
IAO_0000115: A specialized cell involved in gustatory sensory perception.
description: Taste receptor cells, also known as gustatory receptor cells, are specialized epithelial cells that are responsible for detecting taste stimuli. They also play a role in regulating feeding behavior and nutrient intake by signaling the presence of nutrients or toxins in food. These cells are located in taste buds, which are small structures found on the tongue, palate, and throat. Each taste bud is composed of 50-100 taste receptor cells, as well as supporting cells and basal cells. Taste receptor cells are involved in the transduction of taste stimuli into neural signals that can be interpreted by the brain. They detect five primary tastes: sweet, sour, salty, umami (savory), and bitter. Each taste receptor cell is specialized to detect one or more of these tastes, depending on the expression of specific taste receptors on their membrane. For example, sweet taste receptors bind to sugars and artificial sweeteners, while bitter taste receptors recognize many toxins and alkaloids. Mechanistically, when a taste receptor cell is stimulated by a tastant, it depolarizes and releases neurotransmitters that activate sensory nerve fibers, which then transmit the information to the brain. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:67910
has db xref: ZFA:0009126
has exact synonym: taste bud cell
in subset: cellxgene subset

Axiom
annotated source: taste receptor cell
annotated property: IAO_0000115
annotated target: A specialized cell involved in gustatory sensory perception.
has db xref: GOC:tfm
has db xref: ISBN:0618947256

Axiom
annotated source: taste receptor cell
annotated property: description
annotated target: Taste receptor cells, also known as gustatory receptor cells, are specialized epithelial cells that are responsible for detecting taste stimuli. They also play a role in regulating feeding behavior and nutrient intake by signaling the presence of nutrients or toxins in food. These cells are located in taste buds, which are small structures found on the tongue, palate, and throat. Each taste bud is composed of 50-100 taste receptor cells, as well as supporting cells and basal cells. Taste receptor cells are involved in the transduction of taste stimuli into neural signals that can be interpreted by the brain. They detect five primary tastes: sweet, sour, salty, umami (savory), and bitter. Each taste receptor cell is specialized to detect one or more of these tastes, depending on the expression of specific taste receptors on their membrane. For example, sweet taste receptors bind to sugars and artificial sweeteners, while bitter taste receptors recognize many toxins and alkaloids. Mechanistically, when a taste receptor cell is stimulated by a tastant, it depolarizes and releases neurotransmitters that activate sensory nerve fibers, which then transmit the information to the brain. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/nrendo.2015.7
has db xref: DOI:10.1038/nrn.2017.68
has db xref: DOI:10.1111/j.1748-1716.2011.02308.x

Axiom
annotated source: taste receptor cell
annotated property: hasDbXref
annotated target: ZFA:0009126
mapping justification: UnspecifiedMatching

taste receptor cell on CELLxGENE CellGuide
type: Axiom
annotated source: taste receptor cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000209

photoreceptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050908
subclass of: sensory neuron
subclass of: CL_0008028
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050908
IAO_0000115: A cell specialized in detecting light stimuli that are involved in visual perception.
description: Photoreceptor cells are specialized types of neurons found in the retina, responsible for the vital task of converting light into signals that can stimulate a visual response. These cells are called photoreceptor cells because they are light-sensitive, enabling vision in conditions ranging from extremely dim to very bright light. There are two main types of photoreceptor cells in the human eye: rods, which are highly sensitive to light and allow for vision in low-light conditions, and cones, which are responsible for color vision and function best in bright light. The photoreceptor cells function by absorbing light rays and converting them into electrical signals. These signals are then sent to the brain via the optic nerve and are interpreted as visual images. This process begins when the photopigment (a light-sensitive compound) found in photoreceptor cells absorbs light, which triggers a chemical reaction. This reaction leads to changes in the photopigment's configuration and, consequently, alters its electrical properties. This change initiates a signal that is transmitted through the cell and onwards to connecting neurons. Furthermore, photoreceptor cells exhibit a unique and highly specialized structure that reflects their function. Rods, named because of their elongated, rod-shaped structure, consist of an outer segment filled with disks containing rhodopsin, the photopigment responsible for detecting light. Cones, on the other hand, are more conical and have three different types of photopigments, each one sensitive to a different range of wavelengths, allowing for the perception of color. Given the importance of photoreceptor cells in vision, damage or degeneration to these cells can lead to vision impairment or blindness, highlighting their key role in visual perception. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain inf…
has db xref: BTO:0001060
has db xref: CALOHA:TS-0868
has db xref: FBbt:00004211
has db xref: FMA:86740
has db xref: ZFA:0009127
in subset: cellxgene subset

Axiom
annotated source: photoreceptor cell
annotated property: IAO_0000115
annotated target: A cell specialized in detecting light stimuli that are involved in visual perception.
has db xref: MESH:D010786

Axiom
annotated source: photoreceptor cell
annotated property: description
annotated target: Photoreceptor cells are specialized types of neurons found in the retina, responsible for the vital task of converting light into signals that can stimulate a visual response. These cells are called photoreceptor cells because they are light-sensitive, enabling vision in conditions ranging from extremely dim to very bright light. There are two main types of photoreceptor cells in the human eye: rods, which are highly sensitive to light and allow for vision in low-light conditions, and cones, which are responsible for color vision and function best in bright light. The photoreceptor cells function by absorbing light rays and converting them into electrical signals. These signals are then sent to the brain via the optic nerve and are interpreted as visual images. This process begins when the photopigment (a light-sensitive compound) found in photoreceptor cells absorbs light, which triggers a chemical reaction. This reaction leads to changes in the photopigment's configuration and, consequently, alters its electrical properties. This change initiates a signal that is transmitted through the cell and onwards to connecting neurons. Furthermore, photoreceptor cells exhibit a unique and highly specialized structure that reflects their function. Rods, named because of their elongated, rod-shaped structure, consist of an outer segment filled with disks containing rhodopsin, the photopigment responsible for detecting light. Cones, on the other hand, are more conical and have three different types of photopigments, each one sensitive to a different range of wavelengths, allowing for the perception of color. Given the importance of photoreceptor cells in vision, damage or degeneration to these cells can lead to vision impairment or blindness, highlighting their key role in visual perception. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain inf…
has db xref: DOI:10.1016/j.cbpa.2008.04.600
has db xref: DOI:10.1016/j.neubiorev.2017.12.006
has db xref: DOI:10.1038/nrg2717
has db xref: DOI:10.1113/JP282058
has db xref: DOI:10.1242/jcs.175687

Axiom
annotated source: photoreceptor cell
annotated property: hasDbXref
annotated target: FBbt:00004211
mapping justification: ManualMappingCuration

Axiom
annotated source: photoreceptor cell
annotated property: hasDbXref
annotated target: ZFA:0009127
mapping justification: UnspecifiedMatching

photoreceptor cell on CELLxGENE CellGuide
type: Axiom
annotated source: photoreceptor cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000210

electrically active cell
type: Class
subclass of: cell
IAO_0000115: A cell whose function is determined by the generation or the reception of an electric signal.
has db xref: ZFA:0009128

Axiom
annotated source: electrically active cell
annotated property: IAO_0000115
annotated target: A cell whose function is determined by the generation or the reception of an electric signal.
has db xref: FB:ma

Axiom
annotated source: electrically active cell
annotated property: hasDbXref
annotated target: ZFA:0009128
mapping justification: UnspecifiedMatching

synovial cell
type: Class
subclass of: CL_0002078
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002217
IAO_0000115: A cell located in the synovial joint.
has db xref: CALOHA:TS-0995
has db xref: ZFA:0009131
has exact synonym: synoviocyte

Axiom
annotated source: synovial cell
annotated property: subClassOf
annotated target: CL_0002078
is inferred: true

Axiom
annotated source: synovial cell
annotated property: hasDbXref
annotated target: ZFA:0009131
mapping justification: UnspecifiedMatching

Sertoli cell
type: Class
equivalent class: Class
  intersection of: supporting cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001343
subclass of: androgen binding protein secreting cell
subclass of: supporting cell
subclass of: CL_0002625
subclass of: CL_1100001
IAO_0000115: A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier.
description: Sertoli cells, also known as sustentacular cells, are epithelial cells that play a crucial part of the male reproductive system and are situated within the seminiferous tubules of the testes. Functionally, Sertoli cells play diverse and pivotal roles in supporting spermatogenesis, the intricate process of sperm production. To scaffold the developing sperm cells, Sertoli cells morphologically change, interacting directly with the germ cells to provide nutritional support, metabolic regulation, and waste removal, thereby creating an environment conducive to the development of germ cells. In addition to their structural function, Sertoli cells also secrete several bioactive molecules with crucial implications for spermatogenesis. These include anti-mullerian hormone (AMH) during fetal life, inhibin, and androgen binding protein (ABP), as well as several growth factors and transport proteins. They also contribute to the immune-privileged status of the testes by forming the blood-testis barrier, safeguarding sperm antigens from the systemic immune response. Given their extensive roles in maintaining testicular function, impairments in Sertoli cell function can lead to male infertility and are implicated in a range of related disorders. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001238
has db xref: CALOHA:TS-0922
has db xref: FMA:72298
has db xref: VHOG:0001348
has db xref: ZFA:0009133
in subset: cellxgene subset

Axiom
annotated source: Sertoli cell
annotated property: subClassOf
annotated target: supporting cell
is inferred: true

Axiom
annotated source: Sertoli cell
annotated property: IAO_0000115
annotated target: A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier.
has db xref: MESH:D012708

Axiom
annotated source: Sertoli cell
annotated property: description
annotated target: Sertoli cells, also known as sustentacular cells, are epithelial cells that play a crucial part of the male reproductive system and are situated within the seminiferous tubules of the testes. Functionally, Sertoli cells play diverse and pivotal roles in supporting spermatogenesis, the intricate process of sperm production. To scaffold the developing sperm cells, Sertoli cells morphologically change, interacting directly with the germ cells to provide nutritional support, metabolic regulation, and waste removal, thereby creating an environment conducive to the development of germ cells. In addition to their structural function, Sertoli cells also secrete several bioactive molecules with crucial implications for spermatogenesis. These include anti-mullerian hormone (AMH) during fetal life, inhibin, and androgen binding protein (ABP), as well as several growth factors and transport proteins. They also contribute to the immune-privileged status of the testes by forming the blood-testis barrier, safeguarding sperm antigens from the systemic immune response. Given their extensive roles in maintaining testicular function, impairments in Sertoli cell function can lead to male infertility and are implicated in a range of related disorders. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.semcdb.2021.06.016
has db xref: DOI:10.1038/s41419-019-1782-z
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK560631/

Axiom
annotated source: Sertoli cell
annotated property: hasDbXref
annotated target: ZFA:0009133
mapping justification: UnspecifiedMatching

Sertoli cell on CELLxGENE CellGuide
type: Axiom
annotated source: Sertoli cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000216

myelinating Schwann cell
type: Class
subclass of: CL_0002573
subclass of: CL_4023154
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002377
IAO_0000115: A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons.
has broad synonym: Schwann cell
has broad synonym: peripheral neuroglial cell
has db xref: CALOHA:TS-0898
has db xref: FMA:62121
has db xref: ZFA:0009135
has exact synonym: neurilemmal cell
in subset: cellxgene subset

Axiom
annotated source: myelinating Schwann cell
annotated property: IAO_0000115
annotated target: A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons.
has db xref: GOC:cvs
has db xref: GOC:tfm
has db xref: MESH:D012583

Axiom
annotated source: myelinating Schwann cell
annotated property: hasDbXref
annotated target: ZFA:0009135
mapping justification: UnspecifiedMatching

motile cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048870
subclass of: cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048870
IAO_0000115: A cell that moves by its own activities.
has db xref: ZFA:0009136

Axiom
annotated source: motile cell
annotated property: IAO_0000115
annotated target: A cell that moves by its own activities.
has db xref: FB:ma

Axiom
annotated source: motile cell
annotated property: hasDbXref
annotated target: ZFA:0009136
mapping justification: UnspecifiedMatching

ectodermal cell
type: Class
subclass of: eukaryotic cell
subclass of: CL_0002321
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000924
IAO_0000115: A cell of the outer of the three germ layers of the embryo.
has db xref: FMA:72549
has db xref: ZFA:0009137
has exact synonym: ectoderm cell
in subset: cellxgene subset

Axiom
annotated source: ectodermal cell
annotated property: IAO_0000115
annotated target: A cell of the outer of the three germ layers of the embryo.
has db xref: MESH:D004475

Axiom
annotated source: ectodermal cell
annotated property: hasDbXref
annotated target: ZFA:0009137
mapping justification: UnspecifiedMatching

mesodermal cell
type: Class
subclass of: eukaryotic cell
subclass of: CL_0002321
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000926
IAO_0000115: A cell of the middle germ layer of the embryo.
description: Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:72554
has db xref: ZFA:0009138
has exact synonym: mesoblast
has exact synonym: mesoderm cell
in subset: cellxgene subset

Axiom
annotated source: mesodermal cell
annotated property: IAO_0000115
annotated target: A cell of the middle germ layer of the embryo.
has db xref: MESH:D008648

Axiom
annotated source: mesodermal cell
annotated property: description
annotated target: Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.ceb.2019.07.012
has db xref: DOI:10.5535/arm.2016.40.1.162
has db xref: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm

Axiom
annotated source: mesodermal cell
annotated property: hasDbXref
annotated target: ZFA:0009138
mapping justification: UnspecifiedMatching

mesodermal cell on CELLxGENE CellGuide
type: Axiom
annotated source: mesodermal cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000222

endodermal cell
type: Class
subclass of: eukaryotic cell
subclass of: CL_0002321
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000925
IAO_0000115: A cell of the inner of the three germ layers of the embryo.
has db xref: FMA:72555
has db xref: ZFA:0009139
has exact synonym: endoderm cell
in subset: cellxgene subset

Axiom
annotated source: endodermal cell
annotated property: IAO_0000115
annotated target: A cell of the inner of the three germ layers of the embryo.
has db xref: MESH:D004707

Axiom
annotated source: endodermal cell
annotated property: hasDbXref
annotated target: ZFA:0009139
mapping justification: UnspecifiedMatching

anucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001405
subclass of: cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001405
disjoint with: CL_0002242
IAO_0000115: A cell that lacks a nucleus.
has db xref: FMA:68647
has exact synonym: non-nucleated cell

Axiom
annotated source: anucleate cell
annotated property: IAO_0000115
annotated target: A cell that lacks a nucleus.
has db xref: FB:ma

single nucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
subclass of: eukaryotic cell
subclass of: CL_0002242
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001407
IAO_0000115: A cell with a single nucleus.

Axiom
annotated source: single nucleate cell
annotated property: IAO_0000115
annotated target: A cell with a single nucleus.
has db xref: FB:ma
has db xref: GOC:tfm

binucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001406
subclass of: multinucleate cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001406
IAO_0000115: Any cell that has characteristic some binucleate.

Axiom
annotated source: binucleate cell
annotated property: IAO_0000115
annotated target: Any cell that has characteristic some binucleate.
has db xref: FBC:Autogenerated

multinucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001908
subclass of: eukaryotic cell
subclass of: CL_0002242
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001908
IAO_0000115: A cell with more than one nucleus.
has exact synonym: multinucleated cells
has exact synonym: polynuclear cells

Axiom
annotated source: multinucleate cell
annotated property: IAO_0000115
annotated target: A cell with more than one nucleus.
has db xref: FB:ma
has db xref: Wikipedia:Multinucleate

Axiom
annotated source: multinucleate cell
annotated property: hasExactSynonym
annotated target: multinucleated cells
has db xref: Wikipedia:Multinucleate

Axiom
annotated source: multinucleate cell
annotated property: hasExactSynonym
annotated target: polynuclear cells
has db xref: Wikipedia:Multinucleate

erythrocyte
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0005840
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001945
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002039
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0008015
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0015671
subclass of: blood cell
subclass of: oxygen accumulating cell
subclass of: erythroid lineage cell
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0005840
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001945
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0002039
subclass of: Restriction
  on property: RO_0002202
  some values from: reticulocyte
IAO_0000115: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
description: Erythrocytes, also known as red blood cells, are a type of specialized cell that make up the largest percentage of cells in the human body. Erythrocytes are biconcave in shape and lack nuclei and organelles, allowing them to carry oxygen and carbon dioxide through the bloodstream more efficiently. The main function of erythrocytes is to transport oxygen from the lungs to the body's tissues and organs, and to transport carbon dioxide from the body's tissues to the lungs, where it can be exhaled out of the body. Hemoglobin, a protein located inside erythrocytes, is responsible for binding to oxygen. Erythrocytes are produced in the bone marrow and have a lifespan of approximately 120 days before they are broken down and recycled by the body. Erythrocytes are regulated by the hormone erythropoietin, which is produced by the kidneys and liver in response to low oxygen levels in the body, thereby stimulating erythrocyte production . In addition to their role in oxygen transport, erythrocytes also play a key role in regulating the body's pH levels. Without erythrocytes, oxygen would not be able to be transported efficiently throughout the body and tissues would not receive the necessary oxygen to function properly. Overall, erythrocytes are essential for maintaining the health and homeostasis of the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
description: Erythrocytes, also known as red blood cells, are a type of specialized cell whose main function it is to transport oxygen from the lungs to the body's tissues and organs, and to transport carbon dioxide from the body's tissues to the lungs, where it can be exhaled out of the body. In humans, erythrocytes make up the largest percentage of cells in the body. Human erythrocytes are biconcave in shape and lack nuclei and organelles, allowing them to carry oxygen and carbon dioxide through the bloodstream more efficiently. Most mammals have enucleated erythrocytes, while other animals such as birds and reptiles have nucleated erythrocytes. Hemoglobin, a protein located inside erythrocytes, is responsible for binding to oxygen. Erythrocytes are produced in the bone marrow and have a lifespan of approximately 120 days before they are broken down and recycled by the body. Erythrocytes are regulated by the hormone erythropoietin, which is produced by the kidneys and liver in response to low oxygen levels in the body, thereby stimulating erythrocyte production . In addition to their role in oxygen transport, erythrocytes also play a key role in regulating the body's pH levels. Without erythrocytes, oxygen would not be able to be transported efficiently throughout the body and tissues would not receive the necessary oxygen to function properly. Overall, erythrocytes are essential for maintaining the health and homeostasis of the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000424
has db xref: CALOHA:TS-0290
has db xref: FMA:81100
has exact synonym: RBC
has exact synonym: red blood cell
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: erythrocyte
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: erythrocyte
annotated property: IAO_0000115
annotated target: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
has db xref: GOC:tfm
has db xref: MESH:D004912

Axiom
annotated source: erythrocyte
annotated property: description
annotated target: Erythrocytes, also known as red blood cells, are a type of specialized cell that make up the largest percentage of cells in the human body. Erythrocytes are biconcave in shape and lack nuclei and organelles, allowing them to carry oxygen and carbon dioxide through the bloodstream more efficiently. The main function of erythrocytes is to transport oxygen from the lungs to the body's tissues and organs, and to transport carbon dioxide from the body's tissues to the lungs, where it can be exhaled out of the body. Hemoglobin, a protein located inside erythrocytes, is responsible for binding to oxygen. Erythrocytes are produced in the bone marrow and have a lifespan of approximately 120 days before they are broken down and recycled by the body. Erythrocytes are regulated by the hormone erythropoietin, which is produced by the kidneys and liver in response to low oxygen levels in the body, thereby stimulating erythrocyte production . In addition to their role in oxygen transport, erythrocytes also play a key role in regulating the body's pH levels. Without erythrocytes, oxygen would not be able to be transported efficiently throughout the body and tissues would not receive the necessary oxygen to function properly. Overall, erythrocytes are essential for maintaining the health and homeostasis of the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.blre.2012.12.003
has db xref: DOI:10.1056/NEJM199801223380407
has db xref: DOI:10.3389/fphys.2021.655393

Axiom
annotated source: erythrocyte
annotated property: description
annotated target: Erythrocytes, also known as red blood cells, are a type of specialized cell whose main function it is to transport oxygen from the lungs to the body's tissues and organs, and to transport carbon dioxide from the body's tissues to the lungs, where it can be exhaled out of the body. In humans, erythrocytes make up the largest percentage of cells in the body. Human erythrocytes are biconcave in shape and lack nuclei and organelles, allowing them to carry oxygen and carbon dioxide through the bloodstream more efficiently. Most mammals have enucleated erythrocytes, while other animals such as birds and reptiles have nucleated erythrocytes. Hemoglobin, a protein located inside erythrocytes, is responsible for binding to oxygen. Erythrocytes are produced in the bone marrow and have a lifespan of approximately 120 days before they are broken down and recycled by the body. Erythrocytes are regulated by the hormone erythropoietin, which is produced by the kidneys and liver in response to low oxygen levels in the body, thereby stimulating erythrocyte production . In addition to their role in oxygen transport, erythrocytes also play a key role in regulating the body's pH levels. Without erythrocytes, oxygen would not be able to be transported efficiently throughout the body and tissues would not receive the necessary oxygen to function properly. Overall, erythrocytes are essential for maintaining the health and homeostasis of the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.blre.2012.12.003
has db xref: DOI:10.1056/NEJM199801223380407
has db xref: DOI:10.3389/fphys.2021.655393

erythrocyte on CELLxGENE CellGuide
type: Axiom
annotated source: erythrocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000232

platelet
type: Class
subclass of: blood cell
subclass of: anucleate cell
subclass of: serotonin secreting cell
subclass of: myeloid cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001874
subclass of: Restriction
  on property: RO_0002202
  some values from: megakaryocyte
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0007596
IAO_0000115: A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
description: Platelets, also known as thrombocytes, are small, disc-shaped cell fragments devoid of a nucleus, yet remarkably intricate and multi-functional. They originate from the megakaryocytes in the bone marrow via a process called thrombopoiesis. Platelets are central to hemostasis, a process that prevents bleeding from broken or damaged blood vessels and facilitates wound healing. In their resting state, platelets are inactive but become quickly activated when an injury occurs. Platelets function in the initiation and regulation of coagulation or clotting, which is a complex process involving several bioactive molecules. When a blood vessel is injured, the inner lining of the vessel, the endothelium, gets disrupted, exposing the underlying tissue matrix. This leads to platelet activation and adhesion to the injury site, initiating the clotting cascade. Platelets release granules packed with clotting factors, proteins, enzymes, and more platelets, which further propagates the clotting process. When activated, platelets also change their shape from discoid to a spherical form with protruding pseudopods that enables them to adhere more readily to the site of injury and mesh with one another to form a 'platelet plug'. Additionally, platelets serve other physiological roles. They release growth factors enhancing tissue regeneration and wound healing. They also play a significant role in inflammation, innate immunity, and antimicrobial host defense, as they interact with leukocytes and may sequester microbes. Platelets are involved in maintaining the integrity of the blood vessels and angiogenesis, the formation of new blood vessels. Proper functioning of platelets is critical for maintaining homeostasis, while dysregulation can lead to conditions such as thrombosis or bleeding disorders. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain informa…
has db xref: BTO:0000132
has db xref: CALOHA:TS-0803
has db xref: FMA:62851
has exact synonym: anucleate thrombocyte
has exact synonym: blood platelet
has exact synonym: enucleate thrombocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF.

Axiom
annotated source: platelet
annotated property: subClassOf
annotated target: myeloid cell
is inferred: true

Axiom
annotated source: platelet
annotated property: IAO_0000115
annotated target: A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: MESH:D001792
has db xref: PMID:11110672
has db xref: PMID:16987572
has db xref: PMID:17204662
has db xref: PMID:17479180
has db xref: PMID:20414831
has db xref: http://en.wikipedia.org/wiki/Platelet

Axiom
annotated source: platelet
annotated property: description
annotated target: Platelets, also known as thrombocytes, are small, disc-shaped cell fragments devoid of a nucleus, yet remarkably intricate and multi-functional. They originate from the megakaryocytes in the bone marrow via a process called thrombopoiesis. Platelets are central to hemostasis, a process that prevents bleeding from broken or damaged blood vessels and facilitates wound healing. In their resting state, platelets are inactive but become quickly activated when an injury occurs. Platelets function in the initiation and regulation of coagulation or clotting, which is a complex process involving several bioactive molecules. When a blood vessel is injured, the inner lining of the vessel, the endothelium, gets disrupted, exposing the underlying tissue matrix. This leads to platelet activation and adhesion to the injury site, initiating the clotting cascade. Platelets release granules packed with clotting factors, proteins, enzymes, and more platelets, which further propagates the clotting process. When activated, platelets also change their shape from discoid to a spherical form with protruding pseudopods that enables them to adhere more readily to the site of injury and mesh with one another to form a 'platelet plug'. Additionally, platelets serve other physiological roles. They release growth factors enhancing tissue regeneration and wound healing. They also play a significant role in inflammation, innate immunity, and antimicrobial host defense, as they interact with leukocytes and may sequester microbes. Platelets are involved in maintaining the integrity of the blood vessels and angiogenesis, the formation of new blood vessels. Proper functioning of platelets is critical for maintaining homeostasis, while dysregulation can lead to conditions such as thrombosis or bleeding disorders. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain informa…
has db xref: DOI:10.1007/s10555-017-9677-x
has db xref: DOI:10.1016/j.blre.2014.10.003
has db xref: DOI:10.1038/s41569-018-0110-0
has db xref: DOI:10.3389/fimmu.2019.01731

platelet on CELLxGENE CellGuide
type: Axiom
annotated source: platelet
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000233

phagocyte
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0006909
subclass of: motile cell
subclass of: stuff accumulating cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0006909
IAO_0000115: Any cell capable of ingesting particulate matter via phagocytosis.
description: Phagocytes are a heterogeneous group of white blood cells that have the capability to ingest, or ‘phagocytose’, foreign substances, pathogens, and cellular debris with high efficiency, thereby playing a vital role in the immune response. Phagocytes circulate throughout the body, patrolling and guarding against the invasion of pathogens. They are one among many types of cells that originate from hematopoietic stem cells in the bone marrow. Upon detection of an invading microorganism, phagocytes are mobilized by inflammatory mediators (such as bacterial proteins or complement proteins) to the infection site. They recognize surface molecules, specifically antigens, on harmful bacteria or other foreign substances with the help of opsonins, which are proteins that bind to the pathogen and make them more susceptible to phagocytosis. The process of phagocytosis involves the extension of the phagocyte's membrane around the microorganism, completely enclosing it within a microbicidal vacuole, the phagolysosome, which contains various microbicidal chemicals and digestive enzymes such as cathepsins, proteases, lysozymes, and lipases that may be employed to degrade the pathogen. Phagocytes are predominantly neutrophils or monocytes. Neutrophils are the most abundant type of phagocyte and are usually the first to arrive at the site of infection. Monocytes are derived from the bone marrow and can circulate to tissues and mature into local macrophages. Macrophages arrive later at sites of infection and are longer-lived than neutrophils. The process of phagocytosis must be tightly regulated to avoid host tissue damage. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001044
has db xref: FMA:83806
has db xref: MESH:D010586
has db xref: ZFA:0009140
in subset: cellxgene subset

Axiom
annotated source: phagocyte
annotated property: IAO_0000115
annotated target: Any cell capable of ingesting particulate matter via phagocytosis.
has db xref: GOC:add
has db xref: ISBN:0721601464

Axiom
annotated source: phagocyte
annotated property: description
annotated target: Phagocytes are a heterogeneous group of white blood cells that have the capability to ingest, or ‘phagocytose’, foreign substances, pathogens, and cellular debris with high efficiency, thereby playing a vital role in the immune response. Phagocytes circulate throughout the body, patrolling and guarding against the invasion of pathogens. They are one among many types of cells that originate from hematopoietic stem cells in the bone marrow. Upon detection of an invading microorganism, phagocytes are mobilized by inflammatory mediators (such as bacterial proteins or complement proteins) to the infection site. They recognize surface molecules, specifically antigens, on harmful bacteria or other foreign substances with the help of opsonins, which are proteins that bind to the pathogen and make them more susceptible to phagocytosis. The process of phagocytosis involves the extension of the phagocyte's membrane around the microorganism, completely enclosing it within a microbicidal vacuole, the phagolysosome, which contains various microbicidal chemicals and digestive enzymes such as cathepsins, proteases, lysozymes, and lipases that may be employed to degrade the pathogen. Phagocytes are predominantly neutrophils or monocytes. Neutrophils are the most abundant type of phagocyte and are usually the first to arrive at the site of infection. Monocytes are derived from the bone marrow and can circulate to tissues and mature into local macrophages. Macrophages arrive later at sites of infection and are longer-lived than neutrophils. The process of phagocytosis must be tightly regulated to avoid host tissue damage. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:0.3389/fimmu.2020.01066
has db xref: DOI:10.1016/B978-0-08-046884-6.00607-2
has db xref: DOI:10.1016/B978-0-12-809633-8.90746-5
has db xref: DOI:10.1086/374747
has db xref: DOI:10.1182/blood-2007-12-077917

Axiom
annotated source: phagocyte
annotated property: hasDbXref
annotated target: ZFA:0009140
mapping justification: UnspecifiedMatching

phagocyte on CELLxGENE CellGuide
type: Axiom
annotated source: phagocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000234

macrophage
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002504
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0006909
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0031268
subclass of: mononuclear phagocyte
subclass of: professional antigen presenting cell
subclass of: myeloid leukocyte
subclass of: Restriction
  on property: RO_0002202
  some values from: monocyte
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0031268
IAO_0000115: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
description: Macrophages are specialized white blood cells involved in immune responses, inflammation, and tissue repair. Tissue-resident macrophages can be self-renewing and arise from embryo-derived populations. Macrophages can also originate from circulating monocytes that differentiate into macrophages upon migration into body tissues. Macrophages are involved in the detection, phagocytosis, and destruction of bacteria and other pathogens. They are also responsible for engulfing and removing dead cells and debris. Macrophages are also one of the cells that present pathogenic antigens to T cells so that the pathogens may be recognized and killed, or so that an antibody response may be mounted. They can also secrete cytokines, chemokines, and enzymes that further orchestrate the immune response. Tissue-resident macrophages are diverse and heterogenous, likely as a result of the signals received from the tissue environment. The functions of these macrophages are specific to each tissue and contribute to tissue homeostasis. Dysregulation of macrophage functioning may also contribute to the development of various disease processes, such as fibrosis, chronic inflammation, or cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000801
has db xref: CALOHA:TS-0587
has db xref: FMA:63261
has db xref: FMA:83585
has db xref: MESH:D008264
has db xref: ZFA:0009141
has exact synonym: histiocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.

Axiom
annotated source: macrophage
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: macrophage
annotated property: IAO_0000115
annotated target: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:16213494
has db xref: PMID:1919437

Axiom
annotated source: macrophage
annotated property: description
annotated target: Macrophages are specialized white blood cells involved in immune responses, inflammation, and tissue repair. Tissue-resident macrophages can be self-renewing and arise from embryo-derived populations. Macrophages can also originate from circulating monocytes that differentiate into macrophages upon migration into body tissues. Macrophages are involved in the detection, phagocytosis, and destruction of bacteria and other pathogens. They are also responsible for engulfing and removing dead cells and debris. Macrophages are also one of the cells that present pathogenic antigens to T cells so that the pathogens may be recognized and killed, or so that an antibody response may be mounted. They can also secrete cytokines, chemokines, and enzymes that further orchestrate the immune response. Tissue-resident macrophages are diverse and heterogenous, likely as a result of the signals received from the tissue environment. The functions of these macrophages are specific to each tissue and contribute to tissue homeostasis. Dysregulation of macrophage functioning may also contribute to the development of various disease processes, such as fibrosis, chronic inflammation, or cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.immuni.2016.02.015
has db xref: DOI:10.1038/ni.2705
has db xref: DOI:10.1093/intimm/dxy054
has db xref: DOI:10.1146/annurev-immunol-032414-112220
has db xref: DOI:10.3389/fimmu.2021.708186

Axiom
annotated source: macrophage
annotated property: hasDbXref
annotated target: ZFA:0009141
mapping justification: UnspecifiedMatching

macrophage on CELLxGENE CellGuide
type: Axiom
annotated source: macrophage
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000235

B cell
type: Class
equivalent class: Class
  intersection of: lymphocyte of B lineage
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0019724
subclass of: lymphocyte of B lineage
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0019724
IAO_0000115: A lymphocyte of B lineage that is capable of B cell mediated immunity.
has db xref: BTO:0000776
has db xref: CALOHA:TS-0068
has db xref: FMA:62869
has db xref: MESH:D001402
has db xref: VHOG:0001480
has db xref: ZFA:0009142
has exact synonym: B lymphocyte
has exact synonym: B-cell
has exact synonym: B-lymphocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: B cell
annotated property: subClassOf
annotated target: lymphocyte of B lineage
is inferred: true

Axiom
annotated source: B cell
annotated property: IAO_0000115
annotated target: A lymphocyte of B lineage that is capable of B cell mediated immunity.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

Axiom
annotated source: B cell
annotated property: hasDbXref
annotated target: ZFA:0009142
mapping justification: UnspecifiedMatching

keratinizing barrier epithelial cell
type: Class
subclass of: stratified epithelial cell
subclass of: keratin accumulating cell
subclass of: CL_0002077
subclass of: Restriction
  on property: RO_0002202
  some values from: surface ectodermal cell
in subset: cellxgene subset

brush border epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005903
subclass of: columnar/cuboidal epithelial cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005903
IAO_0000115: An epithelial cell characterized by the presence of a brush border on its apical surface, which increases the surface area for absorption.
has db xref: ajpgi.00005.2011
has db xref: PMID:25422372
has db xref: ZFA:0009143
comment: All brush border cells are columnar-cuboidal. The formal logical definition of this term asserts this. Brush border epithelial cells are predominantly found lining the small intestine and the proximal tubules of the kidneys.

Axiom
annotated source: brush border epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009143
mapping justification: UnspecifiedMatching

stratified squamous epithelial cell
type: Class
equivalent class: Class
  intersection of: stratified epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000486
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002254
subclass of: squamous epithelial cell
subclass of: stratified epithelial cell
IAO_0000115: A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus.
description: Stratified squamous epithelial cells are a specific type of epithelial cell that form layers and have a flat shape. These cells are part of the outermost layer of the skin, called the epidermis, and are also found lining surfaces of the body that are subjected to physical or chemical wear and tear, such as the mouth, esophagus, and vagina. The primary role of these cells is to create a barrier that protects underlying tissues from dehydration, abrasion, and infection. The stratified squamous epithelium is able to provide a strong, force-resistant barrier due to the stratified arrangement of the cells; it consists primarily of keratinocytes in various stages of differentiation: The basal layer contains cells that continuously divide and push older cells towards the surface. As the cells move up through the layers, they gradually flatten and become filled with a protein called keratin. In high-abrasion areas like the skin, the outer layers of these cells can become so filled with keratin that they die (they become 'keratinized'), providing an even more robust barrier; eventually, they are shed off in a process known as desquamation. In addition to forming a protective barrier, stratified squamous epithelial cells also play a part in the immune response. They can recognize pathogens, and in response, release chemical signals that attract immune cells to the site of potential infection. Moreover, they also carry out a variety of interactions with the immune system to ensure that invading pathogens cannot penetrate into deeper layers of the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009144
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: stratified squamous epithelial cell
annotated property: IAO_0000115
annotated target: A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus.
has db xref: PMID:30422572
has db xref: Wikipedia:Epithelium
has db xref: Wikipedia:Stratified_squamous_epithelium

Axiom
annotated source: stratified squamous epithelial cell
annotated property: description
annotated target: Stratified squamous epithelial cells are a specific type of epithelial cell that form layers and have a flat shape. These cells are part of the outermost layer of the skin, called the epidermis, and are also found lining surfaces of the body that are subjected to physical or chemical wear and tear, such as the mouth, esophagus, and vagina. The primary role of these cells is to create a barrier that protects underlying tissues from dehydration, abrasion, and infection. The stratified squamous epithelium is able to provide a strong, force-resistant barrier due to the stratified arrangement of the cells; it consists primarily of keratinocytes in various stages of differentiation: The basal layer contains cells that continuously divide and push older cells towards the surface. As the cells move up through the layers, they gradually flatten and become filled with a protein called keratin. In high-abrasion areas like the skin, the outer layers of these cells can become so filled with keratin that they die (they become 'keratinized'), providing an even more robust barrier; eventually, they are shed off in a process known as desquamation. In addition to forming a protective barrier, stratified squamous epithelial cells also play a part in the immune response. They can recognize pathogens, and in response, release chemical signals that attract immune cells to the site of potential infection. Moreover, they also carry out a variety of interactions with the immune system to ensure that invading pathogens cannot penetrate into deeper layers of the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/s00281-018-0701-1
has db xref: DOI:10.1016/j.jdermsci.2004.05.004
has db xref: DOI:10.1016/j.jdermsci.2018.01.012
has db xref: DOI:10.1038/onc.2010.456

Axiom
annotated source: stratified squamous epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009144
mapping justification: UnspecifiedMatching

stratified squamous epithelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: stratified squamous epithelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000240

transitional epithelial cell
type: Class
subclass of: epithelial cell
IAO_0000115: A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium.
has db xref: FMA:66778
has db xref: ZFA:0009148
in subset: human reference atlas

Axiom
annotated source: transitional epithelial cell
annotated property: IAO_0000115
annotated target: A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: transitional epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009148
mapping justification: UnspecifiedMatching

Rohon-Beard neuron
type: Class
subclass of: primary sensory neuron (sensu Teleostei)
IAO_0000115: Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings.
has db xref: AAO:0010316
has db xref: EFO:0003711
has db xref: VHOG:0001484
has db xref: ZFA:0009150
has exact synonym: Rohon Beard cell
has exact synonym: Rohon-Beard cell
has related synonym: RB neuron

Axiom
annotated source: Rohon-Beard neuron
annotated property: IAO_0000115
annotated target: Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings.
has db xref: VHOG:0001484

Axiom
annotated source: Rohon-Beard neuron
annotated property: hasDbXref
annotated target: ZFA:0009150
mapping justification: UnspecifiedMatching

Axiom
annotated source: Rohon-Beard neuron
annotated property: hasExactSynonym
annotated target: Rohon Beard cell
has db xref: VHOG:0001484

Axiom
annotated source: Rohon-Beard neuron
annotated property: hasRelatedSynonym
annotated target: RB neuron
has db xref: VHOG:0001484

eurydendroid cell
type: Class
subclass of: efferent neuron
has db xref: ZFA:0009153
in subset: cellxgene subset

Axiom
annotated source: eurydendroid cell
annotated property: hasDbXref
annotated target: ZFA:0009153
mapping justification: UnspecifiedMatching

eukaryotic cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 2759
subclass of: cell
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 2759
disjoint with: prokaryotic cell
IAO_0000115: Any cell that in taxon some Eukaryota.
has db xref: MESH:D005057

Axiom
annotated source: eukaryotic cell
annotated property: IAO_0000115
annotated target: Any cell that in taxon some Eukaryota.
has db xref: FBC:Autogenerated

eye photoreceptor cell
type: Class
equivalent class: Class
  intersection of: photoreceptor cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000970
subclass of: neuronal receptor cell
subclass of: photoreceptor cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000970
IAO_0000115: Any photoreceptor cell that is part of some eye.
description: Eye photoreceptor cells, also commonly known as photoreceptors, are specialized types of cells found in the retina, the light-sensitive layer at the back of the eye. They are integral to the complex process of vision, as they are directly involved in converting light into electrical signals. This process is known as phototransduction. There are two primary classes of photoreceptor cells; rods, which function mainly in dim light and provide black-and-white vision, and cones, which function in brighter light and allow for the perception of color. Rods and cones carry out their roles through sophisticated biochemical reactions. The main component of these reactions is a protein called opsin, which binds to a small molecule known as retinal. In the presence of light, retinal changes its shape, leading to a series of chemical reactions that result in changes to the cell’s electrical potential, thus creating an electrical signal that travels to the optic nerve. Rod cells possess only one kind of opsin, called rhodopsin, which only allows them to distinguish between light and dark. Conversely, cone cells have three types of opsins, allowing for the differentiation of various colors. The spatial distribution of these cell types throughout the retina also contributes to their function. Rod cells are more numerous and are distributed more at the periphery of the retina, contributing to peripheral and night vision. On the other hand, cone cells are concentrated in the macula, a tiny central region in the retina, and with the highest density in the fovea, a small pit in the macula. This distribution of cones lies at the base of fine detail and color vision in the central visual field. In summary, eye photoreceptor cells carry out the primary function of transforming light into visual signals, a role that is crucial for the overall process of vision. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editor…
has db xref: ZFA:0009154
in subset: cellxgene subset
in subset: eye upper slim
in subset: human reference atlas

Axiom
annotated source: eye photoreceptor cell
annotated property: IAO_0000115
annotated target: Any photoreceptor cell that is part of some eye.
has db xref: FBC:Autogenerated

Axiom
annotated source: eye photoreceptor cell
annotated property: description
annotated target: Eye photoreceptor cells, also commonly known as photoreceptors, are specialized types of cells found in the retina, the light-sensitive layer at the back of the eye. They are integral to the complex process of vision, as they are directly involved in converting light into electrical signals. This process is known as phototransduction. There are two primary classes of photoreceptor cells; rods, which function mainly in dim light and provide black-and-white vision, and cones, which function in brighter light and allow for the perception of color. Rods and cones carry out their roles through sophisticated biochemical reactions. The main component of these reactions is a protein called opsin, which binds to a small molecule known as retinal. In the presence of light, retinal changes its shape, leading to a series of chemical reactions that result in changes to the cell’s electrical potential, thus creating an electrical signal that travels to the optic nerve. Rod cells possess only one kind of opsin, called rhodopsin, which only allows them to distinguish between light and dark. Conversely, cone cells have three types of opsins, allowing for the differentiation of various colors. The spatial distribution of these cell types throughout the retina also contributes to their function. Rod cells are more numerous and are distributed more at the periphery of the retina, contributing to peripheral and night vision. On the other hand, cone cells are concentrated in the macula, a tiny central region in the retina, and with the highest density in the fovea, a small pit in the macula. This distribution of cones lies at the base of fine detail and color vision in the central visual field. In summary, eye photoreceptor cells carry out the primary function of transforming light into visual signals, a role that is crucial for the overall process of vision. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editor…
has db xref: DOI:10.1002/cne.902920402
has db xref: DOI:10.1038/eye.2016.107
has db xref: DOI:10.1098/rstb.2009.0051
has db xref: DOI:10.1146/annurev.biophys.31.082901.134348
has db xref: DOI:10.1186/gb-2005-6-3-213

Axiom
annotated source: eye photoreceptor cell
annotated property: hasDbXref
annotated target: ZFA:0009154
mapping justification: UnspecifiedMatching

eye photoreceptor cell on CELLxGENE CellGuide
type: Axiom
annotated source: eye photoreceptor cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000287

somatotropin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030252
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030252
IAO_0000115: A peptide hormone secreting cell that produces growth hormone, somatotropin.
has db xref: ZFA:0009155
has exact synonym: growth hormone secreting cell
has exact synonym: somatotrophin secreting cell

Axiom
annotated source: somatotropin secreting cell
annotated property: IAO_0000115
annotated target: A peptide hormone secreting cell that produces growth hormone, somatotropin.
has db xref: GOC:tfm
has db xref: SANBI:mhl

Axiom
annotated source: somatotropin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009155
mapping justification: UnspecifiedMatching

gamete
type: Class
equivalent class: Class
  intersection of: germ cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001375
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0009566
subclass of: haploid cell
subclass of: germ cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0009566
IAO_0000115: A mature sexual reproductive cell having a single set of unpaired chromosomes.
description: Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution. (This extended description was generated by ChatGPT and revie…
has db xref: CALOHA:TS-0395
has db xref: FBbt:00005412
has db xref: FMA:18649
has db xref: ZFA:0009156
has exact synonym: haploid nucleated cell
has related synonym: haploid germ cell

Axiom
annotated source: gamete
annotated property: subClassOf
annotated target: germ cell
is inferred: true

Axiom
annotated source: gamete
annotated property: IAO_0000115
annotated target: A mature sexual reproductive cell having a single set of unpaired chromosomes.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: gamete
annotated property: description
annotated target: Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution. (This extended description was generated by ChatGPT and revie…
has db xref: DOI:10.1038/s41586-020-2347-0
has db xref: DOI:10.3389/fcell.2022.1040708
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK10008/
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK553142/

Axiom
annotated source: gamete
annotated property: hasDbXref
annotated target: FBbt:00005412
mapping justification: ManualMappingCuration

Axiom
annotated source: gamete
annotated property: hasDbXref
annotated target: ZFA:0009156
mapping justification: UnspecifiedMatching

gamete on CELLxGENE CellGuide
type: Axiom
annotated source: gamete
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000300

pole cell
type: Class
subclass of: primordial germ cell
IAO_0000115: A primordial germ cell of insects. Such cells form at the posterior pole of the early embryo.
has db xref: FBbt:00000092

Axiom
annotated source: pole cell
annotated property: IAO_0000115
annotated target: A primordial germ cell of insects. Such cells form at the posterior pole of the early embryo.
has db xref: doi:10.1017/CBO9780511818202.015

Axiom
annotated source: pole cell
annotated property: hasDbXref
annotated target: FBbt:00000092
mapping justification: ManualMappingCuration

crystallin accumulating cell
type: Class
subclass of: stuff accumulating cell
has exact synonym: lens cell
in subset: eye upper slim

tracheal epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0003126
subclass of: CL_0002202
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0003126
subclass of: Restriction
  on property: RO_0002202
  some values from: tracheoblast
IAO_0000115: An epithelial cell found in the trachea.
has db xref: FMA:74793
has exact synonym: tracheocyte
comment: This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell'

Axiom
annotated source: tracheal epithelial cell
annotated property: subClassOf
annotated target: CL_0002202
is inferred: true

Axiom
annotated source: tracheal epithelial cell
annotated property: IAO_0000115
annotated target: An epithelial cell found in the trachea.
has db xref: GOC:tfm

keratin accumulating cell
type: Class
subclass of: stuff accumulating cell
description: Keratin-accumulating cells, primarily known as keratinocytes, are a distinctive type of epithelial cells predominantly found in the skin's outermost layer known as the epidermis. These cells are responsible for the production of a unique type of protein called keratin. Keratin is a crucial part of the biological structure and functionality of these cells and is essential in creating a protective barrier for the body. These cells form a protective shield against environmental damage such as UV radiation, harmful microbes, and physical injuries. The primary function of keratinocytes is the synthesis and accumulation of keratin, which undergoes minor modifications such as desquamation and cornification resulting in the formation of a solid and stable protein-rich protective layer on the body's surface. The production of keratin is a highly coordinated and regulated process. The cytoskeleton of these cells is primarily composed of keratin intermediate filaments. During keratinocyte maturation and differentiation, keratin-accumulating cells transit from the basal layer to the outermost layer of the skin during which they synthesize different types of keratins sequentially creating a stratified and structured epidermal layer. Moreover, keratinocytes produce cytokines and chemokines that have defensive roles against pathogenic intruders. Additionally, these cells partake in the inflammation process by signaling immune cells to the area of the injury. Furthermore, keratinocytes play crucial roles in wound healing and skin regeneration. In addition to having a protective and barrier-centric role, keratinocytes are also involved in regulating the rate of water loss from the body, maintaining body temperature, and facilitating sensory perception. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes an…
has db xref: ZFA:0009157

Axiom
annotated source: keratin accumulating cell
annotated property: description
annotated target: Keratin-accumulating cells, primarily known as keratinocytes, are a distinctive type of epithelial cells predominantly found in the skin's outermost layer known as the epidermis. These cells are responsible for the production of a unique type of protein called keratin. Keratin is a crucial part of the biological structure and functionality of these cells and is essential in creating a protective barrier for the body. These cells form a protective shield against environmental damage such as UV radiation, harmful microbes, and physical injuries. The primary function of keratinocytes is the synthesis and accumulation of keratin, which undergoes minor modifications such as desquamation and cornification resulting in the formation of a solid and stable protein-rich protective layer on the body's surface. The production of keratin is a highly coordinated and regulated process. The cytoskeleton of these cells is primarily composed of keratin intermediate filaments. During keratinocyte maturation and differentiation, keratin-accumulating cells transit from the basal layer to the outermost layer of the skin during which they synthesize different types of keratins sequentially creating a stratified and structured epidermal layer. Moreover, keratinocytes produce cytokines and chemokines that have defensive roles against pathogenic intruders. Additionally, these cells partake in the inflammation process by signaling immune cells to the area of the injury. Furthermore, keratinocytes play crucial roles in wound healing and skin regeneration. In addition to having a protective and barrier-centric role, keratinocytes are also involved in regulating the rate of water loss from the body, maintaining body temperature, and facilitating sensory perception. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes an…
has db xref: DOI:10.1007/s00418-008-0435-6
has db xref: DOI:10.1016/j.bbamcr.2013.06.010
has db xref: DOI:10.1083/jcb.201404147
has db xref: DOI:10.1172/jci.insight.142067
has db xref: DOI:10.3390/ijms21228790

Axiom
annotated source: keratin accumulating cell
annotated property: hasDbXref
annotated target: ZFA:0009157
mapping justification: UnspecifiedMatching

keratin accumulating cell on CELLxGENE CellGuide
type: Axiom
annotated source: keratin accumulating cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000311

keratinocyte
type: Class
subclass of: keratinizing barrier epithelial cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002775
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002776
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042060
IAO_0000115: An epithelial cell of stratified squamous tissues, including skin, oral mucosa (Hiroshima et al., 2011), and esophagus (Whelan et al., 2018), that produces keratin proteins and secretes antimicrobial peptides to form a resilient barrier against environmental damage, dehydration, pathogens, and microbial invasion. It undergoes successive stages of differentiation marked by changes in keratin expression, supporting tissue integrity, wound repair, and contributing to immune defense.
has db xref: BTO:0000667
has db xref: CALOHA:TS-0500
has db xref: FMA:62879
has db xref: ZFA:0009158
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: keratinocyte
annotated property: subClassOf
annotated target: keratinizing barrier epithelial cell
is inferred: true

Axiom
annotated source: keratinocyte
annotated property: IAO_0000115
annotated target: An epithelial cell of stratified squamous tissues, including skin, oral mucosa (Hiroshima et al., 2011), and esophagus (Whelan et al., 2018), that produces keratin proteins and secretes antimicrobial peptides to form a resilient barrier against environmental damage, dehydration, pathogens, and microbial invasion. It undergoes successive stages of differentiation marked by changes in keratin expression, supporting tissue integrity, wound repair, and contributing to immune defense.
has db xref: PMID:15749908
has db xref: PMID:19256306
has db xref: PMID:19727116
has db xref: PMID:29713660
has db xref: PMID:37873034

Axiom
annotated source: keratinocyte
annotated property: hasDbXref
annotated target: ZFA:0009158
mapping justification: UnspecifiedMatching

milk secreting cell
type: Class
subclass of: secretory cell

sebocyte
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001821
subclass of: glandular secretory epithelial cell
subclass of: exocrine cell
subclass of: epidermal cell
subclass of: CL_0002308
subclass of: CL_2000021
IAO_0000115: An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents.
has exact synonym: sebum secreting cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: sebocyte
annotated property: IAO_0000115
annotated target: An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents.
has db xref: MESH:D012629
has db xref: PMID:19944183

Axiom
annotated source: sebocyte
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM853.HLFH.534

mucus secreting cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0070254
subclass of: seromucus secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0070254
IAO_0000115: Any cell that is capable of some mucus secretion.
has db xref: BTO:0003689
has db xref: ZFA:0009159
has exact synonym: mucous cell
in subset: cellxgene subset

Axiom
annotated source: mucus secreting cell
annotated property: IAO_0000115
annotated target: Any cell that is capable of some mucus secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: mucus secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009159
mapping justification: UnspecifiedMatching

pulmonary alveolar epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0004821
subclass of: epithelial cell of lung
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004821
IAO_0000115: An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-09-02T08:27:21Z
has db xref: BTO:0000395
has db xref: CALOHA:TS-2168
has db xref: FMA:62499
has db xref: MESH:D056809
has exact synonym: alveolar epithelial cell
has exact synonym: alveolus of lung epithelial cell
has exact synonym: epithelial cell of alveolus of lung
has exact synonym: pneumocyte
has exact synonym: pneumonocyte
in subset: cellxgene subset

Axiom
annotated source: pulmonary alveolar epithelial cell
annotated property: IAO_0000115
annotated target: An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.
has db xref: GOC:tfm
has db xref: PMID:20054144
has db xref: PMID:29463737

Axiom
annotated source: pulmonary alveolar epithelial cell
annotated property: hasExactSynonym
annotated target: pneumocyte
has db xref: PMID:32491474

stuff accumulating cell
type: Class
subclass of: cell
IAO_0000115: A cell that is specialised to accumulate a particular substance(s).
in subset: upper level

Axiom
annotated source: stuff accumulating cell
annotated property: IAO_0000115
annotated target: A cell that is specialised to accumulate a particular substance(s).
has db xref: FB:ma

extracellular matrix secreting cell
type: Class
subclass of: stromal cell
has db xref: ZFA:0009162
in subset: cellxgene subset

Axiom
annotated source: extracellular matrix secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009162
mapping justification: UnspecifiedMatching

oxygen accumulating cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0015671
subclass of: cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0015671
IAO_0000115: Any cell that is capable of some oxygen transport.
has db xref: ZFA:0009164

Axiom
annotated source: oxygen accumulating cell
annotated property: IAO_0000115
annotated target: Any cell that is capable of some oxygen transport.
has db xref: FBC:Autogenerated

Axiom
annotated source: oxygen accumulating cell
annotated property: hasDbXref
annotated target: ZFA:0009164
mapping justification: UnspecifiedMatching

migratory neural crest cell
type: Class
subclass of: motile cell
subclass of: eukaryotic cell
subclass of: CL_0011012
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0007004
IAO_0000115: A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
has db xref: FMA:86667
has db xref: ZFA:0007086

Axiom
annotated source: migratory neural crest cell
annotated property: IAO_0000115
annotated target: A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
has db xref: doi:10.1016/j.stem.2015.02.017

Axiom
annotated source: migratory neural crest cell
annotated property: hasDbXref
annotated target: ZFA:0007086
mapping justification: UnspecifiedMatching

neuroblast (sensu Nematoda and Protostomia)
type: Class
subclass of: neural stem cell
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33317
IAO_0000115: A neural precursor of the central nervous system.
has broad synonym: neuroblast
has db xref: FBbt:00005146
in subset: cellxgene subset

Axiom
annotated source: neuroblast (sensu Nematoda and Protostomia)
annotated property: IAO_0000115
annotated target: A neural precursor of the central nervous system.
has db xref: PMID:1295739

Axiom
annotated source: neuroblast (sensu Nematoda and Protostomia)
annotated property: hasDbXref
annotated target: FBbt:00005146
mapping justification: ManualMappingCuration

glioblast (sensu Vertebrata)
type: Class
subclass of: glioblast
subclass of: neuron associated cell (sensu Vertebrata)
IAO_0000115: An early neural cell developing from the early ependymal cell of the neural tube.
has db xref: FMA:70564
has db xref: ZFA:0009169
has exact synonym: spongioblast
in subset: cellxgene subset

Axiom
annotated source: glioblast (sensu Vertebrata)
annotated property: IAO_0000115
annotated target: An early neural cell developing from the early ependymal cell of the neural tube.
has db xref: GOC:tfm
has db xref: ISBN:0618947256

Axiom
annotated source: glioblast (sensu Vertebrata)
annotated property: hasDbXref
annotated target: ZFA:0009169
mapping justification: UnspecifiedMatching

pigment cell (sensu Nematoda and Protostomia)
type: Class
subclass of: pigment cell
RO_0002161: NCBITaxon_33511

extraembryonic cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000478
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000478
IAO_0000115: Any cell that is part of some extraembryonic structure.
has db xref: ZFA:0009176
in subset: cellxgene subset
in subset: general cell types upper slim

Axiom
annotated source: extraembryonic cell
annotated property: IAO_0000115
annotated target: Any cell that is part of some extraembryonic structure.
has db xref: FBC:Autogenerated

Axiom
annotated source: extraembryonic cell
annotated property: hasDbXref
annotated target: ZFA:0009176
mapping justification: UnspecifiedMatching

amnioserosal cell
type: Class
equivalent class: Class
  intersection of: extraembryonic cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0010302
subclass of: extraembryonic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0010302
IAO_0000115: Any extraembryonic cell that is part of some amnioserosa.

Axiom
annotated source: amnioserosal cell
annotated property: IAO_0000115
annotated target: Any extraembryonic cell that is part of some amnioserosa.
has db xref: FBC:Autogenerated

trophoblast cell
type: Class
subclass of: BFO_0000002
subclass of: extraembryonic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_1000274
IAO_0000115: An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development.
description: Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:83028
has exact synonym: trophoblastic cell

Axiom
annotated source: trophoblast cell
annotated property: subClassOf
annotated target: extraembryonic cell
is inferred: true

Axiom
annotated source: trophoblast cell
annotated property: IAO_0000115
annotated target: An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development.
has db xref: GOC:tfm
has db xref: MESH:D014327
has db xref: PMID:37630754
has db xref: doi:10.1007/978-3-030-84725-8

Axiom
annotated source: trophoblast cell
annotated property: description
annotated target: Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.jri.2023.103811
has db xref: DOI:10.1530/JOE-17-0402
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK53245

Axiom
annotated source: trophoblast cell
annotated property: hasExactSynonym
annotated target: trophoblastic cell
has db xref: doi:10.1007/978-3-030-84725-8

trophoblast cell on CELLxGENE CellGuide
type: Axiom
annotated source: trophoblast cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000351

multi-potent skeletal muscle stem cell
type: Class
equivalent class: Class
  intersection of: multi fate stem cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001134
subclass of: multi fate stem cell
subclass of: cell of skeletal muscle
IAO_0000115: A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.
has db xref: FMA:86767
has db xref: ZFA:0009179
comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo.

Axiom
annotated source: multi-potent skeletal muscle stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: multi-potent skeletal muscle stem cell
annotated property: IAO_0000115
annotated target: A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.
has db xref: PMID:18282570

Axiom
annotated source: multi-potent skeletal muscle stem cell
annotated property: hasDbXref
annotated target: ZFA:0009179
mapping justification: UnspecifiedMatching

stratified epithelial stem cell
type: Class
subclass of: epithelial fate stem cell
has db xref: ZFA:0009180

Axiom
annotated source: stratified epithelial stem cell
annotated property: hasDbXref
annotated target: ZFA:0009180
mapping justification: UnspecifiedMatching

vascular associated smooth muscle cell
type: Class
equivalent class: Class
  intersection of: smooth muscle cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002049
subclass of: smooth muscle cell
subclass of: CL_4033054
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002049
IAO_0000115: A smooth muscle cell associated with the vasculature.
description: Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009181
has exact synonym: VSMC
has exact synonym: vascular smooth muscle cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: subClassOf
annotated target: smooth muscle cell
is inferred: true

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: IAO_0000115
annotated target: A smooth muscle cell associated with the vasculature.
has db xref: GOC:dsd
has db xref: GOC:tfm

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: description
annotated target: Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1093/cvr/cvs135
has db xref: DOI:10.1093/cvr/cvy023
has db xref: DOI:10.1161/ATVBAHA.118.311229
has db xref: DOI:10.3389/fimmu.2020.599415
has db xref: DOI:10.3390/ijms20225694

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: hasDbXref
annotated target: ZFA:0009181
mapping justification: UnspecifiedMatching

vascular associated smooth muscle cell on CELLxGENE CellGuide
type: Axiom
annotated source: vascular associated smooth muscle cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000359

epidermal cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0007376
subclass of: CL_0002159
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0007376
IAO_0000115: An epithelial cell of the integument (the outer layer of an organism).
description: Epidermal cells constitute the outermost layer of the skin in animals and have a multifaceted role in maintaining the body's overall homeostasis. They originate from the ectoderm and form the epidermis, a stratified squamous epithelium that mostly consists of keratinocytes in various stages of differentiation. The primary role of these cells is to act as a physical barrier, shielding the internal organs, tissues, and system from dehydration, infection, and other external influences such as UV radiation. The thickness and stratification of the epidermis vary with its location in the body, depending on the specific demand for protective function. One notable characteristic of epidermal cells is their continuous cycle of renewal. The cells are produced in the deepest layer of the epidermis, known as the basal or germinative layer, where they undergo cell division. As new cells form, they gradually push the older cells towards the skin surface. While ascending, these cells undergo a process known as keratinization, where they become filled with keratin, a protein that provides strength and rigidity. By the time they reach the surface, they are essentially dead and filled with keratin, forming a tough, resistant layer that is regularly shed and replaced by newer cells beneath. This entire process, from cell generation to shedding, usually takes around a month. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001470
has db xref: CALOHA:TS-0283
has db xref: FMA:62411
has db xref: MESH:D000078404
has db xref: ZFA:0009183
has exact synonym: cell of epidermis
has narrow synonym: epithelial cell of skin
in subset: cellxgene subset

Axiom
annotated source: epidermal cell
annotated property: IAO_0000115
annotated target: An epithelial cell of the integument (the outer layer of an organism).
has db xref: Flybase:dsj
has db xref: MA:ma

Axiom
annotated source: epidermal cell
annotated property: description
annotated target: Epidermal cells constitute the outermost layer of the skin in animals and have a multifaceted role in maintaining the body's overall homeostasis. They originate from the ectoderm and form the epidermis, a stratified squamous epithelium that mostly consists of keratinocytes in various stages of differentiation. The primary role of these cells is to act as a physical barrier, shielding the internal organs, tissues, and system from dehydration, infection, and other external influences such as UV radiation. The thickness and stratification of the epidermis vary with its location in the body, depending on the specific demand for protective function. One notable characteristic of epidermal cells is their continuous cycle of renewal. The cells are produced in the deepest layer of the epidermis, known as the basal or germinative layer, where they undergo cell division. As new cells form, they gradually push the older cells towards the skin surface. While ascending, these cells undergo a process known as keratinization, where they become filled with keratin, a protein that provides strength and rigidity. By the time they reach the surface, they are essentially dead and filled with keratin, forming a tough, resistant layer that is regularly shed and replaced by newer cells beneath. This entire process, from cell generation to shedding, usually takes around a month. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.tcb.2018.05.002
has db xref: DOI:10.1146/annurev.cellbio.22.010305.104357
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK513299/#:~:text=The%20stratum%20corneum%20is%20the%20outermost%20layer%20of%20the%20epidermis,potential%20and%20undergo%20programmed%20destruction.

Axiom
annotated source: epidermal cell
annotated property: hasDbXref
annotated target: ZFA:0009183
mapping justification: UnspecifiedMatching

Axiom
annotated source: epidermal cell
annotated property: hasExactSynonym
annotated target: cell of epidermis
has db xref: FMA:62411

Axiom
annotated source: epidermal cell
annotated property: hasNarrowSynonym
annotated target: epithelial cell of skin
has db xref: FMA:62411

epidermal cell on CELLxGENE CellGuide
type: Axiom
annotated source: epidermal cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000362

animal zygote
type: Class
equivalent class: Class
  intersection of: CL_0010017
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon_33208
subclass of: early embryonic cell (metazoa)
subclass of: eukaryotic cell
subclass of: CL_0010017
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_33208
IAO_0000115: Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
has broad synonym: zygote
has db xref: BTO:0000854
has db xref: EHDAA2:0004546
has db xref: FMA:72395

Axiom
annotated source: animal zygote
annotated property: IAO_0000115
annotated target: Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
has db xref: ISBN:0471245208

histoblast
type: Class
subclass of: eukaryotic cell
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_50557
IAO_0000115: A progenitor cell found in the larval epidermis of insects and that gives rise to the adult abdominal epidermis.
has db xref: FBbt:00001789

Axiom
annotated source: histoblast
annotated property: IAO_0000115
annotated target: A progenitor cell found in the larval epidermis of insects and that gives rise to the adult abdominal epidermis.
has db xref: doi:10.1016/j.cub.2022.01.045

Axiom
annotated source: histoblast
annotated property: hasDbXref
annotated target: FBbt:00001789
mapping justification: ManualMappingCuration

tracheoblast
type: Class
subclass of: branched duct epithelial cell

prohemocyte (sensu Nematoda and Protostomia)
type: Class
subclass of: CL_0008001
IAO_0000115: A precursor of mature hemocytes.
RO_0002161: NCBITaxon_33511
has db xref: FBbt:00005062

Axiom
annotated source: prohemocyte (sensu Nematoda and Protostomia)
annotated property: IAO_0000115
annotated target: A precursor of mature hemocytes.
has db xref: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: prohemocyte (sensu Nematoda and Protostomia)
annotated property: hasDbXref
annotated target: FBbt:00005062
mapping justification: ManualMappingCuration

hemocyte (sensu Arthropoda)
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: blood cell (sensu Nematoda and Protostomia)
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6656
subclass of: Restriction
  on property: RO_0002202
  some values from: prohemocyte (sensu Nematoda and Protostomia)
IAO_0000115: A blood cell of the circulatory system of arthropods.
has db xref: FBbt:00005063

Axiom
annotated source: hemocyte (sensu Arthropoda)
annotated property: IAO_0000115
annotated target: A blood cell of the circulatory system of arthropods.
has db xref: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: hemocyte (sensu Arthropoda)
annotated property: hasDbXref
annotated target: FBbt:00005063
mapping justification: ManualMappingCuration

tendon cell
type: Class
equivalent class: Class
  intersection of: fibroblast
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000043
subclass of: CL_1000307
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000043
IAO_0000115: An elongated fibroblast that is part of a tendon. Its cytoplasm is stretched between the collagen fibres of the tendon, and it possesses a central nucleus with a prominent nucleolus. Tendon cell has a well-developed rough endoplasmic reticulum, and it is responsible for the synthesis and turnover of tendon fibres and ground substance.
description: Tendon cells are specialized elongated fibroblasts that are predominantly found in tendons, the fibrous connective tissue that connects muscle to bone. These cells are biologically unique and essential for the formation and repair of tendons. Tendon cells possess elongated cell bodies and have a spindle or stellate-like shape with thin and long cytoplasmic extensions. They are predominantly positioned longitudinally along the collagen fibers. Their primary function is to produce and maintain the extracellular matrix of tendons, which comprises primarily of collagen, proteoglycans, and other non-collagenous proteins. Tendon cells are actively involved in tendon homeostasis and adaptation to mechanical loading. When tendons are regularly subjected to mechanical strain, these cells react by synthesizing more matrix proteins, thus strengthening the tendon structure. In response to tendon injury or degenerative changes, tendon cells can proliferate and increase their matrix synthesis to repair and regenerate the damaged tissue. However, excessive mechanical loading or aging can result in abnormal responses, leading to pathologic changes in tendon structure and function. In addition, tendon cells also have immunomodulatory functions. They can orchestrate local immune responses by producing a variety of cytokines and chemokines, and by interacting with immune cells that infiltrate the tendon tissue under pathologic conditions. Moreover, tendon cells are capable of expressing genes related to nociception and have a potential role in tendon pain mechanisms. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009189
has exact synonym: muscle attachment cell
has related synonym: tenocyte
in subset: cellxgene subset

Axiom
annotated source: tendon cell
annotated property: IAO_0000115
annotated target: An elongated fibroblast that is part of a tendon. Its cytoplasm is stretched between the collagen fibres of the tendon, and it possesses a central nucleus with a prominent nucleolus. Tendon cell has a well-developed rough endoplasmic reticulum, and it is responsible for the synthesis and turnover of tendon fibres and ground substance.
has db xref: GOC:NV
has db xref: GOC:tfm
has db xref: PMID:37894875
has db xref: PMID:957445

Axiom
annotated source: tendon cell
annotated property: description
annotated target: Tendon cells are specialized elongated fibroblasts that are predominantly found in tendons, the fibrous connective tissue that connects muscle to bone. These cells are biologically unique and essential for the formation and repair of tendons. Tendon cells possess elongated cell bodies and have a spindle or stellate-like shape with thin and long cytoplasmic extensions. They are predominantly positioned longitudinally along the collagen fibers. Their primary function is to produce and maintain the extracellular matrix of tendons, which comprises primarily of collagen, proteoglycans, and other non-collagenous proteins. Tendon cells are actively involved in tendon homeostasis and adaptation to mechanical loading. When tendons are regularly subjected to mechanical strain, these cells react by synthesizing more matrix proteins, thus strengthening the tendon structure. In response to tendon injury or degenerative changes, tendon cells can proliferate and increase their matrix synthesis to repair and regenerate the damaged tissue. However, excessive mechanical loading or aging can result in abnormal responses, leading to pathologic changes in tendon structure and function. In addition, tendon cells also have immunomodulatory functions. They can orchestrate local immune responses by producing a variety of cytokines and chemokines, and by interacting with immune cells that infiltrate the tendon tissue under pathologic conditions. Moreover, tendon cells are capable of expressing genes related to nociception and have a potential role in tendon pain mechanisms. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.jbiomech.2005.05.011
has db xref: DOI:10.1038/nrrheum.2015.26
has db xref: DOI:10.1152/physrev.00031.2003
has db xref: DOI:10.1515/sjpain-2022-0018/html
has db xref: DOI:10.3390/cells11030434

Axiom
annotated source: tendon cell
annotated property: hasDbXref
annotated target: ZFA:0009189
mapping justification: UnspecifiedMatching

tendon cell on CELLxGENE CellGuide
type: Axiom
annotated source: tendon cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000388

blood cell (sensu Nematoda and Protostomia)
type: Class
subclass of: blood cell
RO_0002161: NCBITaxon_33511

crystal cell
type: Class
subclass of: hemocyte (sensu Arthropoda)
subclass of: Restriction
  on property: RO_0002202
  some values from: procrystal cell
IAO_0000115: A hemocyte that synthesizes and secretes melanins as part of the antimicrobial immune response. It is characterized morphologically by crystal inclusions of phenoloxidases in its cytoplasm, hence its name.

Axiom
annotated source: crystal cell
annotated property: IAO_0000115
annotated target: A hemocyte that synthesizes and secretes melanins as part of the antimicrobial immune response. It is characterized morphologically by crystal inclusions of phenoloxidases in its cytoplasm, hence its name.
has db xref: doi:10.1016/B978-012369493-5.50008-0

electrically responsive cell
type: Class
subclass of: electrically active cell
IAO_0000115: A cell whose function is determined by its response to an electric signal.
has db xref: ZFA:0009190

Axiom
annotated source: electrically responsive cell
annotated property: IAO_0000115
annotated target: A cell whose function is determined by its response to an electric signal.
has db xref: FB:ma

Axiom
annotated source: electrically responsive cell
annotated property: hasDbXref
annotated target: ZFA:0009190
mapping justification: UnspecifiedMatching

plasmatocyte
type: Class
subclass of: hemocyte (sensu Arthropoda)
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035010
IAO_0000115: A phagocytic hemocyte, responsible for the engulfment of small particles, microbes, and apoptotic tissue debris. It may also secretes antimicrobial peptides and contribute to the production and secretion of proteins of the hemolymph.
has db xref: FBbt:00001685
has related synonym: macrophage
in subset: cellxgene subset

Axiom
annotated source: plasmatocyte
annotated property: IAO_0000115
annotated target: A phagocytic hemocyte, responsible for the engulfment of small particles, microbes, and apoptotic tissue debris. It may also secretes antimicrobial peptides and contribute to the production and secretion of proteins of the hemolymph.
has db xref: https://doi.org/10.1016/B978-012369493-5.50008-0

Axiom
annotated source: plasmatocyte
annotated property: hasDbXref
annotated target: FBbt:00001685
mapping justification: ManualMappingCuration

procrystal cell
type: Class
subclass of: prohemocyte (sensu Nematoda and Protostomia)
IAO_0000115: A precursor of mature crystal cells.
has db xref: FBbt:00001689

Axiom
annotated source: procrystal cell
annotated property: IAO_0000115
annotated target: A precursor of mature crystal cells.
has db xref: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: procrystal cell
annotated property: hasDbXref
annotated target: FBbt:00001689
mapping justification: ManualMappingCuration

lamellocyte
type: Class
subclass of: hemocyte (sensu Arthropoda)
IAO_0000115: A hemocyte found in immuno-stimulated larvae.
has db xref: FBbt:00001687

Axiom
annotated source: lamellocyte
annotated property: IAO_0000115
annotated target: A hemocyte found in immuno-stimulated larvae.
has db xref: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: lamellocyte
annotated property: hasDbXref
annotated target: FBbt:00001687
mapping justification: ManualMappingCuration

ganglion interneuron
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: RO_0002100
    some values from: UBERON_0000045
subclass of: interneuron
subclass of: Restriction
  on property: RO_0002100
  some values from: UBERON_0000045
IAO_0000115: Any interneuron that has its soma located in some ganglion.
description: Ganglion interneurons, sometimes classified under 'relay neurons,' are complex cellular structures prominently found in the nervous system across various organisms. These cells serve as intermediaries or connectors, conducting impulses between afferent (or sensory) neurons and efferent (or motor) neurons within the body. They have specialized roles in sensory-motor integration within the nervous system and play a pivotal part in defining the complexity and precision of the nervous system. These highly specialized neurons are predominantly located in the spinal cord and brain, particularly abundant in the gray matter of these regions, forming complex neural networks. The increased presence of glial cells around interneurons acts as an insulator enhancing the speed of impulse transmission. Ganglion interneurons receive informational input through dendrites from sensory neurons; this information is then converted into electrical impulses, which are processed and transmitted to other neurons or effectors, such as muscles or glands, through axons. Furthermore, these ganglion interneurons have significant roles in the formulation and execution of motor reflexes and serve as integral components of reflex arcs. They also participate in the modulation and filtration of relevant sensory information, ensuring that signals reaching the late-stage processing units (like the brain) are refined and critical to the organism's survival. Consequently, these neurons significantly influence the organism's behavior based on the incoming sensory information. Overall, they are responsible for creating connections amongst various neural circuits, making them pivotal in producing integrated responses and maintaining the proper functioning of the nervous system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes a…
in subset: cellxgene subset

Axiom
annotated source: ganglion interneuron
annotated property: subClassOf
annotated target: interneuron
is inferred: true

Axiom
annotated source: ganglion interneuron
annotated property: IAO_0000115
annotated target: Any interneuron that has its soma located in some ganglion.
has db xref: FBC:Autogenerated

Axiom
annotated source: ganglion interneuron
annotated property: description
annotated target: Ganglion interneurons, sometimes classified under 'relay neurons,' are complex cellular structures prominently found in the nervous system across various organisms. These cells serve as intermediaries or connectors, conducting impulses between afferent (or sensory) neurons and efferent (or motor) neurons within the body. They have specialized roles in sensory-motor integration within the nervous system and play a pivotal part in defining the complexity and precision of the nervous system. These highly specialized neurons are predominantly located in the spinal cord and brain, particularly abundant in the gray matter of these regions, forming complex neural networks. The increased presence of glial cells around interneurons acts as an insulator enhancing the speed of impulse transmission. Ganglion interneurons receive informational input through dendrites from sensory neurons; this information is then converted into electrical impulses, which are processed and transmitted to other neurons or effectors, such as muscles or glands, through axons. Furthermore, these ganglion interneurons have significant roles in the formulation and execution of motor reflexes and serve as integral components of reflex arcs. They also participate in the modulation and filtration of relevant sensory information, ensuring that signals reaching the late-stage processing units (like the brain) are refined and critical to the organism's survival. Consequently, these neurons significantly influence the organism's behavior based on the incoming sensory information. Overall, they are responsible for creating connections amongst various neural circuits, making them pivotal in producing integrated responses and maintaining the proper functioning of the nervous system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes a…
has db xref: DOI:10.1038/nn.2707
has db xref: DOI:10.1111/j.1748-1716.1962.tb02497.x
has db xref: DOI:10.1152/jn.1992.68.4.1384
has db xref: DOI:10.1371/journal.pcbi.1002626
has db xref: DOI:10.1523/JNEUROSCI.5570-03.2004

ganglion interneuron on CELLxGENE CellGuide
type: Axiom
annotated source: ganglion interneuron
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000397

electrically signaling cell
type: Class
subclass of: electrically active cell
IAO_0000115: A cell that initiates an electrical signal and passes that signal to another cell.
has db xref: ZFA:0009193

Axiom
annotated source: electrically signaling cell
annotated property: IAO_0000115
annotated target: A cell that initiates an electrical signal and passes that signal to another cell.
has db xref: FB:ma

Axiom
annotated source: electrically signaling cell
annotated property: hasDbXref
annotated target: ZFA:0009193
mapping justification: UnspecifiedMatching

male gamete
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001375
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0009566
subclass of: male germ cell
subclass of: gamete
IAO_0000115: Any male germ cell that has characteristic some haploid and is capable of some fertilization.
description: The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001277
has db xref: CALOHA:TS-0949

Axiom
annotated source: male gamete
annotated property: subClassOf
annotated target: male germ cell
is inferred: true

Axiom
annotated source: male gamete
annotated property: subClassOf
annotated target: gamete
is inferred: true

Axiom
annotated source: male gamete
annotated property: IAO_0000115
annotated target: Any male germ cell that has characteristic some haploid and is capable of some fertilization.
has db xref: FBC:Autogenerated

Axiom
annotated source: male gamete
annotated property: description
annotated target: The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.semcdb.2016.04.009
has db xref: DOI:10.1242/dev.202046
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK26843/
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK553142/

male gamete on CELLxGENE CellGuide
type: Axiom
annotated source: male gamete
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000408

polyploid cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001377
subclass of: cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001377
IAO_0000115: A cell that contains more than two haploid sets of chromosomes.
description: A polyploid cell is a unique type of cell characterized by the possession of more than two sets of chromosomes. This is much higher than the typical diploid nature of other somatic cells. This cellular phenomenon known as polyploidy results from errors during cell division leading to the generation of non-standard polyploid cells, a property that is common to both plant and animal cells. These cells occur naturally and can also be formed through genetic manipulation. Polyploid cells play a critical role in the overall growth and development of organisms. In plant cells, polyploidy often contributes to speciation and diversity. A notable characteristic of many plant species is their ability to tolerate polyploidy, a trait that often leads to increased cell size, altered gene expression, and may enhance the physiological and adaptive traits of a plant. In animals, polyploidy is less common but still plays a significant role in liver function and injury repair. Polyploidization in hepatocytes aids in maintaining genetic stability and also allows for cellular adaptation to liver injury. Polyploid cells also play a potential role in cancer development. Some cancer cells are polyploid or aneuploid (having an abnormal number of chromosomes) indicating a relationship between chromosome status and cancer progression. Polyploidy in cancer cells may contribute to increased mutation rates, adaptation to adverse environments, and resistance to chemotherapy. Overall, polyploid cells may lead to pathological conditions like cancer, however, many are part of normal healthy biological systems, playing an integral role in the diversity and evolution of life. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)

Axiom
annotated source: polyploid cell
annotated property: IAO_0000115
annotated target: A cell that contains more than two haploid sets of chromosomes.
has db xref: FB:ma
has db xref: PMID:32646579
has db xref: https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy

Axiom
annotated source: polyploid cell
annotated property: description
annotated target: A polyploid cell is a unique type of cell characterized by the possession of more than two sets of chromosomes. This is much higher than the typical diploid nature of other somatic cells. This cellular phenomenon known as polyploidy results from errors during cell division leading to the generation of non-standard polyploid cells, a property that is common to both plant and animal cells. These cells occur naturally and can also be formed through genetic manipulation. Polyploid cells play a critical role in the overall growth and development of organisms. In plant cells, polyploidy often contributes to speciation and diversity. A notable characteristic of many plant species is their ability to tolerate polyploidy, a trait that often leads to increased cell size, altered gene expression, and may enhance the physiological and adaptive traits of a plant. In animals, polyploidy is less common but still plays a significant role in liver function and injury repair. Polyploidization in hepatocytes aids in maintaining genetic stability and also allows for cellular adaptation to liver injury. Polyploid cells also play a potential role in cancer development. Some cancer cells are polyploid or aneuploid (having an abnormal number of chromosomes) indicating a relationship between chromosome status and cancer progression. Polyploidy in cancer cells may contribute to increased mutation rates, adaptation to adverse environments, and resistance to chemotherapy. Overall, polyploid cells may lead to pathological conditions like cancer, however, many are part of normal healthy biological systems, playing an integral role in the diversity and evolution of life. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.tcb.2013.06.002
has db xref: DOI:10.1016/j.tig.2015.03.011
has db xref: DOI:10.1038/cddis.2017.167
has db xref: DOI:10.1038/nrm1276
has db xref: DOI:10.1146/annurev-cellbio-092910-154234

polyploid cell on CELLxGENE CellGuide
type: Axiom
annotated source: polyploid cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000412

haploid cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001375
subclass of: cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001375
IAO_0000115: A cell whose nucleus contains a single haploid genome.
description: A haploid cell is a unique class of cell characterized by having a single set of chromosomes. The formation of haploid cells occurs through meiosis, a process where a diploid cell, containing two sets of chromosomes, undergoes division, resulting in four haploid cells. Haploid cells play an important role in the sexual reproduction of various organisms. Serving as gametes, they transmit genetic information to successive generations, contributing to genetic diversity. Their single set of chromosomes results in unique trait combinations in offspring, enhancing adaptability to changing environments. Furthermore, haploid cells facilitate the study of recessive traits in genetic research, as each gene is present in a single copy, without the influence of a dominant gene. It's important to note that certain organisms, such as some fungi and algae, follow a haploid dominant life cycle, spending the majority of their life cycle in the haploid phase. This phase accelerates the generation of genetic diversity among offspring, proving advantageous in rapidly changing environments. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)

Axiom
annotated source: haploid cell
annotated property: IAO_0000115
annotated target: A cell whose nucleus contains a single haploid genome.
has db xref: FB:ma
has db xref: GOC:tfm

Axiom
annotated source: haploid cell
annotated property: description
annotated target: A haploid cell is a unique class of cell characterized by having a single set of chromosomes. The formation of haploid cells occurs through meiosis, a process where a diploid cell, containing two sets of chromosomes, undergoes division, resulting in four haploid cells. Haploid cells play an important role in the sexual reproduction of various organisms. Serving as gametes, they transmit genetic information to successive generations, contributing to genetic diversity. Their single set of chromosomes results in unique trait combinations in offspring, enhancing adaptability to changing environments. Furthermore, haploid cells facilitate the study of recessive traits in genetic research, as each gene is present in a single copy, without the influence of a dominant gene. It's important to note that certain organisms, such as some fungi and algae, follow a haploid dominant life cycle, spending the majority of their life cycle in the haploid phase. This phase accelerates the generation of genetic diversity among offspring, proving advantageous in rapidly changing environments. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1186/s13287-017-0657-4
has db xref: https://bccampusbiology.pressbooks.tru.ca/chapter/sexual-reproduction/
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK26840/

haploid cell on CELLxGENE CellGuide
type: Axiom
annotated source: haploid cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000413

endopolyploid cell
type: Class
subclass of: polyploid cell
description: Endopolyploid cells are a specialized cell type characterized by having multiple complete sets of chromosomes, far exceeding the amount found in typical diploid cells. The process known as endoreplication results in variant cycles of DNA replication without subsequent cell divisions, leading to an increase in cell volume, an alteration in gene expression, and polyploidy. These cells are commonly found throughout the plant and animal kingdoms, indicating their foundational role in organismal biology. Endopolyploid cells serve critical roles in maintaining an organism's biological system by regulating tissue growth and development, cellular differentiation, and physiological response to environmental stimuli. For instance, in plants, endopolyploidy serves as a mechanism for increased cell size leading to larger fruits and broader leaves. In animals, these cells are fundamental in liver regeneration. Therefore, their prominence in adaptive and developmental processes across diverse organisms reflects their evolutionary importance. Endopolyploid cells also play a role in pathological conditions, primarily cancer development, where endoreplication can lead to genomic instability resulting in malignant progression. However, these cells also possess inherent potential for therapeutic applications. For example, stimulating endoreplication in cancer cells can trigger senescence and reduction in tumor growth. Furthermore, endopolyploid cells can be harnessed for regenerative medicine purposes, as they have demonstrated potential for differentiation and tissue repair. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)

Axiom
annotated source: endopolyploid cell
annotated property: description
annotated target: Endopolyploid cells are a specialized cell type characterized by having multiple complete sets of chromosomes, far exceeding the amount found in typical diploid cells. The process known as endoreplication results in variant cycles of DNA replication without subsequent cell divisions, leading to an increase in cell volume, an alteration in gene expression, and polyploidy. These cells are commonly found throughout the plant and animal kingdoms, indicating their foundational role in organismal biology. Endopolyploid cells serve critical roles in maintaining an organism's biological system by regulating tissue growth and development, cellular differentiation, and physiological response to environmental stimuli. For instance, in plants, endopolyploidy serves as a mechanism for increased cell size leading to larger fruits and broader leaves. In animals, these cells are fundamental in liver regeneration. Therefore, their prominence in adaptive and developmental processes across diverse organisms reflects their evolutionary importance. Endopolyploid cells also play a role in pathological conditions, primarily cancer development, where endoreplication can lead to genomic instability resulting in malignant progression. However, these cells also possess inherent potential for therapeutic applications. For example, stimulating endoreplication in cancer cells can trigger senescence and reduction in tumor growth. Furthermore, endopolyploid cells can be harnessed for regenerative medicine purposes, as they have demonstrated potential for differentiation and tissue repair. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.cellbi.2005.10.013
has db xref: DOI:10.1016/j.tcb.2018.02.006
has db xref: DOI:10.1038/s41418-017-0040-0
has db xref: DOI:10.1101/gad.1829209
has db xref: DOI:10.1242/dev.080531

endopolyploid cell on CELLxGENE CellGuide
type: Axiom
annotated source: endopolyploid cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000417

mitogenic signaling cell
type: Class
subclass of: cell
IAO_0000115: A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment.

Axiom
annotated source: mitogenic signaling cell
annotated property: IAO_0000115
annotated target: A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment.
has db xref: FB:ma

tip cell
type: Class
subclass of: mitogenic signaling cell
in subset: cellxgene subset

excretory cell
type: Class
subclass of: cell
IAO_0000115: A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
has db xref: WBbt:0005812

Axiom
annotated source: excretory cell
annotated property: IAO_0000115
annotated target: A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
has db xref: GOC:tfm
has db xref: PMID:19783135

xanthophore cell
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0005002
IAO_0000115: A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red.
has db xref: ZFA:0009198
has related synonym: xanthophore

Axiom
annotated source: xanthophore cell
annotated property: IAO_0000115
annotated target: A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red.
has db xref: SANBI:mhl

Axiom
annotated source: xanthophore cell
annotated property: hasDbXref
annotated target: ZFA:0009198
mapping justification: UnspecifiedMatching

iridophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0005001
IAO_0000115: A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color.
has db xref: ZFA:0009199
has related synonym: guanophore

Axiom
annotated source: iridophore
annotated property: IAO_0000115
annotated target: A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color.
has db xref: SANBI:mhl

Axiom
annotated source: iridophore
annotated property: hasDbXref
annotated target: ZFA:0009199
mapping justification: UnspecifiedMatching

luteinizing hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032275
subclass of: secretory cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032275
IAO_0000115: A peptide hormone secreting cell pituitary that produces luteinizing hormone.
has db xref: ZFA:0009203

Axiom
annotated source: luteinizing hormone secreting cell
annotated property: IAO_0000115
annotated target: A peptide hormone secreting cell pituitary that produces luteinizing hormone.
has db xref: GOC:tfm

Axiom
annotated source: luteinizing hormone secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009203
mapping justification: UnspecifiedMatching

prolactin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0070459
subclass of: protein secreting cell
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0070459
IAO_0000115: A peptide hormone cell that secretes prolactin.
has db xref: ZFA:0009204

Axiom
annotated source: prolactin secreting cell
annotated property: IAO_0000115
annotated target: A peptide hormone cell that secretes prolactin.
has db xref: GOC:tfm
has db xref: SANBI:mhl

Axiom
annotated source: prolactin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009204
mapping justification: UnspecifiedMatching

melanocyte stimulating hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0036160
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0036160
IAO_0000115: A cell of the intermediate pituitary that produces melanocyte stimulating hormone.
has db xref: BTO:0002277
has db xref: ZFA:0009205
has exact synonym: melanotrope
has exact synonym: melanotroph

Axiom
annotated source: melanocyte stimulating hormone secreting cell
annotated property: IAO_0000115
annotated target: A cell of the intermediate pituitary that produces melanocyte stimulating hormone.
has db xref: SANBI:mhl

Axiom
annotated source: melanocyte stimulating hormone secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009205
mapping justification: UnspecifiedMatching

follicle stem cell (sensu Arthropoda)
type: Class
subclass of: epithelial fate stem cell
subclass of: Restriction
IAO_0000115: A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods.
has broad synonym: somatic stem cell
has db xref: FBbt:00004903

Axiom
annotated source: follicle stem cell (sensu Arthropoda)
annotated property: IAO_0000115
annotated target: A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods.
has db xref: doi:10.1016/B978-012369493-5.50005-5
has db xref: doi:10.1038/s41467-020-19361-0
has db xref: doi:10.1242/dev.121.11.3797

Axiom
annotated source: follicle stem cell (sensu Arthropoda)
annotated property: hasBroadSynonym
annotated target: somatic stem cell
has db xref: doi:10.1016/j.devcel.2005.08.012

Axiom
annotated source: follicle stem cell (sensu Arthropoda)
annotated property: hasDbXref
annotated target: FBbt:00004903
mapping justification: ManualMappingCuration

follicular dendritic cell
type: Class
subclass of: dendritic cell
IAO_0000115: A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response.
description: Follicular dendritic cells (FDCs) are specialized cells found in B cell follicles in secondary lymphoid organs such as lymph nodes and spleen. FDCs play a key role in the immune response by presenting antigens to B-cells, which are responsible for producing antibodies. They accomplish this by acquiring antigens via multiple pathways and retaining them in non-degradative endosomal vesicles which cycle to the cell surface, allowing B-cells to encounter and recognize native antigens. In addition, FDCs secrete various cytokines and chemokines that direct immune cells to sites of infection or inflammation. FDCs are unique among immune cells in that they do not originate from hematopoietic stem cells, but rather from stromal cells in the lymphoid tissues. They are characterized by their distinctive shape, with long, branching processes that form a network within the follicle. FDCs are also distinguished by the presence of complement receptors, Fc receptors, and other molecules that enable them to capture and present antigens to B-cells. Because of their important role in antigen presentation and immune regulation, FDCs have been studied extensively in the context of infectious diseases, autoimmunity, and cancer. Notably, FDCs appear to function as a reservoir for HIV, contribute to autoimmune pathology by presenting autoantigens, and drive FDC sarcoma. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0004267
has db xref: FMA:83037
has db xref: MESH:D020566
in subset: cellxgene subset
in subset: human reference atlas
comment: Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451.

Axiom
annotated source: follicular dendritic cell
annotated property: IAO_0000115
annotated target: A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response.
has db xref: ISBN:127520252

Axiom
annotated source: follicular dendritic cell
annotated property: description
annotated target: Follicular dendritic cells (FDCs) are specialized cells found in B cell follicles in secondary lymphoid organs such as lymph nodes and spleen. FDCs play a key role in the immune response by presenting antigens to B-cells, which are responsible for producing antibodies. They accomplish this by acquiring antigens via multiple pathways and retaining them in non-degradative endosomal vesicles which cycle to the cell surface, allowing B-cells to encounter and recognize native antigens. In addition, FDCs secrete various cytokines and chemokines that direct immune cells to sites of infection or inflammation. FDCs are unique among immune cells in that they do not originate from hematopoietic stem cells, but rather from stromal cells in the lymphoid tissues. They are characterized by their distinctive shape, with long, branching processes that form a network within the follicle. FDCs are also distinguished by the presence of complement receptors, Fc receptors, and other molecules that enable them to capture and present antigens to B-cells. Because of their important role in antigen presentation and immune regulation, FDCs have been studied extensively in the context of infectious diseases, autoimmunity, and cancer. Notably, FDCs appear to function as a reservoir for HIV, contribute to autoimmune pathology by presenting autoantigens, and drive FDC sarcoma. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/jcp.30662
has db xref: DOI:10.1038/nri3689
has db xref: DOI:10.3389/fimmu.2016.00225

follicular dendritic cell on CELLxGENE CellGuide
type: Axiom
annotated source: follicular dendritic cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000442

Axiom
annotated source: follicular dendritic cell
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM355.ZFMS.256

Axiom
annotated source: follicular dendritic cell
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM559.FNBB.6273

calcitonin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0036161
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0036161
IAO_0000115: Any secretory cell that is capable of some calcitonin secretion.
has db xref: ZFA:0009206

Axiom
annotated source: calcitonin secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some calcitonin secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: calcitonin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009206
mapping justification: UnspecifiedMatching

carbohydrate secreting cell
type: Class
subclass of: secretory cell

white adipocyte
type: Class
subclass of: adipocyte
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001347
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002334
IAO_0000115: An adipocyte with light coloration and few mitochondria. It contains a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole.
description: White fat cells, also known as white adipocytes, are cells found primarily in the white adipose tissue, a specialized type of connective tissue that functions as the major storage site for energy in the form of lipids. This type of adipose cell is characterized by its large droplets of liquid fat, called triglycerides, which almost completely fill the cell pushing the nucleus and other organelles to the periphery. They appear white or yellowish in color due to their high cytoplasm lipid content. White fat cells are involved in lipogenesis, the metabolic process where excess glucose and other energy-rich compounds are converted into neutral fats for storage. Conversely, these cells also play a pivotal role in lipolysis, the breakdown of triglycerides to release glycerol and fatty acids, when required by the body. Moreover, these cells act as thermal insulators, helping to maintain the body's temperature. Importantly, white fat cells are crucial for the proper functioning of numerous physiological processes including appetite regulation, inflammatory response, and immunity. They are also known to secrete various hormones and cytokines, such as leptin and adiponectin, which are instrumental in regulating metabolic activities and maintaining overall metabolic homeostasis. Dysregulation of these cells, along with an accumulation of excess white fat, has been linked to several health issues including obesity, metabolic syndrome, and type 2 diabetes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: CALOHA:TS-1119
has db xref: FMA:83434
has exact synonym: white adipose cell
has related synonym: white fat cell

Axiom
annotated source: white adipocyte
annotated property: IAO_0000115
annotated target: An adipocyte with light coloration and few mitochondria. It contains a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole.
has db xref: GOC:tfm
has db xref: MESH:D052438

Axiom
annotated source: white adipocyte
annotated property: description
annotated target: White fat cells, also known as white adipocytes, are cells found primarily in the white adipose tissue, a specialized type of connective tissue that functions as the major storage site for energy in the form of lipids. This type of adipose cell is characterized by its large droplets of liquid fat, called triglycerides, which almost completely fill the cell pushing the nucleus and other organelles to the periphery. They appear white or yellowish in color due to their high cytoplasm lipid content. White fat cells are involved in lipogenesis, the metabolic process where excess glucose and other energy-rich compounds are converted into neutral fats for storage. Conversely, these cells also play a pivotal role in lipolysis, the breakdown of triglycerides to release glycerol and fatty acids, when required by the body. Moreover, these cells act as thermal insulators, helping to maintain the body's temperature. Importantly, white fat cells are crucial for the proper functioning of numerous physiological processes including appetite regulation, inflammatory response, and immunity. They are also known to secrete various hormones and cytokines, such as leptin and adiponectin, which are instrumental in regulating metabolic activities and maintaining overall metabolic homeostasis. Dysregulation of these cells, along with an accumulation of excess white fat, has been linked to several health issues including obesity, metabolic syndrome, and type 2 diabetes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.arcmed.2008.09.005
has db xref: DOI:10.1038/s41574-019-0230-6
has db xref: DOI:10.1038/s41574-021-00471-8
has db xref: DOI:10.1038/s42255-021-00493-6
has db xref: DOI:10.1146/annurev.nutr.27.061406.093734

white adipocyte on CELLxGENE CellGuide
type: Axiom
annotated source: white adipocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000448

brown adipocyte
type: Class
subclass of: adipocyte
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001348
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002335
IAO_0000115: A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation.
description: Brown fat cells, also known as brown adipocytes, form a type of adipose tissue that regulates energy by thermogenesis (heat production). These cells are rich in mitochondria, which lends them their characteristic brown colouring. Mitochondria are crucial to the brown fat cell's function since they contain an integral protein called uncoupling protein 1 (UCP1). This protein permits protons to leak across the mitochondrial inner membrane, disrupting the usual pathway of ATP production. Instead of generating ATP, the energy derived from glucose and fatty acids is dissipated as heat. This unique function makes brown fat cells an important biological tool for regulating body temperature, especially in infants and hibernating animals. While historically believed to be primarily relevant in newborns, recent findings highlight a role of brown fat cells in adults as well. They provide significant health benefits by metabolising excess glucose in the body and burning unwanted fat, and thereby raising the possibilities of using brown fat cells therapeutically for conditions like obesity or diabetes. Furthermore, stimulation of brown fat activity in adults is linked with improved overall metabolic health and lower risk of metabolic syndrome. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: CALOHA:TS-0099
has db xref: FMA:83435
has exact synonym: brown adipose cell
has exact synonym: brown fat cell
in subset: cellxgene subset

Axiom
annotated source: brown adipocyte
annotated property: IAO_0000115
annotated target: A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation.
has db xref: MESH:D002001

Axiom
annotated source: brown adipocyte
annotated property: description
annotated target: Brown fat cells, also known as brown adipocytes, form a type of adipose tissue that regulates energy by thermogenesis (heat production). These cells are rich in mitochondria, which lends them their characteristic brown colouring. Mitochondria are crucial to the brown fat cell's function since they contain an integral protein called uncoupling protein 1 (UCP1). This protein permits protons to leak across the mitochondrial inner membrane, disrupting the usual pathway of ATP production. Instead of generating ATP, the energy derived from glucose and fatty acids is dissipated as heat. This unique function makes brown fat cells an important biological tool for regulating body temperature, especially in infants and hibernating animals. While historically believed to be primarily relevant in newborns, recent findings highlight a role of brown fat cells in adults as well. They provide significant health benefits by metabolising excess glucose in the body and burning unwanted fat, and thereby raising the possibilities of using brown fat cells therapeutically for conditions like obesity or diabetes. Furthermore, stimulation of brown fat activity in adults is linked with improved overall metabolic health and lower risk of metabolic syndrome. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/164_2018_118
has db xref: DOI:10.1042/BJ20130457
has db xref: DOI:10.1074/jbc.M000547200
has db xref: DOI:10.1097/MED.0b013e328337a81f
has db xref: DOI:10.4161/adip.18951

brown adipocyte on CELLxGENE CellGuide
type: Axiom
annotated source: brown adipocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000449

dendritic cell
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042613
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001003
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001816
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002504
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0019882
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045580
subclass of: mononuclear phagocyte
subclass of: professional antigen presenting cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042613
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001003
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001816
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045580
disjoint with: lymphocyte
IAO_0000115: A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
description: Dendritic cells, named for their tree-like extensions called dendrites, are a type of immune cell that form a critical bridge between the innate and adaptive immune systems. They are derived from hematopoietic bone marrow progenitor cells and can be found throughout the body poised as sentinels in locations such as the skin, lungs, or liver, as well as immune organs such as the thymus, lymph nodes, or spleen. They can also be found in an immature state in the blood. Dendritic cells serve as antigen-presenting cells, with a primary function of processing and presenting antigens to T-cells to facilitate an immune response. Upon encountering an antigen, dendritic cells engulf the pathogen via phagocytosis and subsequently process the pathogen into antigens. These antigens are then presented on the surface of the dendritic cell in the context of major histocompatibility complex (MHC) molecules. The dendritic cell migrates to the lymph nodes, containing naive T-cells, and presents the antigens to them. This process triggers the activation of cognate T-cells into effector T-cells, which can then recognize and eradicate cells bearing the same antigen. Additionally, the dendritic cells can influence the type of immune response the body will mount. They communicate with T-cells through the use of co-stimulatory molecules and cytokines. Depending on the type of co-stimulatory molecules used and the set of cytokines released, dendritic cells can promote the development of a cellular immune response, dominated by cytotoxic T cells effective against intracellular pathogens such as viruses, a humoral response, mediated by B cells and effective against extracellular bacteria and toxins, or a tolerogenic response. Thus, dendritic cells play a pivotal role in immunity, helping the body to effectively combat infections, prevent autoimmune diseases, and maintain tolerance to healthy self-tissues. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, w…
has db xref: BTO:0002042
has db xref: CALOHA:TS-0194
has db xref: FMA:83036
has db xref: MESH:D003713
has db xref: ZFA:0009209
has related synonym: interdigitating cell
has related synonym: veiled cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: dendritic cell
annotated property: IAO_0000115
annotated target: A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
has db xref: GOC:add
has db xref: ISBN:0781735149

Axiom
annotated source: dendritic cell
annotated property: description
annotated target: Dendritic cells, named for their tree-like extensions called dendrites, are a type of immune cell that form a critical bridge between the innate and adaptive immune systems. They are derived from hematopoietic bone marrow progenitor cells and can be found throughout the body poised as sentinels in locations such as the skin, lungs, or liver, as well as immune organs such as the thymus, lymph nodes, or spleen. They can also be found in an immature state in the blood. Dendritic cells serve as antigen-presenting cells, with a primary function of processing and presenting antigens to T-cells to facilitate an immune response. Upon encountering an antigen, dendritic cells engulf the pathogen via phagocytosis and subsequently process the pathogen into antigens. These antigens are then presented on the surface of the dendritic cell in the context of major histocompatibility complex (MHC) molecules. The dendritic cell migrates to the lymph nodes, containing naive T-cells, and presents the antigens to them. This process triggers the activation of cognate T-cells into effector T-cells, which can then recognize and eradicate cells bearing the same antigen. Additionally, the dendritic cells can influence the type of immune response the body will mount. They communicate with T-cells through the use of co-stimulatory molecules and cytokines. Depending on the type of co-stimulatory molecules used and the set of cytokines released, dendritic cells can promote the development of a cellular immune response, dominated by cytotoxic T cells effective against intracellular pathogens such as viruses, a humoral response, mediated by B cells and effective against extracellular bacteria and toxins, or a tolerogenic response. Thus, dendritic cells play a pivotal role in immunity, helping the body to effectively combat infections, prevent autoimmune diseases, and maintain tolerance to healthy self-tissues. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, w…
has db xref: DOI:10.1016/bs.ircmb.2019.07.004
has db xref: DOI:10.1038/nri.2016.116
has db xref: DOI:10.1111/imm.12888
has db xref: DOI:10.1146/annurev-immunol-061020-053707
has db xref: DOI:10.1146/annurev-immunol-100311-102839

Axiom
annotated source: dendritic cell
annotated property: hasDbXref
annotated target: ZFA:0009209
mapping justification: UnspecifiedMatching

dendritic cell on CELLxGENE CellGuide
type: Axiom
annotated source: dendritic cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000451

Langerhans cell
type: Class
equivalent class: Class
  intersection of: conventional dendritic cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001293
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002828
subclass of: myeloid leukocyte
subclass of: conventional dendritic cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001293
subclass of: Restriction
  on property: RO_0002202
  some values from: myeloid cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002828
IAO_0000115: Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus.
has db xref: BTO:0000705
has db xref: CALOHA:TS-2375
has db xref: FMA:63072
has db xref: MESH:D007801
has exact synonym: LC
in subset: cellxgene subset
in subset: human reference atlas
comment: Originally described in the dendritic cell ontology (DC_CL:0000021 )(PMID:19243617). These cells are also CD1a-high, CD14-negative, CD207-positive (langerin), CD324-positive (E-cadherin), and DCIR-positive. They reside in the epidermis.

Axiom
annotated source: Langerhans cell
annotated property: subClassOf
annotated target: conventional dendritic cell
is inferred: true

Axiom
annotated source: Langerhans cell
annotated property: IAO_0000115
annotated target: Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GO_REF:0000031
has db xref: ISBN:0721601464
has db xref: ISBN:0781735149
has db xref: PMCID:PMC2346585
has db xref: PMID:17850486

epinephrine secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048242
subclass of: biogenic amine secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048242
IAO_0000115: A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types.
has db xref: ZFA:0009211
has exact synonym: adrenaline secreting cell
has exact synonym: epinephrin secreting cell

Axiom
annotated source: epinephrine secreting cell
annotated property: IAO_0000115
annotated target: A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types.
has db xref: GOC:tfm
has db xref: PMID:12438093

Axiom
annotated source: epinephrine secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009211
mapping justification: UnspecifiedMatching

Axiom
annotated source: epinephrine secreting cell
annotated property: hasExactSynonym
annotated target: adrenaline secreting cell
has db xref: GO:0048242

mineralocorticoid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0035931
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035931
IAO_0000115: Any secretory cell that is capable of some mineralocorticoid secretion.

Axiom
annotated source: mineralocorticoid secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some mineralocorticoid secretion.
has db xref: FBC:Autogenerated

biogenic amine secreting cell
type: Class
subclass of: secretory cell
has db xref: ZFA:0009212

Axiom
annotated source: biogenic amine secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009212
mapping justification: UnspecifiedMatching

serotonin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001820
subclass of: biogenic amine secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001820
IAO_0000115: A cell type that secretes 5-Hydroxytryptamine (serotonin).
has db xref: ZFA:0009213
has exact synonym: 5-HT secreting cell
has exact synonym: 5-Hydroxytryptamine secreting cell

Axiom
annotated source: serotonin secreting cell
annotated property: IAO_0000115
annotated target: A cell type that secretes 5-Hydroxytryptamine (serotonin).
has db xref: GOC:tfm
has db xref: PMID:19630576

Axiom
annotated source: serotonin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009213
mapping justification: UnspecifiedMatching

noradrenergic cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048243
subclass of: biogenic amine secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048243
IAO_0000115: A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.
has db xref: ZFA:0009214
has exact synonym: noradrenaline secreting cell
has exact synonym: norepinephrin secreting cell
has exact synonym: norepinephrine secreting cell
in subset: cellxgene subset

Axiom
annotated source: noradrenergic cell
annotated property: IAO_0000115
annotated target: A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.
has db xref: GOC:tfm
has db xref: ISBN:068340007X

Axiom
annotated source: noradrenergic cell
annotated property: hasDbXref
annotated target: ZFA:0009214
mapping justification: UnspecifiedMatching

glucocorticoid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0035933
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035933
IAO_0000115: Any secretory cell that is capable of some glucocorticoid secretion.
has db xref: ZFA:0009215

Axiom
annotated source: glucocorticoid secreting cell
annotated property: IAO_0000115
annotated target: Any secretory cell that is capable of some glucocorticoid secretion.
has db xref: FBC:Autogenerated

Axiom
annotated source: glucocorticoid secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009215
mapping justification: UnspecifiedMatching

adrenocorticotropic hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0051458
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0051458
IAO_0000115: A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin.
has db xref: ZFA:0009216
has exact synonym: ACTH secreting cell
has exact synonym: adrenocorticotrophic hormone secreting cell
has exact synonym: corticotrophin hormone secreting cell
has exact synonym: corticotropin hormone secreting cell
has exact synonym: corticotropin secreting cell

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: IAO_0000115
annotated target: A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin.
has db xref: GOC:tfm
has db xref: SANBI:mhl

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009216
mapping justification: UnspecifiedMatching

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: hasExactSynonym
annotated target: ACTH secreting cell
has db xref: GO:0051458

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: hasExactSynonym
annotated target: corticotropin secreting cell
has db xref: GO:0051458

ganglion mother cell
type: Class
subclass of: CL_0011020
subclass of: Restriction
  on property: RO_0002202
  some values from: neuroblast (sensu Nematoda and Protostomia)
IAO_0000115: A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells.
has db xref: FBbt:00005149

Axiom
annotated source: ganglion mother cell
annotated property: hasDbXref
annotated target: FBbt:00005149
mapping justification: ManualMappingCuration

pericardial nephrocyte
type: Class
subclass of: phagocyte (sensu Nematoda and Protostomia)
subclass of: CL_0002520
IAO_0000115: An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel.
has db xref: FBbt:00005058
has narrow synonym: pericardial cell

Axiom
annotated source: pericardial nephrocyte
annotated property: IAO_0000115
annotated target: An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel.
has db xref: FBbt:00003184
has db xref: GO:0061320
has db xref: GOC:tfm
has db xref: PMID:19783135

Axiom
annotated source: pericardial nephrocyte
annotated property: hasDbXref
annotated target: FBbt:00005058
mapping justification: ManualMappingCuration

Axiom
annotated source: pericardial nephrocyte
annotated property: hasNarrowSynonym
annotated target: pericardial cell
has db xref: FBbt:00005058
has db xref: GO:0061320

thyrotroph
type: Class
subclass of: basophil cell of pars distalis of adenohypophysis
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0070460
IAO_0000115: A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center.
has db xref: FMA:83099
has db xref: MESH:D052684
has db xref: ZFA:0009218
has exact synonym: beta-basophil
has exact synonym: thyroid stimulating hormone secreting cell
has exact synonym: thyrotrope

Axiom
annotated source: thyrotroph
annotated property: IAO_0000115
annotated target: A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center.
has db xref: ISBN:0517223651
has db xref: SANBI:mhl

Axiom
annotated source: thyrotroph
annotated property: hasDbXref
annotated target: ZFA:0009218
mapping justification: UnspecifiedMatching

follicle cell of egg chamber
type: Class
subclass of: BFO_0000002
subclass of: follicular epithelial cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000992
subclass of: Restriction
  on property: RO_0002202
  some values from: follicle stem cell (sensu Arthropoda)
IAO_0000115: A somatic epithelial cell of the insect egg chamber.
has broad synonym: follicle cell
has broad synonym: ovarian follicle cell
has db xref: FBbt:00004904

Axiom
annotated source: follicle cell of egg chamber
annotated property: hasDbXref
annotated target: FBbt:00004904
mapping justification: ManualMappingCuration

juvenile hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045443
subclass of: secretory cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045443
IAO_0000115: An endocrine cell that secretes juvenile hormone.
has db xref: FBbt:00058020

Axiom
annotated source: juvenile hormone secreting cell
annotated property: IAO_0000115
annotated target: An endocrine cell that secretes juvenile hormone.
has db xref: GO:tfm

Axiom
annotated source: juvenile hormone secreting cell
annotated property: hasDbXref
annotated target: FBbt:00058020
mapping justification: ManualMappingCuration

connective tissue type mast cell
type: Class
equivalent class: Class
  intersection of: mast cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002384
subclass of: mast cell
subclass of: CL_0002320
IAO_0000115: Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent.
has exact synonym: MC(TC)
has exact synonym: MCTC
has exact synonym: TC mast cells
in subset: human reference atlas
comment: They are CD88-positive. The cytoplasmic granules contain high levels of histamine and heparin (mouse) or major neutral proteases, tryptase, chymase, carboxypeptidase A, and cathepsin G (humans). Reportedly, they cannot produce leukotrienes (LTC4) and IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype.

Axiom
annotated source: connective tissue type mast cell
annotated property: subClassOf
annotated target: mast cell
is inferred: true

Axiom
annotated source: connective tissue type mast cell
annotated property: IAO_0000115
annotated target: Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: PMID:19923473
has db xref: PMID:9354811

mucosal type mast cell
type: Class
equivalent class: Class
  intersection of: mast cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001961
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002540
subclass of: mast cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001961
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002540
IAO_0000115: Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype.
has exact synonym: MC(T)
has exact synonym: MCT
has exact synonym: T mast cells
in subset: human reference atlas
comment: They are CD88-negative. The cytoplasmic granules contain low levels of histamine and high levels of chondroitin sulfate (mouse) or major neutral proteases and tryptase (humans). Additionally, they can produce leukotrienes (LTC4), IL-5, IL-6, and low levels of IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype.

Axiom
annotated source: mucosal type mast cell
annotated property: subClassOf
annotated target: mast cell
is inferred: true

Axiom
annotated source: mucosal type mast cell
annotated property: IAO_0000115
annotated target: Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: PMID:19923473
has db xref: PMID:9354811

garland cell
type: Class
subclass of: binucleate cell
subclass of: phagocyte (sensu Nematoda and Protostomia)
subclass of: CL_0002520
IAO_0000115: A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae.
has broad synonym: garland nephrocyte
has db xref: BTO:0004596
has db xref: FBbt:00005059

Axiom
annotated source: garland cell
annotated property: IAO_0000115
annotated target: A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae.
has db xref: GOC:tfm
has db xref: PMID:19783135
has db xref: fbbt:00005059

Axiom
annotated source: garland cell
annotated property: hasBroadSynonym
annotated target: garland nephrocyte
has db xref: GO:0061321

Axiom
annotated source: garland cell
annotated property: hasDbXref
annotated target: FBbt:00005059
mapping justification: ManualMappingCuration

oenocyte
type: Class
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6656
IAO_0000115: A secretory cell of ectodermal origin. This cell may have important functions in fatty acid and hydrocarbon metabolism and is metabolically linked to the fat body and tracheae. This cell is exclusive of arthropods.
has db xref: FBbt:00004995
comment: Oenocytes are highly variable in size, shape, cluster formation and anatomical location. In adults, oenocytes tend to be smaller but more numerous than in larvae. While oenocytes have been found in arachnids and crustaceans, they have been most abundantly described in insects.

Axiom
annotated source: oenocyte
annotated property: IAO_0000115
annotated target: A secretory cell of ectodermal origin. This cell may have important functions in fatty acid and hydrocarbon metabolism and is metabolically linked to the fat body and tracheae. This cell is exclusive of arthropods.
has db xref: GOC:bf
has db xref: PMID:11171397
has db xref: PMID:24397521
has db xref: PMID:34208190
has db xref: https://www.merriam-webster.com/dictionary/oenocyte

Axiom
annotated source: oenocyte
annotated property: hasDbXref
annotated target: FBbt:00004995
mapping justification: ManualMappingCuration

Axiom
annotated source: oenocyte
annotated property: comment
annotated target: Oenocytes are highly variable in size, shape, cluster formation and anatomical location. In adults, oenocytes tend to be smaller but more numerous than in larvae. While oenocytes have been found in arachnids and crustaceans, they have been most abundantly described in insects.
has db xref: PMID:24397521
has db xref: PMID:34208190

visible light photoreceptor cell
type: Class
equivalent class: Class
  intersection of: photoreceptor cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0009584
subclass of: photoreceptor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0009584
IAO_0000115: A photoreceptor cell that detects visible light.
has db xref: ZFA:0009219

Axiom
annotated source: visible light photoreceptor cell
annotated property: IAO_0000115
annotated target: A photoreceptor cell that detects visible light.
has db xref: GOC:tfm

Axiom
annotated source: visible light photoreceptor cell
annotated property: hasDbXref
annotated target: ZFA:0009219
mapping justification: UnspecifiedMatching

CD4-positive helper T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001816
subclass of: CD4-positive, alpha-beta T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD4-positive, alpha-beta T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001816
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030217
IAO_0000115: A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions.
description: The CD4-positive helper T cells are a subpopulation of T lymphocytes, which are part of the adaptive immune system. These cells play a vital role in establishing and maximizing the capability of the immune system to combat infections. Like all T lymphocytes, CD4+ helper T cells are uniquely characterized by the expression of a T-cell receptor (TCR) complex on their cell surface. The subset of CD4+ cells express the CD4 glycoprotein on their cell surface that serves as a co-receptor for the T-cell receptor. The CD4 co-receptor enables these cells to interact with antigen-presenting cells and perform their influential role in adaptive immune response. CD4+ helper T cells are primarily responsible for assisting other cells in the immunological processes. This involves recognition, interaction, and processing of antigens. Once an antigen-presenting cell presents a foreign antigen such as peptides derived from pathogens or transformed cells to the CD4+ helper T cell, it becomes activated, proliferates, and differentiates into subtypes such as Th1, Th2, Th17, or Treg, each with a specific role in the immune response. Th1 cells produces various cytokines. including IFN‐γ, IL-2 and TNF-β, and aid cell-mediated immune responses against intracellular pathogens. Th2 cells produce IL-4, IL-5 and IL13 and assist in antibody-mediated immune responses. Th17 cells release IL-17 and convey protective immunity against extracellular bacteria and fungi as well as contributing to inflammation and autoimmunity, while Treg cells are immunosuppressive cells and maintain immune homeostasis and provide tolerance to self-antigens. Finally, follicular T helper (Tfh) cells are thought to help B cells build up antibody responses by assisting germinal center formation, affinity maturation, and possibly immunoglobulin class switch recombination In addition to their critical role in immune response, CD4+ helper T cells are notably the main target of HIV infection, where the virus depletes the numbe…
has db xref: CALOHA:TS-1146
has db xref: FMA:70572
has exact synonym: CD4-positive T-helper cell
has exact synonym: CD4-positive helper T lymphocyte
has exact synonym: CD4-positive helper T-cell
has exact synonym: CD4-positive helper T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD4-positive helper T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive helper T cell
annotated property: IAO_0000115
annotated target: A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: MESH:D006377

Axiom
annotated source: CD4-positive helper T cell
annotated property: description
annotated target: The CD4-positive helper T cells are a subpopulation of T lymphocytes, which are part of the adaptive immune system. These cells play a vital role in establishing and maximizing the capability of the immune system to combat infections. Like all T lymphocytes, CD4+ helper T cells are uniquely characterized by the expression of a T-cell receptor (TCR) complex on their cell surface. The subset of CD4+ cells express the CD4 glycoprotein on their cell surface that serves as a co-receptor for the T-cell receptor. The CD4 co-receptor enables these cells to interact with antigen-presenting cells and perform their influential role in adaptive immune response. CD4+ helper T cells are primarily responsible for assisting other cells in the immunological processes. This involves recognition, interaction, and processing of antigens. Once an antigen-presenting cell presents a foreign antigen such as peptides derived from pathogens or transformed cells to the CD4+ helper T cell, it becomes activated, proliferates, and differentiates into subtypes such as Th1, Th2, Th17, or Treg, each with a specific role in the immune response. Th1 cells produces various cytokines. including IFN‐γ, IL-2 and TNF-β, and aid cell-mediated immune responses against intracellular pathogens. Th2 cells produce IL-4, IL-5 and IL13 and assist in antibody-mediated immune responses. Th17 cells release IL-17 and convey protective immunity against extracellular bacteria and fungi as well as contributing to inflammation and autoimmunity, while Treg cells are immunosuppressive cells and maintain immune homeostasis and provide tolerance to self-antigens. Finally, follicular T helper (Tfh) cells are thought to help B cells build up antibody responses by assisting germinal center formation, affinity maturation, and possibly immunoglobulin class switch recombination In addition to their critical role in immune response, CD4+ helper T cells are notably the main target of HIV infection, where the virus depletes the numbe…
has db xref: DOI:10.1002/ctd2.199
has db xref: DOI:10.1038/s43018-023-00521-2
has db xref: DOI:10.1111/imcb.12662
has db xref: DOI:10.1146/annurev-immunol-103019-085803
has db xref: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/t-helper-cell

CD4-positive helper T cell on CELLxGENE CellGuide
type: Axiom
annotated source: CD4-positive helper T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000492

UV sensitive photoreceptor cell
type: Class
equivalent class: Class
  intersection of: photoreceptor cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0009589
subclass of: photoreceptor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0009589
IAO_0000115: A photoreceptor cell that detects ultraviolet light.
has db xref: ZFA:0009221

Axiom
annotated source: UV sensitive photoreceptor cell
annotated property: IAO_0000115
annotated target: A photoreceptor cell that detects ultraviolet light.
has db xref: GOC:tfm

Axiom
annotated source: UV sensitive photoreceptor cell
annotated property: hasDbXref
annotated target: ZFA:0009221
mapping justification: UnspecifiedMatching

inhibitory interneuron
type: Class
subclass of: interneuron
IAO_0000115: An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS).
description: Inhibitory interneurons, often referred to as local circuit neurons, are integral components of the central nervous system where they play key roles in refining neural circuits and shaping network activity. Known for their inhibitory nature, these neurons form connections mainly within the same region of the brain or spinal cord where they are located. This localization allows them to impact the activities of nearby excitatory neurons by means of inhibitory networks to inhibit or reduce the likelihood of the firing of these excitatory neurons. Functionally, Inhibitory Interneurons serve as primary regulators and modulators of the output of nerve cells, orchestrating a balance between excitatory and inhibitory activities in neural networks. It is through their characteristic release of inhibitory neurotransmitters, such as gamma-aminobutyric acid (GABA) and glycine, that they manage to suppress postsynaptic potentials, preventing or reducing the propagation of action potentials. This regulation is not only essential for maintaining equilibrium within the nervous system, but also helps prevent conditions that arise from excessive neuronal activities, such as epilepsy. Inhibitory Interneurons, while relatively small in number compared to their excitatory counterparts, exhibit considerable diversity in their structure, function, and neurochemical expression. They are broadly categorized into multiple subtypes, each with its unique influence on neural circuit behavior and role in different behaviors or cognitive processes. For instance, certain subtypes are involved with timing and synchrony of neural activity, while others participate in contrast enhancement in sensory processing or in isolating specific activity patterns. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so…
has db xref: FMA:84776
has db xref: ZFA:0009225
in subset: cellxgene subset

Axiom
annotated source: inhibitory interneuron
annotated property: IAO_0000115
annotated target: An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS).
has db xref: GOC:tfm
has db xref: http://en.wikipedia.org/wiki/Interneuron

Axiom
annotated source: inhibitory interneuron
annotated property: description
annotated target: Inhibitory interneurons, often referred to as local circuit neurons, are integral components of the central nervous system where they play key roles in refining neural circuits and shaping network activity. Known for their inhibitory nature, these neurons form connections mainly within the same region of the brain or spinal cord where they are located. This localization allows them to impact the activities of nearby excitatory neurons by means of inhibitory networks to inhibit or reduce the likelihood of the firing of these excitatory neurons. Functionally, Inhibitory Interneurons serve as primary regulators and modulators of the output of nerve cells, orchestrating a balance between excitatory and inhibitory activities in neural networks. It is through their characteristic release of inhibitory neurotransmitters, such as gamma-aminobutyric acid (GABA) and glycine, that they manage to suppress postsynaptic potentials, preventing or reducing the propagation of action potentials. This regulation is not only essential for maintaining equilibrium within the nervous system, but also helps prevent conditions that arise from excessive neuronal activities, such as epilepsy. Inhibitory Interneurons, while relatively small in number compared to their excitatory counterparts, exhibit considerable diversity in their structure, function, and neurochemical expression. They are broadly categorized into multiple subtypes, each with its unique influence on neural circuit behavior and role in different behaviors or cognitive processes. For instance, certain subtypes are involved with timing and synchrony of neural activity, while others participate in contrast enhancement in sensory processing or in isolating specific activity patterns. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so…
has db xref: DOI:10.1007/s12576-016-0442-7
has db xref: DOI:10.1016/j.neuropharm.2014.09.011
has db xref: DOI:10.1038/nature25999
has db xref: DOI:10.1152/physrev.00007.2017
has db xref: DOI:10.1523/JNEUROSCI.23-02-00622.2003

Axiom
annotated source: inhibitory interneuron
annotated property: hasDbXref
annotated target: ZFA:0009225
mapping justification: UnspecifiedMatching

inhibitory interneuron on CELLxGENE CellGuide
type: Axiom
annotated source: inhibitory interneuron
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000498

stromal cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0002320
subclass of: Restriction
  on property: RO_0002202
  some values from: mesenchymal stem cell
IAO_0000115: A connective tissue cell of an organ found in the loose connective tissue.
description: Stromal cells constitute a significant portion of the structural cellular milieu (stroma) that supports the function of parenchymal (functional) cells within an organ. The stroma is the connective, supportive framework of biological tissues with various functions depending on the specific organ and cell type. Stromal cells, derived from the mesenchymal lineage, play crucial roles in creating, maintaining, and repairing the tissue microenvironment in virtually all mammalian organs, making these cells indispensable to biological function. Additionally, stromal cells secrete growth factors, cytokines, and extracellular matrix (ECM) molecules to constitute an interactive cellular network and ensure an optimal environment for the functional cells. Beyond mere structural support, these cells are instrumental in wound healing, inflammation, and maintaining tissue integrity. They may also influence the behavior of other cell types through direct cell-cell interactions or paracrine signaling. Clinically and in research, stromal cells often draw attention due to their interaction with tumors in the cancer microenvironment. Over the past years, the role of stromal cells as facilitators of tumor growth and metastasis has been recognized increasingly. They contribute to cancer progression not only by modulating the ECM but also through the secretion of various bioactive molecules and interacting with immune cells, thereby influencing the immunologic responses to tumors. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0002064
has db xref: FMA:83624
has db xref: ZFA:0009226
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: stromal cell
annotated property: IAO_0000115
annotated target: A connective tissue cell of an organ found in the loose connective tissue.
has db xref: GOC:tfm
has db xref: MESH:D017154

Axiom
annotated source: stromal cell
annotated property: description
annotated target: Stromal cells constitute a significant portion of the structural cellular milieu (stroma) that supports the function of parenchymal (functional) cells within an organ. The stroma is the connective, supportive framework of biological tissues with various functions depending on the specific organ and cell type. Stromal cells, derived from the mesenchymal lineage, play crucial roles in creating, maintaining, and repairing the tissue microenvironment in virtually all mammalian organs, making these cells indispensable to biological function. Additionally, stromal cells secrete growth factors, cytokines, and extracellular matrix (ECM) molecules to constitute an interactive cellular network and ensure an optimal environment for the functional cells. Beyond mere structural support, these cells are instrumental in wound healing, inflammation, and maintaining tissue integrity. They may also influence the behavior of other cell types through direct cell-cell interactions or paracrine signaling. Clinically and in research, stromal cells often draw attention due to their interaction with tumors in the cancer microenvironment. Over the past years, the role of stromal cells as facilitators of tumor growth and metastasis has been recognized increasingly. They contribute to cancer progression not only by modulating the ECM but also through the secretion of various bioactive molecules and interacting with immune cells, thereby influencing the immunologic responses to tumors. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/nri2588
has db xref: DOI:10.1038/s41536-019-0083-6
has db xref: DOI:10.1186/s13058-016-0740-2
has db xref: DOI:10.1634/stemcells.2007-0637
has db xref: DOI:10.3389/fcell.2020.555378

Axiom
annotated source: stromal cell
annotated property: hasDbXref
annotated target: ZFA:0009226
mapping justification: UnspecifiedMatching

stromal cell on CELLxGENE CellGuide
type: Axiom
annotated source: stromal cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000499

follicular epithelial cell
type: Class
subclass of: epithelial cell
IAO_0000115: An epithelial somatic cell associated with a maturing oocyte.

granulosa cell
type: Class
subclass of: BFO_0000002
subclass of: steroid hormone secreting cell
subclass of: CL_0002174
subclass of: CL_1100001
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_4033066
IAO_0000115: A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors.
description: Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000542
has db xref: CALOHA:TS-0729
has db xref: FMA:18718
has db xref: ZFA:0009227
has exact synonym: granulosa cell of ovary
in subset: cellxgene subset

Axiom
annotated source: granulosa cell
annotated property: IAO_0000115
annotated target: A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors.
has db xref: MESH:D006107

Axiom
annotated source: granulosa cell
annotated property: description
annotated target: Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.ejogrb.2004.01.010
has db xref: DOI:10.1093/humrep/del408
has db xref: DOI:10.1093/humupd/6.3.279
has db xref: DOI:10.1210/jcem-28-3-355
has db xref: DOI:10.3389/fendo.2019.00832/full

Axiom
annotated source: granulosa cell
annotated property: hasDbXref
annotated target: ZFA:0009227
mapping justification: UnspecifiedMatching

granulosa cell on CELLxGENE CellGuide
type: Axiom
annotated source: granulosa cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000501

type D enteroendocrine cell
type: Class
subclass of: enteroendocrine cell
subclass of: neuroendocrine cell
subclass of: somatostatin secreting cell
IAO_0000115: A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.
description: Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:62935
has db xref: ZFA:0009228
has exact synonym: D cell
in subset: cellxgene subset

Axiom
annotated source: type D enteroendocrine cell
annotated property: IAO_0000115
annotated target: A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.
has db xref: MESH:D019864

Axiom
annotated source: type D enteroendocrine cell
annotated property: description
annotated target: Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.pharmthera.2015.05.007
has db xref: DOI:10.1038/s41574-018-0020-6
has db xref: DOI:10.1093/annonc/mdh216
has db xref: https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell

Axiom
annotated source: type D enteroendocrine cell
annotated property: hasDbXref
annotated target: ZFA:0009228
mapping justification: UnspecifiedMatching

type D enteroendocrine cell on CELLxGENE CellGuide
type: Axiom
annotated source: type D enteroendocrine cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000502

enkephalin secreting cell
type: Class
subclass of: endorphin secreting cell
IAO_0000115: An endorphine cell that secretes enkephalin.
has db xref: ZFA:0009231

Axiom
annotated source: enkephalin secreting cell
annotated property: IAO_0000115
annotated target: An endorphine cell that secretes enkephalin.
has db xref: GO:tfm

Axiom
annotated source: enkephalin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009231
mapping justification: UnspecifiedMatching

endorphin secreting cell
type: Class
subclass of: peptide hormone secreting cell
IAO_0000115: A peptide hormone secreting cell that secretes endorphin.
has db xref: ZFA:0009232

Axiom
annotated source: endorphin secreting cell
annotated property: IAO_0000115
annotated target: A peptide hormone secreting cell that secretes endorphin.
has db xref: GO:tfm

Axiom
annotated source: endorphin secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009232
mapping justification: UnspecifiedMatching

type G enteroendocrine cell
type: Class
subclass of: enteroendocrine cell
subclass of: neuroendocrine cell
subclass of: enkephalin secreting cell
subclass of: gastrin secreting cell
IAO_0000115: An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.
has db xref: BTO:0004108
has db xref: FMA:67609
has exact synonym: G cell
in subset: cellxgene subset

Axiom
annotated source: type G enteroendocrine cell
annotated property: IAO_0000115
annotated target: An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.
has db xref: GOC:tfm
has db xref: ISBN:0517223651
has db xref: MESH:D019863
has db xref: PMID:10700044
has db xref: PMID:35674015
has db xref: PMID:37240181

gastrin secreting cell
type: Class
subclass of: peptide hormone secreting cell
IAO_0000115: A peptide hormone secreting cell that secretes gastrin.
in subset: human reference atlas

Axiom
annotated source: gastrin secreting cell
annotated property: IAO_0000115
annotated target: A peptide hormone secreting cell that secretes gastrin.
has db xref: GO:tfm

androgen binding protein secreting cell
type: Class
subclass of: protein secreting cell
IAO_0000115: A peptide hormone secreting cell that secretes androgen binding protein.

Axiom
annotated source: androgen binding protein secreting cell
annotated property: IAO_0000115
annotated target: A peptide hormone secreting cell that secretes androgen binding protein.
has db xref: GO:tfm

cardiac muscle myoblast
type: Class
equivalent class: Class
  intersection of: myoblast
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001133
  intersection of: Restriction
    on property: RO_0002203
    some values from: cardiac muscle cell
subclass of: CL_0002494
subclass of: CL_0010021
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001133
IAO_0000115: A precursor cell destined to differentiate into cardiac muscle cell.
has db xref: FMA:84797
has db xref: ZFA:0009234
has exact synonym: cardiac muscle progenitor cell
has exact synonym: cardiomyocyte progenitor cell
in subset: cellxgene subset

Axiom
annotated source: cardiac muscle myoblast
annotated property: IAO_0000115
annotated target: A precursor cell destined to differentiate into cardiac muscle cell.
has db xref: GOC:tfm
has db xref: MESH:D032386

Axiom
annotated source: cardiac muscle myoblast
annotated property: hasDbXref
annotated target: ZFA:0009234
mapping justification: UnspecifiedMatching

smooth muscle myoblast
type: Class
equivalent class: Class
  intersection of: myoblast
  intersection of: Restriction
    on property: RO_0002203
    some values from: smooth muscle cell
subclass of: myoblast
subclass of: Restriction
  on property: RO_0002203
  some values from: smooth muscle cell
IAO_0000115: A precursor cell destined to differentiate into smooth muscle myocytes.
description: A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:84798
has db xref: ZFA:0009235
has exact synonym: myoblast, smooth muscle
has related synonym: satellite cell
in subset: cellxgene subset

Axiom
annotated source: smooth muscle myoblast
annotated property: IAO_0000115
annotated target: A precursor cell destined to differentiate into smooth muscle myocytes.
has db xref: GOC:tfm
has db xref: MESH:D032390

Axiom
annotated source: smooth muscle myoblast
annotated property: description
annotated target: A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1074/jbc.RA118.001739
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK544225/
has db xref: https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle

Axiom
annotated source: smooth muscle myoblast
annotated property: hasDbXref
annotated target: ZFA:0009235
mapping justification: UnspecifiedMatching

Axiom
annotated source: smooth muscle myoblast
annotated property: hasExactSynonym
annotated target: myoblast, smooth muscle
has db xref: MESH:D032390

smooth muscle myoblast on CELLxGENE CellGuide
type: Axiom
annotated source: smooth muscle myoblast
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000514

skeletal muscle myoblast
type: Class
equivalent class: Class
  intersection of: myoblast
  intersection of: Restriction
    on property: RO_0002203
    some values from: CL_0008002
subclass of: myoblast
subclass of: Restriction
  on property: RO_0002202
  some values from: multi-potent skeletal muscle stem cell
subclass of: Restriction
  on property: RO_0002203
  some values from: CL_0008002
IAO_0000115: A myoblast that differentiates into skeletal muscle fibers.
has db xref: FMA:84799
has db xref: ZFA:0009236
has exact synonym: skeletal myoblast
in subset: cellxgene subset

Axiom
annotated source: skeletal muscle myoblast
annotated property: IAO_0000115
annotated target: A myoblast that differentiates into skeletal muscle fibers.
has db xref: SANBI:mhl

Axiom
annotated source: skeletal muscle myoblast
annotated property: hasDbXref
annotated target: ZFA:0009236
mapping justification: UnspecifiedMatching

macrophage derived foam cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: foam cell
subclass of: Restriction
  on property: RO_0002202
  some values from: macrophage
IAO_0000115: A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
has exact synonym: lipophage

Axiom
annotated source: macrophage derived foam cell
annotated property: IAO_0000115
annotated target: A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
has db xref: GOC:add
has db xref: PMID:20213546

phagocyte (sensu Vertebrata)
type: Class
subclass of: phagocyte
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
IAO_0000115: A phagocyte in vertebrates that is able to phagocytosis.

Axiom
annotated source: phagocyte (sensu Vertebrata)
annotated property: IAO_0000115
annotated target: A phagocyte in vertebrates that is able to phagocytosis.
has db xref: GOC:tfm

phagocyte (sensu Nematoda and Protostomia)
type: Class
subclass of: phagocyte
IAO_0000115: A phagocyte from organisms in the Nematoda or Protostomia clades.
RO_0002161: NCBITaxon_33511

Axiom
annotated source: phagocyte (sensu Nematoda and Protostomia)
annotated property: IAO_0000115
annotated target: A phagocyte from organisms in the Nematoda or Protostomia clades.
has db xref: GOC:tfm

prokaryotic cell
type: Class
subclass of: cell
RO_0002161: NCBITaxon 2759
has db xref: MESH:D011387

fungal cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 4751
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 4751
IAO_0000115: Any cell that in taxon some Fungi.

Axiom
annotated source: fungal cell
annotated property: IAO_0000115
annotated target: Any cell that in taxon some Fungi.
has db xref: FBC:Autogenerated

syncytiotrophoblast cell
type: Class
equivalent class: Class
  intersection of: trophoblast cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001908
subclass of: trophoblast cell
subclass of: CL_4052002
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000371
IAO_0000115: A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.
has db xref: FMA:83043
has exact synonym: syncytial trophoblast cell
has exact synonym: syncytiotrophoblastic cell
has related synonym: plasmidotrophoblast cell
has related synonym: syntrophoblast cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: syncytiotrophoblast cell
annotated property: IAO_0000115
annotated target: A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.
has db xref: GOC:tfm
has db xref: ISBN:0323052908

Axiom
annotated source: syncytiotrophoblast cell
annotated property: hasExactSynonym
annotated target: syncytial trophoblast cell
has db xref: PMID:11787150

Axiom
annotated source: syncytiotrophoblast cell
annotated property: hasExactSynonym
annotated target: syncytiotrophoblastic cell
has db xref: PMID:21733368

afferent neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron which conveys sensory information centrally from the periphery.
has db xref: FMA:87653
has db xref: ZFA:0009238
has exact synonym: input neuron
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: afferent neuron
annotated property: IAO_0000115
annotated target: A neuron which conveys sensory information centrally from the periphery.
has db xref: GOC:tfm
has db xref: MESH:D009475

Axiom
annotated source: afferent neuron
annotated property: hasDbXref
annotated target: ZFA:0009238
mapping justification: UnspecifiedMatching

efferent neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron which sends impulses peripherally to activate muscles or secretory cells.
has db xref: ZFA:0009239
has exact synonym: output neuron
in subset: cellxgene subset

Axiom
annotated source: efferent neuron
annotated property: IAO_0000115
annotated target: A neuron which sends impulses peripherally to activate muscles or secretory cells.
has db xref: MESH:D009476

Axiom
annotated source: efferent neuron
annotated property: hasDbXref
annotated target: ZFA:0009239
mapping justification: UnspecifiedMatching

primary neuron (sensu Teleostei)
type: Class
subclass of: BFO_0000002
subclass of: CL_2000029
subclass of: Restriction
  on property: RO_0002100
  some values from: UBERON_0002240
IAO_0000115: A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed.
has db xref: ZFA:0009242

Axiom
annotated source: primary neuron (sensu Teleostei)
annotated property: IAO_0000115
annotated target: A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed.
has db xref: PMID:1842357
has db xref: doi:10.1242/dev.108.1.121

Axiom
annotated source: primary neuron (sensu Teleostei)
annotated property: hasDbXref
annotated target: ZFA:0009242
mapping justification: UnspecifiedMatching

primary sensory neuron (sensu Teleostei)
type: Class
equivalent class: Class
  intersection of: sensory neuron
  intersection of: primary neuron (sensu Teleostei)
subclass of: sensory neuron
subclass of: primary neuron (sensu Teleostei)
IAO_0000115: A primary neuron (sensu Teleostei) that has a sensory function.
in subset: cellxgene subset

Axiom
annotated source: primary sensory neuron (sensu Teleostei)
annotated property: IAO_0000115
annotated target: A primary neuron (sensu Teleostei) that has a sensory function.
has db xref: PMID:1842357

neuron
type: Class
equivalent class: Restriction
  on property: RO_0020104
  has self: true
subclass of: electrically responsive cell
subclass of: electrically signaling cell
subclass of: CL_0002319
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0019226
IAO_0000115: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
has db xref: BTO:0000938
has db xref: CALOHA:TS-0683
has db xref: FBbt:00005106
has db xref: FMA:54527
has db xref: VHOG:0001483
has db xref: WBbt:0003679
has db xref: ZFA:0009248
has exact synonym: nerve cell
in subset: cellxgene subset
in subset: human reference atlas
comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.

Axiom
annotated source: neuron
annotated property: IAO_0000115
annotated target: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
has db xref: MESH:D009474
has db xref: http://en.wikipedia.org/wiki/Neuron

Axiom
annotated source: neuron
annotated property: hasDbXref
annotated target: FBbt:00005106
mapping justification: ManualMappingCuration

Axiom
annotated source: neuron
annotated property: hasDbXref
annotated target: ZFA:0009248
mapping justification: UnspecifiedMatching

melanoblast
type: Class
subclass of: eukaryotic cell
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002202
  some values from: migratory neural crest cell
IAO_0000115: A cell that originates from the neural crest and differentiates into a pigment cell.
has db xref: BTO:0003217
has db xref: FMA:83377
has db xref: ZFA:0009249
comment: Derived from UBERON:0002342 neural crest.

Axiom
annotated source: melanoblast
annotated property: IAO_0000115
annotated target: A cell that originates from the neural crest and differentiates into a pigment cell.
has db xref: GOC:tfm
has db xref: SANBI:mhl

Axiom
annotated source: melanoblast
annotated property: hasDbXref
annotated target: ZFA:0009249
mapping justification: UnspecifiedMatching

lymphocyte
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017500
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000792
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0040072
subclass of: mononuclear leukocyte
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017500
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000792
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0040072
subclass of: Restriction
  on property: RO_0002202
  some values from: common lymphoid progenitor
disjoint with: myeloid leukocyte
IAO_0000115: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
has db xref: BTO:0000775
has db xref: CALOHA:TS-0583
has db xref: FMA:62863
has db xref: MESH:D008214
has db xref: VHOG:0001535
has db xref: ZFA:0009250
in subset: cellxgene subset
in subset: human reference atlas
comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)

Axiom
annotated source: lymphocyte
annotated property: IAO_0000115
annotated target: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
has db xref: GOC:add
has db xref: ISBN:0683073696
has db xref: ISBN:0781735149

Axiom
annotated source: lymphocyte
annotated property: hasDbXref
annotated target: ZFA:0009250
mapping justification: UnspecifiedMatching

T-helper 1 cell
type: Class
equivalent class: Class
  intersection of: CD4-positive helper T cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001835
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001202
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001207
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032609
subclass of: CD4-positive helper T cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001835
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001202
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001207
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032609
IAO_0000115: A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma.
description: T-helper 1 (Th1) cells are a subset of mature T lymphocytes. These cells are integral parts of the adaptive immune system, and their primary function is in cell-mediated immunity. Th1 cells play a pivotal role in the immune response against intracellular pathogens. Activation of naive T lymphocytes produces different effector cell phenotypes based upon the cytokine signals they receive during activation. Th1 differentiation is favored by interleukin-12 (IL-12), IL-18, type 1 interferons, and interferon-gamma (IFN-γ). Th1 cells exert their immune function by producing and releasing certain types of cytokines such as IFN-γ and IL-2. IFN-γ activates macrophages and enhances their ability to destroy intracellular pathogens, including viruses and certain bacteria. These cytokines also play a role in activating macrophages, natural killer (NK) cells, CD8+ T cells, and B cells, thus perpetuating the immune response. Release of cytokines by Th1 cells at the site of infection, dependent on the cell’s recognition of the antigen via MHC-II molecules, helps to direct the immune response. Some Th1 effector cells appear to develop into memory T cells. This enables them to react more swiftly and robustly if the same pathogen is encountered again. These cells Th1 cells are also involved in the pathogenesis of several types of autoimmune diseases, such as multiple sclerosis and type 1 diabetes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001678
has db xref: FMA:84382
has exact synonym: T helper cells type 1
has exact synonym: T(H)-1 cell
has exact synonym: Th1 CD4+ T cell
has exact synonym: Th1 T cell
has exact synonym: Th1 T lymphocyte
has exact synonym: Th1 T-cell
has exact synonym: Th1 T-lymphocyte
has exact synonym: Th1 cell
has exact synonym: helper T cell type 1
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'Th1 CD4+ T cell', but its logical definition includes additional known characteristics of T-helper 1 T cells.

Axiom
annotated source: T-helper 1 cell
annotated property: subClassOf
annotated target: CD4-positive helper T cell
is inferred: true

Axiom
annotated source: T-helper 1 cell
annotated property: IAO_0000115
annotated target: A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:19375293
has db xref: PMID:20303875
has db xref: PMID:22343568

Axiom
annotated source: T-helper 1 cell
annotated property: description
annotated target: T-helper 1 (Th1) cells are a subset of mature T lymphocytes. These cells are integral parts of the adaptive immune system, and their primary function is in cell-mediated immunity. Th1 cells play a pivotal role in the immune response against intracellular pathogens. Activation of naive T lymphocytes produces different effector cell phenotypes based upon the cytokine signals they receive during activation. Th1 differentiation is favored by interleukin-12 (IL-12), IL-18, type 1 interferons, and interferon-gamma (IFN-γ). Th1 cells exert their immune function by producing and releasing certain types of cytokines such as IFN-γ and IL-2. IFN-γ activates macrophages and enhances their ability to destroy intracellular pathogens, including viruses and certain bacteria. These cytokines also play a role in activating macrophages, natural killer (NK) cells, CD8+ T cells, and B cells, thus perpetuating the immune response. Release of cytokines by Th1 cells at the site of infection, dependent on the cell’s recognition of the antigen via MHC-II molecules, helps to direct the immune response. Some Th1 effector cells appear to develop into memory T cells. This enables them to react more swiftly and robustly if the same pathogen is encountered again. These cells Th1 cells are also involved in the pathogenesis of several types of autoimmune diseases, such as multiple sclerosis and type 1 diabetes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/B978-0-12-374279-7.08002-4
has db xref: DOI:10.1016/B978-0-7020-6896-6.00016-8
has db xref: DOI:10.1016/j.jaci.2014.11.001
has db xref: DOI:10.1146/annurev-immunol-103019-085803

Axiom
annotated source: T-helper 1 cell
annotated property: hasExactSynonym
annotated target: T helper cells type 1
has db xref: PMID:9419219

Axiom
annotated source: T-helper 1 cell
annotated property: hasExactSynonym
annotated target: Th1 CD4+ T cell
has db xref: PMID:22343568

T-helper 1 cell on CELLxGENE CellGuide
type: Axiom
annotated source: T-helper 1 cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000545

T-helper 2 cell
type: Class
equivalent class: Class
  intersection of: CD4-positive helper T cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001941
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001202
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001207
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
subclass of: CD4-positive helper T cell
subclass of: CL_0001051
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001941
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
IAO_0000115: A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4.
description: T-helper 2 cells (Th2 cells) are a subset of CD4+ T lymphocytes, which play central roles in cell-mediated immunity. All T lymphocytes are uniquely characterized by the expression of a T-cell receptor (TCR) complex on their cell surface. Th2 cells express the CD4 co-receptor which enables the T-cell receptor to engage with antigen-presenting cells and perform their influential role in adaptive immune response. Th2 cells differentiate from naïve CD4+ T cells following TCR ligation and specific cytokine signaling. Th2 cell development and stabilization requires the master regulatory transcription factor GATA-3. Furthermore, IL-4-mediated activation of STAT6 is thought to play an important role in Th2 cell differentiation. The primary function of Th2 cells is to coordinate the immune response against extracellular pathogens, particularly parasitic helminths. They achieve this primarily through the secretion of their signature cytokines – the interleukins IL-4, IL-5, and IL-13. For instance, IL-4 promotes the differentiation of B cells into plasma cells that produce immunoglobulin E (IgE), a class of antibodies that mediate the immune response to parasites and are involved in allergic reactions. IL-5 promotes the activation and survival of eosinophils, a type of white blood cell that is effective against certain parasites. IL-13 works alongside IL-4 but also influences mucus production in the respiratory tract, an important defense mechanism against parasites. Despite their critical roles in host defense, an overactive Th2 response can also lead to pathological outcomes such as allergy and asthma. These health issues are typically characterized by excessive IgE production, eosinophilic inflammation, and mucus hypersecretion, all hallmarks of a Th2 response. In these instances, the immune system reacts excessively to normally harmless substances like pollen, dust mites, or certain foods, with the Th2 cells driving this overreaction. As such, understanding the precise pat…
has db xref: BTO:0001679
has db xref: FMA:84385
has db xref: MESH:D018418
has exact synonym: T helper cells type 2
has exact synonym: T(H)-2 cell
has exact synonym: Th2 T cell
has exact synonym: Th2 T lymphocyte
has exact synonym: Th2 T-cell
has exact synonym: Th2 T-lymphocyte
has exact synonym: Th2 cell
has exact synonym: helper T cell type 2
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'non-Th1/Th17 CD4+ T cell' (see CL:0001051), but includes the additional necessary and sufficient conditions to allow classification as a T-helper 2 T cell.

Axiom
annotated source: T-helper 2 cell
annotated property: subClassOf
annotated target: CD4-positive helper T cell
is inferred: true

Axiom
annotated source: T-helper 2 cell
annotated property: IAO_0000115
annotated target: A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:19375293
has db xref: PMID:20103781
has db xref: PMID:22343568

Axiom
annotated source: T-helper 2 cell
annotated property: description
annotated target: T-helper 2 cells (Th2 cells) are a subset of CD4+ T lymphocytes, which play central roles in cell-mediated immunity. All T lymphocytes are uniquely characterized by the expression of a T-cell receptor (TCR) complex on their cell surface. Th2 cells express the CD4 co-receptor which enables the T-cell receptor to engage with antigen-presenting cells and perform their influential role in adaptive immune response. Th2 cells differentiate from naïve CD4+ T cells following TCR ligation and specific cytokine signaling. Th2 cell development and stabilization requires the master regulatory transcription factor GATA-3. Furthermore, IL-4-mediated activation of STAT6 is thought to play an important role in Th2 cell differentiation. The primary function of Th2 cells is to coordinate the immune response against extracellular pathogens, particularly parasitic helminths. They achieve this primarily through the secretion of their signature cytokines – the interleukins IL-4, IL-5, and IL-13. For instance, IL-4 promotes the differentiation of B cells into plasma cells that produce immunoglobulin E (IgE), a class of antibodies that mediate the immune response to parasites and are involved in allergic reactions. IL-5 promotes the activation and survival of eosinophils, a type of white blood cell that is effective against certain parasites. IL-13 works alongside IL-4 but also influences mucus production in the respiratory tract, an important defense mechanism against parasites. Despite their critical roles in host defense, an overactive Th2 response can also lead to pathological outcomes such as allergy and asthma. These health issues are typically characterized by excessive IgE production, eosinophilic inflammation, and mucus hypersecretion, all hallmarks of a Th2 response. In these instances, the immune system reacts excessively to normally harmless substances like pollen, dust mites, or certain foods, with the Th2 cells driving this overreaction. As such, understanding the precise pat…
has db xref: DOI:10.1038/nri.2017.118
has db xref: DOI:10.1146/annurev-immunol-051116-052350
has db xref: DOI:10.3389/fimmu.2019.02318
has db xref: DOI:10.3389/fimmu.2022.974066

Axiom
annotated source: T-helper 2 cell
annotated property: hasExactSynonym
annotated target: T helper cells type 2
has db xref: PMID:9419219

T-helper 2 cell on CELLxGENE CellGuide
type: Axiom
annotated source: T-helper 2 cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000546

proerythroblast
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017503
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005730
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002505
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0040072
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001945
subclass of: erythroid lineage cell
subclass of: CL_0002242
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017503
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005730
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0040072
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001945
subclass of: Restriction
  on property: RO_0002202
  some values from: erythroid progenitor cell
IAO_0000115: An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
has db xref: FMA:83518
has exact synonym: rubriblast
has related synonym: pronormoblast
in subset: blood and immune upper slim
in subset: cellxgene subset

Axiom
annotated source: proerythroblast
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: proerythroblast
annotated property: IAO_0000115
annotated target: An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
has db xref: ISBN:0721601464
has db xref: PMID:1638021

Axiom
annotated source: proerythroblast
annotated property: hasExactSynonym
annotated target: rubriblast
has db xref: ISBN:0721601464

basophilic erythroblast
type: Class
equivalent class: Class
  intersection of: erythroblast
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017503
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000792
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001945
subclass of: erythroblast
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017503
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000792
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001945
IAO_0000115: A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
has db xref: FMA:83505
has db xref: ZFA:0005236
has exact synonym: basophilic normoblast
has exact synonym: early erythroblast
has exact synonym: early normoblast
has exact synonym: prorubricyte
in subset: cellxgene subset

Axiom
annotated source: basophilic erythroblast
annotated property: subClassOf
annotated target: erythroblast
is inferred: true

Axiom
annotated source: basophilic erythroblast
annotated property: IAO_0000115
annotated target: A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
has db xref: GOC:tfm
has db xref: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: hasDbXref
annotated target: ZFA:0005236
mapping justification: UnspecifiedMatching

Axiom
annotated source: basophilic erythroblast
annotated property: hasExactSynonym
annotated target: basophilic normoblast
has db xref: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: hasExactSynonym
annotated target: early erythroblast
has db xref: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: hasExactSynonym
annotated target: early normoblast
has db xref: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: hasExactSynonym
annotated target: prorubricyte
has db xref: ISBN:0721601464

polychromatophilic erythroblast
type: Class
equivalent class: Class
  intersection of: erythroblast
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017504
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000792
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001945
subclass of: erythroblast
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017504
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000792
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001945
subclass of: Restriction
  on property: RO_0002202
  some values from: basophilic erythroblast
IAO_0000115: A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
has db xref: FMA:83506
has db xref: ZFA:0005241
has exact synonym: intermediate erythroblast
has exact synonym: intermediate normoblast
has exact synonym: polychromatic erythroblast
has exact synonym: polychromatic normoblast
has exact synonym: polychromatophilic normoblast
has exact synonym: rubricyte
in subset: cellxgene subset

Axiom
annotated source: polychromatophilic erythroblast
annotated property: subClassOf
annotated target: erythroblast
is inferred: true

Axiom
annotated source: polychromatophilic erythroblast
annotated property: IAO_0000115
annotated target: A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
has db xref: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: hasDbXref
annotated target: ZFA:0005241
mapping justification: UnspecifiedMatching

Axiom
annotated source: polychromatophilic erythroblast
annotated property: hasExactSynonym
annotated target: intermediate erythroblast
has db xref: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: hasExactSynonym
annotated target: intermediate normoblast
has db xref: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: hasExactSynonym
annotated target: polychromatic erythroblast
has db xref: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: hasExactSynonym
annotated target: polychromatic normoblast
has db xref: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: hasExactSynonym
annotated target: polychromatophilic normoblast
has db xref: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: hasExactSynonym
annotated target: rubricyte
has db xref: ISBN:0721601464

orthochromatic erythroblast
type: Class
equivalent class: Class
  intersection of: erythroblast
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017502
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0030263
subclass of: erythroblast
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017502
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0030263
subclass of: Restriction
  on property: RO_0002202
  some values from: polychromatophilic erythroblast
IAO_0000115: The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
has db xref: FMA:84646
has exact synonym: acidophilic erythroblast
has exact synonym: eosinophilic erythroblast
has exact synonym: late erythoblast
has exact synonym: orthochromatic normoblast
has exact synonym: pyknotic eto enrythroblast
in subset: cellxgene subset

Axiom
annotated source: orthochromatic erythroblast
annotated property: subClassOf
annotated target: erythroblast
is inferred: true

Axiom
annotated source: orthochromatic erythroblast
annotated property: IAO_0000115
annotated target: The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
has db xref: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: hasExactSynonym
annotated target: acidophilic erythroblast
has db xref: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: hasExactSynonym
annotated target: eosinophilic erythroblast
has db xref: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: hasExactSynonym
annotated target: orthochromatic normoblast
has db xref: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: hasExactSynonym
annotated target: pyknotic eto enrythroblast
has db xref: ISBN:0721601464

megakaryocyte progenitor cell
type: Class
equivalent class: Class
  intersection of: myeloid lineage restricted progenitor cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007113
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030219
subclass of: myeloid cell
subclass of: myeloid lineage restricted progenitor cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: RO_0002202
  some values from: megakaryocyte-erythroid progenitor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007113
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030219
IAO_0000115: The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
has db xref: BTO:0001164
has db xref: CALOHA:TS-0610
has db xref: FMA:84235
has db xref: MESH:D055016
has exact synonym: CFU-Meg
has exact synonym: Meg-CFC
has exact synonym: MkP
has exact synonym: colony-forming unit-megakaryocyte
has exact synonym: megacaryoblast
has exact synonym: megacaryocyte progenitor cell
has exact synonym: megakaryoblast
has exact synonym: megakaryocytic progenitor cell
has related synonym: promegacaryocyte
has related synonym: promegakaryocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: subClassOf
annotated target: myeloid lineage restricted progenitor cell
is inferred: true

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: IAO_0000115
annotated target: The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0721601464

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: hasExactSynonym
annotated target: CFU-Meg
has db xref: PMID:11722431
has db xref: PMID:12482498

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: hasExactSynonym
annotated target: Meg-CFC
has db xref: PMCID:PMC1794060

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: hasExactSynonym
annotated target: MkP
has db xref: PMID:21116988

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: hasExactSynonym
annotated target: megakaryocytic progenitor cell
has db xref: PMID:12482498

megakaryocyte
type: Class
subclass of: myeloid cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001393
subclass of: Restriction
  on property: RO_0002202
  some values from: megakaryocyte progenitor cell
disjoint with: erythroid lineage cell
IAO_0000115: A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release.
description: A megakaryocyte is a large, unique, and complex cell type found primarily in the bone marrow, the spongy, semi-solid tissue located in the medullary cavities of certain bones. The term ‘megakaryocyte’ is derived from the Greek 'mega', meaning great, and 'karyon', referring to the nucleus. Megakaryocytes are characterized by their large size, typically with a diameter of 50-100 µm in humans, and the presence of a multilobulated nucleus; they are the largest hematopoietic cells in the bone marrow but also the rarest cells. The primary function of a megakaryocyte is the production of platelets, also known as thrombocytes. Platelets are small, anucleate cell fragments that play a crucial role in the process of hemostasis, the arrest of blood loss from a damaged blood vessel. The process begins when the megakaryocyte extends long, branching processes called proplatelets, into the sinusoidal blood vessels present in the bone marrow. These proplatelets then fragment into the discoid structures recognized as platelets. Each megakaryocyte can produce thousands of platelets during its lifespan. Apart from platelet production, megakaryocytes are involved in several other functions. They express immune-sensing receptors such as Fc-γ receptor and Toll-like receptors and produce factors such as platelet factor 4 and platelet-derived growth factor that can stimulate the immune system. Also, in certain pathological conditions, megakaryocytes release TGF-β and PDGF and contribute to bone marrow fibrosis, a condition characterized by excessive accumulation of fibrous tissue in the bone marrow leading to anemia. Recent studies have also highlighted the role of megakaryocytes in regulating hematopoiesis, the process of blood cell production. They can influence the bone marrow microenvironment and control the behavior of hematopoietic stem cells, the progenitors of all types of blood cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added…
has db xref: BTO:0000843
has db xref: CALOHA:TS-0611
has db xref: FMA:83555
has exact synonym: megacaryocyte
has exact synonym: megalocaryocyte
has exact synonym: megalokaryocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Megakaryocytes are reportedly CD181-positive and CD182-positive.

Axiom
annotated source: megakaryocyte
annotated property: subClassOf
annotated target: myeloid cell
is inferred: true

Axiom
annotated source: megakaryocyte
annotated property: IAO_0000115
annotated target: A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release.
has db xref: ISBN:0721601464
has db xref: MESH:D008533
has db xref: PMID:31043076
has db xref: http://en.wikipedia.org/wiki/Megakaryocyte

Axiom
annotated source: megakaryocyte
annotated property: description
annotated target: A megakaryocyte is a large, unique, and complex cell type found primarily in the bone marrow, the spongy, semi-solid tissue located in the medullary cavities of certain bones. The term ‘megakaryocyte’ is derived from the Greek 'mega', meaning great, and 'karyon', referring to the nucleus. Megakaryocytes are characterized by their large size, typically with a diameter of 50-100 µm in humans, and the presence of a multilobulated nucleus; they are the largest hematopoietic cells in the bone marrow but also the rarest cells. The primary function of a megakaryocyte is the production of platelets, also known as thrombocytes. Platelets are small, anucleate cell fragments that play a crucial role in the process of hemostasis, the arrest of blood loss from a damaged blood vessel. The process begins when the megakaryocyte extends long, branching processes called proplatelets, into the sinusoidal blood vessels present in the bone marrow. These proplatelets then fragment into the discoid structures recognized as platelets. Each megakaryocyte can produce thousands of platelets during its lifespan. Apart from platelet production, megakaryocytes are involved in several other functions. They express immune-sensing receptors such as Fc-γ receptor and Toll-like receptors and produce factors such as platelet factor 4 and platelet-derived growth factor that can stimulate the immune system. Also, in certain pathological conditions, megakaryocytes release TGF-β and PDGF and contribute to bone marrow fibrosis, a condition characterized by excessive accumulation of fibrous tissue in the bone marrow leading to anemia. Recent studies have also highlighted the role of megakaryocytes in regulating hematopoiesis, the process of blood cell production. They can influence the bone marrow microenvironment and control the behavior of hematopoietic stem cells, the progenitors of all types of blood cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added…
has db xref: DOI:10.1002/JLB.MR0718-261RR
has db xref: DOI:10.1083/jcb.201304054
has db xref: DOI:10.1161/ATVBAHA.119.312129
has db xref: DOI:10.1186/s12967-023-04393-z
has db xref: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/megakaryocyte

megakaryocyte on CELLxGENE CellGuide
type: Axiom
annotated source: megakaryocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000556

granulocyte monocyte progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002032
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002371
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001944
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000005307
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000007857
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000007858
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001865
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030225
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030851
subclass of: myeloid cell
subclass of: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor
subclass of: CL_1001610
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001944
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000005307
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000007857
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000007858
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001865
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030225
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030851
IAO_0000115: A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.
description: Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has broad synonym: CFU-C , Colony forming unit in culture
has db xref: ZFA:0009251
has exact synonym: colony forming unit granulocyte macrophage
has exact synonym: granulocyte-macrophage progenitor
has exact synonym: granulocyte/monocyte precursor
has exact synonym: granulocyte/monocyte progenitor
has related synonym: CFU-GM
has related synonym: GMP
in subset: cellxgene subset
in subset: human reference atlas
comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: IAO_0000115
annotated target: A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.
has db xref: GOC:amm
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0721601464
has db xref: MESH:D055014
has db xref: PMCID:PMC2213186
has db xref: PMCID:PMC548021
has db xref: PMID:16551251
has db xref: PMID:16647566
has db xref: http://en.wikipedia.org/wiki/CFU-GM
has db xref: http://www.copewithcytokines.de

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: description
annotated target: Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.immuni.2017.10.021
has db xref: DOI:10.1146/annurev-immunol-081022113627
has db xref: DOI:10.1186/2050-7771-2-1

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: hasBroadSynonym
annotated target: CFU-C , Colony forming unit in culture
has db xref: http://www.copewithcytokines.de

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: hasDbXref
annotated target: ZFA:0009251
mapping justification: UnspecifiedMatching

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: hasExactSynonym
annotated target: colony forming unit granulocyte macrophage
has db xref: ISBN:0721601464
has db xref: PMCID:PMC2213186
has db xref: PMCID:PMC548021

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: hasExactSynonym
annotated target: granulocyte-macrophage progenitor
has db xref: ISBN:0721601464
has db xref: PMCID:PMC2213186
has db xref: PMCID:PMC548021

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: hasRelatedSynonym
annotated target: CFU-GM
has db xref: ISBN:0721601464
has db xref: PMCID:PMC2213186
has db xref: PMCID:PMC548021
has synonym type: OMO_0003000

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: hasRelatedSynonym
annotated target: GMP
has db xref: ISBN:0721601464
has db xref: PMCID:PMC2213186
has db xref: PMCID:PMC548021
has synonym type: OMO_0003000

granulocyte monocyte progenitor cell on CELLxGENE CellGuide
type: Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000557

reticulocyte
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001945
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0071971
subclass of: erythroid lineage cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001945
subclass of: Restriction
  on property: RO_0002202
  some values from: orthochromatic erythroblast
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0071971
IAO_0000115: An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
has db xref: BTO:0001173
has db xref: CALOHA:TS-0864
has db xref: MESH:D012156
has db xref: ZFA:0009252
in subset: blood and immune upper slim
in subset: cellxgene subset

Axiom
annotated source: reticulocyte
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: reticulocyte
annotated property: IAO_0000115
annotated target: An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:15946868
has db xref: PMID:2037622

Axiom
annotated source: reticulocyte
annotated property: hasDbXref
annotated target: ZFA:0009252
mapping justification: UnspecifiedMatching

promonocyte
type: Class
equivalent class: Class
  intersection of: CL_0002194
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042582
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030224
subclass of: myeloid cell
subclass of: CL_0002194
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042582
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002202
  some values from: monoblast
IAO_0000115: A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules.
description: Promonocytes are precursor cells in the mononuclear phagocyte system, which includes the progenitors in the bone marrow, circulating monocytes and macrophages in various tissues. During monocytopoiesis, promonocytes form after monoblasts differentiate, and precede the development of monocytes and macrophages, which play an integral role in the immune system. Promonocytes are large, often round cells with a high nucleus to cytoplasm ratio. Their cytoplasm is laden with small azurophilic granules, and they are similar in appearance to myelocytes and metamyelocytes. The maturation into monocytes is the key function of promonocytes. Once matured, they navigate their way to the bloodstream and their primary role comes into effect. Monocytes circulate in the blood for a few days before migrating to tissues to become either macrophages or dendritic cells. These cells then proceed to ingest pathogens like bacteria and viruses, helping to keep the body healthy. Thus, promonocytes play a central role in the immune system by paving the way for the development of cells that fight off toxins and attacks. Beyond their immune response role through differentiation, promonocytes may participate in processes such as wound healing and inflammation regulation. Defects or disruptions in promonocyte function have been linked to health disorders, including monocytic-lineage leukemias such as chronic myelomonocytic leukemia (CMML), although it is worth noting that morphologic distinction between promonocytes and other monocytic cells of various differentiation levels is difficult. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0004657
has db xref: FMA:83551
has db xref: ZFA:0009253
in subset: cellxgene subset
in subset: human reference atlas
comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.

Axiom
annotated source: promonocyte
annotated property: subClassOf
annotated target: CL_0002194
is inferred: true

Axiom
annotated source: promonocyte
annotated property: IAO_0000115
annotated target: A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules.
has db xref: GOC:tfm
has db xref: ISBN:0721601464

Axiom
annotated source: promonocyte
annotated property: description
annotated target: Promonocytes are precursor cells in the mononuclear phagocyte system, which includes the progenitors in the bone marrow, circulating monocytes and macrophages in various tissues. During monocytopoiesis, promonocytes form after monoblasts differentiate, and precede the development of monocytes and macrophages, which play an integral role in the immune system. Promonocytes are large, often round cells with a high nucleus to cytoplasm ratio. Their cytoplasm is laden with small azurophilic granules, and they are similar in appearance to myelocytes and metamyelocytes. The maturation into monocytes is the key function of promonocytes. Once matured, they navigate their way to the bloodstream and their primary role comes into effect. Monocytes circulate in the blood for a few days before migrating to tissues to become either macrophages or dendritic cells. These cells then proceed to ingest pathogens like bacteria and viruses, helping to keep the body healthy. Thus, promonocytes play a central role in the immune system by paving the way for the development of cells that fight off toxins and attacks. Beyond their immune response role through differentiation, promonocytes may participate in processes such as wound healing and inflammation regulation. Defects or disruptions in promonocyte function have been linked to health disorders, including monocytic-lineage leukemias such as chronic myelomonocytic leukemia (CMML), although it is worth noting that morphologic distinction between promonocytes and other monocytic cells of various differentiation levels is difficult. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/B978-0-323-35762-3.00027-5
has db xref: DOI:10.1111/ijlh.13212
has db xref: DOI:10.1182/blood.2022015850
has db xref: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/promonocyte

Axiom
annotated source: promonocyte
annotated property: hasDbXref
annotated target: ZFA:0009253
mapping justification: UnspecifiedMatching

promonocyte on CELLxGENE CellGuide
type: Axiom
annotated source: promonocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000559

amacrine cell
type: Class
subclass of: BFO_0000002
subclass of: interneuron
subclass of: CL_0009004
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000966
subclass of: Restriction
  on property: RO_0002120
  some values from: retinal ganglion cell
IAO_0000115: Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons.
has db xref: BTO:0004044
has db xref: FMA:67766
has db xref: ZFA:0009255
has exact synonym: amacrine neuron
has related synonym: AC
has related synonym: ACs
in subset: cellxgene subset
in subset: eye upper slim
in subset: human reference atlas

Axiom
annotated source: amacrine cell
annotated property: IAO_0000115
annotated target: Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons.
has db xref: GOC:tfm
has db xref: MESH:D025042
has db xref: WikipediaVersioned:Amacrine_cell&oldid=1023572246

Axiom
annotated source: amacrine cell
annotated property: hasDbXref
annotated target: ZFA:0009255
mapping justification: UnspecifiedMatching

Axiom
annotated source: amacrine cell
annotated property: hasRelatedSynonym
annotated target: AC
has db xref: doi:10.1038/s41598-020-66092-9
has synonym type: OMO_0003000

Axiom
annotated source: amacrine cell
annotated property: hasRelatedSynonym
annotated target: ACs
has db xref: doi:10.1038/s41598-020-66092-9
has synonym type: OMO_0003000
has synonym type: OMO_0003004

nucleate erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002505
subclass of: erythrocyte
subclass of: CL_0002242
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002421
IAO_0000115: An erythrocyte having a nucleus.
has broad synonym: RBC
has broad synonym: red blood cell
has db xref: ZFA:0009256

Axiom
annotated source: nucleate erythrocyte
annotated property: subClassOf
annotated target: erythrocyte
is inferred: true

Axiom
annotated source: nucleate erythrocyte
annotated property: IAO_0000115
annotated target: An erythrocyte having a nucleus.
has db xref: GOC:add
has db xref: GOc:tfm

Axiom
annotated source: nucleate erythrocyte
annotated property: hasDbXref
annotated target: ZFA:0009256
mapping justification: UnspecifiedMatching

endospore
type: Class
subclass of: prokaryotic cell
IAO_0000115: A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged.
has db xref: BTO:0002779
has exact synonym: bacterial spore

Axiom
annotated source: endospore
annotated property: IAO_0000115
annotated target: A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged.
has db xref: GOC:tfm
has db xref: ISBN:0618947256

neutrophilic promyelocyte
type: Class
equivalent class: Class
  intersection of: promyelocyte
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001944
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000005307
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007857
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000010543
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000014362
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000009978
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030223
subclass of: neutrophil progenitor cell
subclass of: promyelocyte
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001944
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000005307
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007857
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000010543
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000014362
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000009978
subclass of: Restriction
  on property: RO_0002202
  some values from: neutrophilic myeloblast
IAO_0000115: A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression.
has db xref: FMA:84196
has db xref: ZFA:0009257
has exact synonym: neutrophilic premyelocyte
has exact synonym: neutrophilic progranulocyte
comment: These cells are CD11b-negative, CD15-positive, CD16-negative, CD49d-positive, CD68-positive, CD35-negative, and fMLP receptor-negative. They are found in the Band 3 fraction.

Axiom
annotated source: neutrophilic promyelocyte
annotated property: subClassOf
annotated target: promyelocyte
is inferred: true

Axiom
annotated source: neutrophilic promyelocyte
annotated property: IAO_0000115
annotated target: A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: PMID:12560239
has db xref: PMID:15514007

Axiom
annotated source: neutrophilic promyelocyte
annotated property: hasDbXref
annotated target: ZFA:0009257
mapping justification: UnspecifiedMatching

angioblastic mesenchymal cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001444
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002112
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000016043
subclass of: mesenchymal stem cell
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001444
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002112
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000016043
subclass of: Restriction
  on property: RO_0002202
  some values from: mesenchymal stem cell
IAO_0000115: A mesenchymal stem cell capable of developing into blood vessel endothelium.
has db xref: ZFA:0009258
has exact synonym: angioblast
has exact synonym: chondroplast
comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.

Axiom
annotated source: angioblastic mesenchymal cell
annotated property: subClassOf
annotated target: mesenchymal stem cell
is inferred: true

Axiom
annotated source: angioblastic mesenchymal cell
annotated property: IAO_0000115
annotated target: A mesenchymal stem cell capable of developing into blood vessel endothelium.
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: PMID:12768659

Axiom
annotated source: angioblastic mesenchymal cell
annotated property: hasDbXref
annotated target: ZFA:0009258
mapping justification: UnspecifiedMatching

amine precursor uptake and decarboxylation cell
type: Class
subclass of: neuroendocrine cell
IAO_0000115: A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell.
has db xref: BTO:0003866
has db xref: FMA:83114
has db xref: MESH:D001078
has exact synonym: APUD cell

Axiom
annotated source: amine precursor uptake and decarboxylation cell
annotated property: IAO_0000115
annotated target: A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

cardiac mesenchymal cell
type: Class
equivalent class: Class
  intersection of: CL_0008019
  intersection of: Restriction
    on property: RO_0002203
    some values from: CL_0002494
subclass of: CL_0008019
subclass of: CL_2000073
subclass of: Restriction
  on property: RO_0002203
  some values from: CL_0002494
IAO_0000115: A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.
has db xref: ZFA:0009259
in subset: cellxgene subset

Axiom
annotated source: cardiac mesenchymal cell
annotated property: IAO_0000115
annotated target: A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.
has db xref: PMID:18816864

Axiom
annotated source: cardiac mesenchymal cell
annotated property: hasDbXref
annotated target: ZFA:0009259
mapping justification: UnspecifiedMatching

parafollicular cell
type: Class
equivalent class: Class
  intersection of: neurecto-epithelial cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001024
  intersection of: Restriction
    on property: RO_0002215
    some values from: Class
      intersection of: GO_0001820
      intersection of: Restriction
        on property: RO_0002339
        some values from: UBERON_0001009
  intersection of: Restriction
    on property: RO_0002215
    some values from: Class
      intersection of: GO_0036161
      intersection of: Restriction
        on property: RO_0002339
        some values from: UBERON_0001009
subclass of: endocrine cell
subclass of: calcitonin secreting cell
subclass of: serotonin secreting cell
subclass of: neurecto-epithelial cell
subclass of: CL_0002257
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001747
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001024
subclass of: Restriction
  on property: RO_0002202
  some values from: migratory neural crest cell
subclass of: Restriction
  on property: RO_0002215
  some values from: Class
    intersection of: GO_0001820
    intersection of: Restriction
      on property: RO_0002339
      some values from: UBERON_0001009
subclass of: Restriction
  on property: RO_0002215
  some values from: Class
    intersection of: GO_0036161
    intersection of: Restriction
      on property: RO_0002339
      some values from: UBERON_0001009
IAO_0000115: A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. This cell expresses a form of the neural cell adhesion molecule (N-CAM) on its surface and secretes calcitonin and serotonin (5-hydroxytryptamine).
has db xref: FMA:68653
has db xref: SCTID:176770005
has db xref: ZFA:0009260
has exact synonym: C cell
has exact synonym: C cell of thyroid gland
has exact synonym: clear cell of thyroid gland
has exact synonym: parafollicular cell of thyroid gland
has exact synonym: thyroid parafollicular cell

Axiom
annotated source: parafollicular cell
annotated property: subClassOf
annotated target: neurecto-epithelial cell
is inferred: true

Axiom
annotated source: parafollicular cell
annotated property: IAO_0000115
annotated target: A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. This cell expresses a form of the neural cell adhesion molecule (N-CAM) on its surface and secretes calcitonin and serotonin (5-hydroxytryptamine).
has db xref: GOC:tfm
has db xref: ISBN:0517223651

Axiom
annotated source: parafollicular cell
annotated property: hasDbXref
annotated target: ZFA:0009260
mapping justification: UnspecifiedMatching

Axiom
annotated source: parafollicular cell
annotated property: hasExactSynonym
annotated target: C cell of thyroid gland
has db xref: FMA:68653

Axiom
annotated source: parafollicular cell
annotated property: hasExactSynonym
annotated target: clear cell of thyroid gland
has db xref: FMA:68653

Axiom
annotated source: parafollicular cell
annotated property: hasExactSynonym
annotated target: parafollicular cell of thyroid gland
has db xref: FMA:68653

Axiom
annotated source: parafollicular cell
annotated property: hasExactSynonym
annotated target: thyroid parafollicular cell
has db xref: FMA:68653

leucophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0005003
IAO_0000115: A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light.
has db xref: ZFA:0009261

Axiom
annotated source: leucophore
annotated property: IAO_0000115
annotated target: A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light.
has db xref: SANBI:mhl

Axiom
annotated source: leucophore
annotated property: hasDbXref
annotated target: ZFA:0009261
mapping justification: UnspecifiedMatching

retinal cone cell
type: Class
subclass of: CL_0010009
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002672
IAO_0000115: One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.
description: Retinal cone cells, or simply cone cells, are one out of the two types of photoreceptor cells in the retina, the other being retinal rod cells. They function by converting light into signals that can lead to a visual perception. These cells are less sensitive to light compared to rod cells, but they play a crucial role in our vision system for their ability to perceive color and provide sharp visual acuity. They are responsible for our daylight and color vision, enabling an individual to perceive fine detail and rapid changes in light levels. Cone cells are specialized and named based on the absorption spectra of the visual pigments they contain, giving rise to three types of cone cells: short-wavelength S-cones (blue cones), middle-wavelength M-cones (green cones), and long-wavelength L-cones (red cones). The distribution of these cones across the retina differs, with greater densities at the central fovea region, contributing to why our central vision is so sharp and color-detailed compared to peripheral vision. The outer segments of retinal cone cells house the photopigments that absorb light and initiate the process of phototransduction, a biochemical event by which the light signal is transformed into an electrical signal. When a cone cell is stimulated by light, an electrochemical reaction triggers nerve impulses, which are then transmitted to the brain by the optic nerve. There, these impulses are processed into the images that we see. Each type of cone responds to different wavelengths of light, enabling us to perceive a spectrum of color. By working in conjunction with rod cells, which are adapted for low-light vision scenarios, the cone cells provide us with a comprehensive and adaptable vision system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should…
has db xref: BTO:0001036
has db xref: CALOHA:TS-0866
has db xref: FMA:67748
has db xref: ZFA:0009262
has related synonym: cone
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: retinal cone cell
annotated property: IAO_0000115
annotated target: One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.
has db xref: MESH:D017949

Axiom
annotated source: retinal cone cell
annotated property: description
annotated target: Retinal cone cells, or simply cone cells, are one out of the two types of photoreceptor cells in the retina, the other being retinal rod cells. They function by converting light into signals that can lead to a visual perception. These cells are less sensitive to light compared to rod cells, but they play a crucial role in our vision system for their ability to perceive color and provide sharp visual acuity. They are responsible for our daylight and color vision, enabling an individual to perceive fine detail and rapid changes in light levels. Cone cells are specialized and named based on the absorption spectra of the visual pigments they contain, giving rise to three types of cone cells: short-wavelength S-cones (blue cones), middle-wavelength M-cones (green cones), and long-wavelength L-cones (red cones). The distribution of these cones across the retina differs, with greater densities at the central fovea region, contributing to why our central vision is so sharp and color-detailed compared to peripheral vision. The outer segments of retinal cone cells house the photopigments that absorb light and initiate the process of phototransduction, a biochemical event by which the light signal is transformed into an electrical signal. When a cone cell is stimulated by light, an electrochemical reaction triggers nerve impulses, which are then transmitted to the brain by the optic nerve. There, these impulses are processed into the images that we see. Each type of cone responds to different wavelengths of light, enabling us to perceive a spectrum of color. By working in conjunction with rod cells, which are adapted for low-light vision scenarios, the cone cells provide us with a comprehensive and adaptable vision system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should…
has db xref: DOI:10.1016/j.preteyeres.2009.05.003
has db xref: DOI:10.1016/j.preteyeres.2010.11.001
has db xref: DOI:10.1113/JP282058
has db xref: DOI:10.1126/science.3576186
has db xref: DOI:10.1364/JOSAA.10.002491

Axiom
annotated source: retinal cone cell
annotated property: hasDbXref
annotated target: ZFA:0009262
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal cone cell
annotated property: hasRelatedSynonym
annotated target: cone
has db xref: doi:10.1038/s41598-020-66092-9

retinal cone cell on CELLxGENE CellGuide
type: Axiom
annotated source: retinal cone cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000573

erythrophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0005004
IAO_0000115: A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance.
has db xref: ZFA:0009263

Axiom
annotated source: erythrophore
annotated property: IAO_0000115
annotated target: A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance.
has db xref: SANBI:mhl

Axiom
annotated source: erythrophore
annotated property: hasDbXref
annotated target: ZFA:0009263
mapping justification: UnspecifiedMatching

corneal epithelial cell
type: Class
equivalent class: Class
  intersection of: squamous epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001772
subclass of: squamous epithelial cell
subclass of: CL_0002159
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001772
IAO_0000115: An epithelial cell of the cornea.
description: Corneal epithelial cells are a specialized cell type that form the outermost layer of the cornea, the transparent dome-shaped tissue that covers the front of the eye. The corneal epithelium is 5-7 cells thick and is comprised of inner basal cells, middle wing cells and superficial squamous cells. The corneal epithelium plays a crucial role in the maintenance of corneal transparency, protection against external insults, and the refractive power of the cornea. This cell type is responsible for the formation of tight junctions, desmosomes, and hemidesmosomes, which provide structural support to the corneal epithelium and prevent the infiltration of foreign particles and microorganisms. Corneal epithelial cells also have a unique and highly organized cytoskeleton that confers mechanical integrity and limits the penetration of foreign substances. Additionally, corneal epithelial cells secrete a variety of proteins and lipids that help to maintain the hydration and clarity of the cornea. These include mucins, which form a lubricating layer that facilitates blinking and limits dryness, and crystallins, which appear to protect against UV- and oxidative stress-induced apoptosis. Dysfunction of corneal epithelial cells due to infections, inflammation, or injury can lead to corneal opacity, scarring, and impaired vision. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0004298
has db xref: CALOHA:TS-0173
has db xref: FMA:70551
has db xref: ZFA:0009264
has exact synonym: epithelial cell of cornea
in subset: cellxgene subset
in subset: eye upper slim
in subset: human reference atlas

Axiom
annotated source: corneal epithelial cell
annotated property: IAO_0000115
annotated target: An epithelial cell of the cornea.
has db xref: GOC:tfm

Axiom
annotated source: corneal epithelial cell
annotated property: description
annotated target: Corneal epithelial cells are a specialized cell type that form the outermost layer of the cornea, the transparent dome-shaped tissue that covers the front of the eye. The corneal epithelium is 5-7 cells thick and is comprised of inner basal cells, middle wing cells and superficial squamous cells. The corneal epithelium plays a crucial role in the maintenance of corneal transparency, protection against external insults, and the refractive power of the cornea. This cell type is responsible for the formation of tight junctions, desmosomes, and hemidesmosomes, which provide structural support to the corneal epithelium and prevent the infiltration of foreign particles and microorganisms. Corneal epithelial cells also have a unique and highly organized cytoskeleton that confers mechanical integrity and limits the penetration of foreign substances. Additionally, corneal epithelial cells secrete a variety of proteins and lipids that help to maintain the hydration and clarity of the cornea. These include mucins, which form a lubricating layer that facilitates blinking and limits dryness, and crystallins, which appear to protect against UV- and oxidative stress-induced apoptosis. Dysfunction of corneal epithelial cells due to infections, inflammation, or injury can lead to corneal opacity, scarring, and impaired vision. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/S1350-9462(98)00001-9
has db xref: DOI:10.1016/j.semcdb.2007.09.015
has db xref: DOI:10.1097/ACI.0b013e32830e6b04
has db xref: DOI:10.1242/jcs.198119
has db xref: DOI:10.3390/cells10092302

Axiom
annotated source: corneal epithelial cell
annotated property: hasDbXref
annotated target: ZFA:0009264
mapping justification: UnspecifiedMatching

Axiom
annotated source: corneal epithelial cell
annotated property: hasExactSynonym
annotated target: epithelial cell of cornea
has db xref: FMA:70551

corneal epithelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: corneal epithelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000575

monocyte
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030225
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030316
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0043011
subclass of: mononuclear phagocyte
subclass of: myeloid leukocyte
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002202
  some values from: promonocyte
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030225
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030316
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0043011
IAO_0000115: Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
description: Monocytes are a type of white blood cell that constitute part of the mononuclear phagocyte system. They feature prominently in the human body's first line of defense against foreign substances as a part of the innate immune system. Monocytes are the largest of all circulating leukocytes and are identified by their bean-shaped nucleus. They are produced in the bone marrow and circulate in the bloodstream; in some conditions, they may enter tissues and differentiate into macrophages or dendritic cells or a distinct monocyte-derived cell. Monocytes function effectively as phagocytes, devouring harmful pathogens in the body. They engulf and destroy microbes, foreign substances, cancer cells, and other materials detrimental to the body's well-being. This process, known as phagocytosis, is vital for the body's immune response. Monocytes are also equipped to identify harmful pathogens and alert other immune cells to their presence. This is achieved by producing proinflammatory cytokines that recruit other immune cells to the affected area, amplifying the immune response. Beyond their role in fighting infections, monocytes play an important role in the repair and healing of tissues. After an infection or inflammation subsides, monocytes can transition into different types of cells and assist in healing by clearing dead cells and debris and facilitating tissue regeneration. They are crucial in wound healing, control of microbial growth, and tissue development. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000876
has db xref: CALOHA:TS-0638
has db xref: FMA:62864
has db xref: ZFA:0009265
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.

Axiom
annotated source: monocyte
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: monocyte
annotated property: IAO_0000115
annotated target: Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
has db xref: GO_REF:0000031
has db xref: MESH:D009000

Axiom
annotated source: monocyte
annotated property: description
annotated target: Monocytes are a type of white blood cell that constitute part of the mononuclear phagocyte system. They feature prominently in the human body's first line of defense against foreign substances as a part of the innate immune system. Monocytes are the largest of all circulating leukocytes and are identified by their bean-shaped nucleus. They are produced in the bone marrow and circulate in the bloodstream; in some conditions, they may enter tissues and differentiate into macrophages or dendritic cells or a distinct monocyte-derived cell. Monocytes function effectively as phagocytes, devouring harmful pathogens in the body. They engulf and destroy microbes, foreign substances, cancer cells, and other materials detrimental to the body's well-being. This process, known as phagocytosis, is vital for the body's immune response. Monocytes are also equipped to identify harmful pathogens and alert other immune cells to their presence. This is achieved by producing proinflammatory cytokines that recruit other immune cells to the affected area, amplifying the immune response. Beyond their role in fighting infections, monocytes play an important role in the repair and healing of tissues. After an infection or inflammation subsides, monocytes can transition into different types of cells and assist in healing by clearing dead cells and debris and facilitating tissue regeneration. They are crucial in wound healing, control of microbial growth, and tissue development. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.immuni.2018.10.005
has db xref: DOI:10.1126/science.1178331
has db xref: DOI:10.1146/annurev.immunol.021908.132557

Axiom
annotated source: monocyte
annotated property: hasDbXref
annotated target: ZFA:0009265
mapping justification: UnspecifiedMatching

monocyte on CELLxGENE CellGuide
type: Axiom
annotated source: monocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000576

type EC enteroendocrine cell
type: Class
subclass of: enteroendocrine cell
subclass of: chromaffin cell
subclass of: serotonin secreting cell
subclass of: enkephalin secreting cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0004786
IAO_0000115: A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain).
description: Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:62934
has db xref: FMA:83132
has db xref: MESH:D004759
has exact synonym: Kulchitsky cell
has exact synonym: argentaffin cell
has exact synonym: enterochromaffin cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: type EC enteroendocrine cell
annotated property: IAO_0000115
annotated target: A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain).
has db xref: PMID:9505449

Axiom
annotated source: type EC enteroendocrine cell
annotated property: description
annotated target: Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/0166-4328(96)00075-7
has db xref: DOI:10.1016/j.cell.2017.05.034
has db xref: DOI:10.1038/s41574-019-0168-8
has db xref: DOI:10.1073/pnas.1804938115

type EC enteroendocrine cell on CELLxGENE CellGuide
type: Axiom
annotated source: type EC enteroendocrine cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000577

border follicle cell
type: Class
subclass of: follicle cell of egg chamber
IAO_0000115: A follicle cell that migrates from the anterior pole of the insect egg chamber to the anterior of the oocyte where they participate in the formation of the micropyle.
has db xref: FBbt:00004905

Axiom
annotated source: border follicle cell
annotated property: IAO_0000115
annotated target: A follicle cell that migrates from the anterior pole of the insect egg chamber to the anterior of the oocyte where they participate in the formation of the micropyle.
has db xref: FBbt:00004905

Axiom
annotated source: border follicle cell
annotated property: hasDbXref
annotated target: FBbt:00004905
mapping justification: ManualMappingCuration

enterocyte
type: Class
subclass of: brush border epithelial cell
subclass of: gut absorptive cell
subclass of: CL_0002563
IAO_0000115: An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen.
has db xref: BTO:0000398
has db xref: FMA:62122
has db xref: MESH:D020895
has db xref: ZFA:0009269
has narrow synonym: differentiated enterocyte
has narrow synonym: mature enterocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: enterocyte
annotated property: IAO_0000115
annotated target: An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen.
has db xref: SANBI:mhl

Axiom
annotated source: enterocyte
annotated property: hasDbXref
annotated target: ZFA:0009269
mapping justification: UnspecifiedMatching

Axiom
annotated source: enterocyte
annotated property: hasNarrowSynonym
annotated target: differentiated enterocyte
has db xref: PMID:33290721
has db xref: https://orcid.org/0000-0001-9610-7627

Axiom
annotated source: enterocyte
annotated property: hasNarrowSynonym
annotated target: mature enterocyte
has db xref: PMID:33290721
has db xref: https://orcid.org/0000-0001-9610-7627

germ cell
type: Class
subclass of: germ line cell
subclass of: Restriction
  on property: RO_0002216
  some values from: GO_0009566
IAO_0000115: The reproductive cell in multicellular organisms.
has db xref: BTO:0000535
has db xref: NCIT:C12597
has db xref: VHOG:0001534
has db xref: WBbt:0006796
in subset: cellxgene subset

Axiom
annotated source: germ cell
annotated property: subClassOf
annotated target: germ line cell
is inferred: true

Axiom
annotated source: germ cell
annotated property: IAO_0000115
annotated target: The reproductive cell in multicellular organisms.
has db xref: MESH:D005854

odontoclast
type: Class
equivalent class: Class
  intersection of: osteoclast
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0042483
subclass of: osteoclast
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042483
IAO_0000115: A specialized osteoclast associated with the absorption and removal of cementum.
has db xref: BTO:0002516
has db xref: FMA:83027
has db xref: ZFA:0009270

Axiom
annotated source: odontoclast
annotated property: subClassOf
annotated target: osteoclast
is inferred: true

Axiom
annotated source: odontoclast
annotated property: IAO_0000115
annotated target: A specialized osteoclast associated with the absorption and removal of cementum.
has db xref: GOC:add

Axiom
annotated source: odontoclast
annotated property: hasDbXref
annotated target: ZFA:0009270
mapping justification: UnspecifiedMatching

androgen secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0035935
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0035935
IAO_0000115: A steroid hormone secreting cell that secretes androgen.
has db xref: ZFA:0009271

Axiom
annotated source: androgen secreting cell
annotated property: IAO_0000115
annotated target: A steroid hormone secreting cell that secretes androgen.
has db xref: GOC:tfm

Axiom
annotated source: androgen secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009271
mapping justification: UnspecifiedMatching

skeletal muscle satellite cell
type: Class
subclass of: cell of skeletal muscle
subclass of: muscle precursor cell
IAO_0000115: An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers.
description: Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009272
in subset: cellxgene subset
comment: Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle satellite cell population.

Axiom
annotated source: skeletal muscle satellite cell
annotated property: IAO_0000115
annotated target: An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers.
has db xref: GOC:tfm
has db xref: MESH:D032496
has db xref: PMID:21849021
has db xref: PMID:23303905

Axiom
annotated source: skeletal muscle satellite cell
annotated property: description
annotated target: Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/s1357-2725(03)00042-6
has db xref: DOI:10.1152/physrev.00061.2017
has db xref: DOI:10.1186/s13287-022-02706-5
has db xref: DOI:10.1369/0022155411426780
has db xref: DOI:10.22074/cellj.2016.4714

Axiom
annotated source: skeletal muscle satellite cell
annotated property: hasDbXref
annotated target: ZFA:0009272
mapping justification: UnspecifiedMatching

skeletal muscle satellite cell on CELLxGENE CellGuide
type: Axiom
annotated source: skeletal muscle satellite cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000594

enucleate erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001405
subclass of: anucleate cell
subclass of: erythrocyte
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002422
IAO_0000115: An erythrocyte lacking a nucleus.
has broad synonym: red blood cell
has related synonym: RBC
in subset: cellxgene subset

Axiom
annotated source: enucleate erythrocyte
annotated property: subClassOf
annotated target: erythrocyte
is inferred: true

Axiom
annotated source: enucleate erythrocyte
annotated property: IAO_0000115
annotated target: An erythrocyte lacking a nucleus.
has db xref: GOC:add
has db xref: GOC:tfm

Axiom
annotated source: enucleate erythrocyte
annotated property: hasRelatedSynonym
annotated target: RBC
has synonym type: OMO_0003000

sexual spore
type: Class
subclass of: CL_0002369
IAO_0000115: A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature.
has db xref: FAO:0000017
has exact synonym: meiotically-derived spore

Axiom
annotated source: sexual spore
annotated property: IAO_0000115
annotated target: A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature.
has db xref: FAO:0000017
has db xref: GOC:tfm
has db xref: SGD:clt

pyramidal neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0070015
subclass of: CL_2000029
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0070015
IAO_0000115: Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala.
description: Pyramidal neurons, or pyramidal cells, are a distinctive type of neuron named for the triangular shape of their soma, or cell body. The primary characteristic of these neurons is a large apical dendrite that ascends toward the cortical surface, numerous basal dendrites, and a single axon. These neurons are found within parts of the brain including the cerebral cortex, the hippocampus, and the amygdala, playing a critical role in cortex communication, cognitive function, and the relay of information within the brain's neural network. Functional roles of pyramidal neurons depend largely on their localization. However, all types of these neurons serve as principal cells within the grey matter of the brain, transmitting signals over long distances. Primarily, pyramidal cells function as excitatory neurons; they disseminate action potential outputs to other neurons which they are connected to across the synapse. In the cerebral cortex, pyramidal neurons are paramount for sensory perception and motor command, while those located in the hippocampus involve in memory and learning processes. Firing properties of these neurons such as regular spiking and bursting are notable features thought to play a role in synaptic plasticity and signaling. Together, their unique anatomical structure and intricate connectivity underpin their critical function in brain neural networks, significantly contributing to human cognitive abilities. In addition, abnormalities in pyramidal neurons have been linked to a range of neurodegenerative and psychiatric disorders, emphasizing their importance in maintaining healthy neural function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0003102
has db xref: FMA:67310
has db xref: FMA:86775
has db xref: NIFSTD:sao862606388
has db xref: ZFA:0009273
has exact synonym: projection neuron
has exact synonym: pyramidal cell
in subset: BDS subset
in subset: cellxgene subset

Axiom
annotated source: pyramidal neuron
annotated property: IAO_0000115
annotated target: Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala.
has db xref: GOC:tfm
has db xref: MESH:D017966

Axiom
annotated source: pyramidal neuron
annotated property: description
annotated target: Pyramidal neurons, or pyramidal cells, are a distinctive type of neuron named for the triangular shape of their soma, or cell body. The primary characteristic of these neurons is a large apical dendrite that ascends toward the cortical surface, numerous basal dendrites, and a single axon. These neurons are found within parts of the brain including the cerebral cortex, the hippocampus, and the amygdala, playing a critical role in cortex communication, cognitive function, and the relay of information within the brain's neural network. Functional roles of pyramidal neurons depend largely on their localization. However, all types of these neurons serve as principal cells within the grey matter of the brain, transmitting signals over long distances. Primarily, pyramidal cells function as excitatory neurons; they disseminate action potential outputs to other neurons which they are connected to across the synapse. In the cerebral cortex, pyramidal neurons are paramount for sensory perception and motor command, while those located in the hippocampus involve in memory and learning processes. Firing properties of these neurons such as regular spiking and bursting are notable features thought to play a role in synaptic plasticity and signaling. Together, their unique anatomical structure and intricate connectivity underpin their critical function in brain neural networks, significantly contributing to human cognitive abilities. In addition, abnormalities in pyramidal neurons have been linked to a range of neurodegenerative and psychiatric disorders, emphasizing their importance in maintaining healthy neural function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/jnr.23978
has db xref: DOI:10.1016/S0896-6273(01)00447-0
has db xref: DOI:10.1038/nrn2286
has db xref: DOI:10.1038/s41583-019-0125-5
has db xref: DOI:10.1093/cercor/bhg093

Axiom
annotated source: pyramidal neuron
annotated property: hasDbXref
annotated target: ZFA:0009273
mapping justification: UnspecifiedMatching

pyramidal neuron on CELLxGENE CellGuide
type: Axiom
annotated source: pyramidal neuron
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000598

conidium
type: Class
subclass of: fungal asexual spore
IAO_0000115: An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm.
has db xref: BTO:0000283
has db xref: FAO:0000024

Axiom
annotated source: conidium
annotated property: IAO_0000115
annotated target: An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm.
has db xref: ISBN:08199377X
has db xref: PMID:2524423
has db xref: PMID:9529886
has db xref: SGD:clt

cochlear outer hair cell
type: Class
subclass of: CL_4023120
IAO_0000115: A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea.
has db xref: BTO:0003666
has db xref: FMA:62366

Axiom
annotated source: cochlear outer hair cell
annotated property: IAO_0000115
annotated target: A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea.
has db xref: MESH:D018072

retinal rod cell
type: Class
subclass of: CL_0010009
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002672
IAO_0000115: One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
description: Retinal rod cells, often referred to simply as "rod cells”, are a specialized type of photoreceptor cells found in the retina. Their primary function is to detect and convert light into electrochemical signals, which are then transmitted to the brain via nerve impulses. Compared to other types of photoreceptor cells, namely retinal cone cells, rod cells are more sensitive to light, and thus play a crucial role in night and peripheral vision. Rod cells are named for their long, cylindrical shape, which is distinct from the cone-like shape of retinal cone cells. The structure of a rod cell is complex, with different sections responsible for various aspects of its function. The outer segment contains densely packed, light-sensitive membrane discs filled with a pigment called rhodopsin. When light hits rhodopsin, it prompts a chemical reaction that leads to the generation of electrochemical signals. These signals are processed in the cell's inner segment, which contains the cell's primary organelles, including the nucleus and mitochondria, and transmitted through the cell's synaptic terminal to the secondary neurons in the retina. Rod cells are distributed across the majority of the retina, with the highest density found in the peripheral edges. This distribution, coupled with their high sensitivity to light, explains why rod cells contribute significantly to peripheral and low-light vision. However, they do not pick up color and have low spatial acuity, which means that while rod cells can detect the presence of light and movement, the finer details and colors of an image are processed mainly by cone cells. Together, rod cells and cone cells work in concert to enable a wide range of visual capabilities, making vision a complex and intricate biological process. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies on…
has db xref: BTO:0001024
has db xref: CALOHA:TS-0870
has db xref: FMA:67747
has db xref: ZFA:0009275
has related synonym: rod
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: retinal rod cell
annotated property: IAO_0000115
annotated target: One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
has db xref: MESH:D017948

Axiom
annotated source: retinal rod cell
annotated property: description
annotated target: Retinal rod cells, often referred to simply as "rod cells”, are a specialized type of photoreceptor cells found in the retina. Their primary function is to detect and convert light into electrochemical signals, which are then transmitted to the brain via nerve impulses. Compared to other types of photoreceptor cells, namely retinal cone cells, rod cells are more sensitive to light, and thus play a crucial role in night and peripheral vision. Rod cells are named for their long, cylindrical shape, which is distinct from the cone-like shape of retinal cone cells. The structure of a rod cell is complex, with different sections responsible for various aspects of its function. The outer segment contains densely packed, light-sensitive membrane discs filled with a pigment called rhodopsin. When light hits rhodopsin, it prompts a chemical reaction that leads to the generation of electrochemical signals. These signals are processed in the cell's inner segment, which contains the cell's primary organelles, including the nucleus and mitochondria, and transmitted through the cell's synaptic terminal to the secondary neurons in the retina. Rod cells are distributed across the majority of the retina, with the highest density found in the peripheral edges. This distribution, coupled with their high sensitivity to light, explains why rod cells contribute significantly to peripheral and low-light vision. However, they do not pick up color and have low spatial acuity, which means that while rod cells can detect the presence of light and movement, the finer details and colors of an image are processed mainly by cone cells. Together, rod cells and cone cells work in concert to enable a wide range of visual capabilities, making vision a complex and intricate biological process. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies on…
has db xref: DOI:10.1002/cne.902920402
has db xref: DOI:10.1016/0968-0004(83)90235-9
has db xref: DOI:10.1016/j.preteyeres.2016.06.002
has db xref: DOI:10.1038/eye.2015.236
has db xref: DOI:10.1113/JP282058

Axiom
annotated source: retinal rod cell
annotated property: hasDbXref
annotated target: ZFA:0009275
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal rod cell
annotated property: hasRelatedSynonym
annotated target: rod
has db xref: doi:10.1038/s41598-020-66092-9

retinal rod cell on CELLxGENE CellGuide
type: Axiom
annotated source: retinal rod cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000604

fungal asexual spore
type: Class
subclass of: CL_0002369
IAO_0000115: A spore formed following mitosis or mitoses.
has db xref: FAO:0000023

Axiom
annotated source: fungal asexual spore
annotated property: IAO_0000115
annotated target: A spore formed following mitosis or mitoses.
has db xref: GOC:tfm
has db xref: PMID:2524423
has db xref: PMID:9529886
has db xref: SGD:clt

macroconidium
type: Class
subclass of: conidium
IAO_0000115: The larger of two types of asexual spores formed by some fungi; usually round or oblong.
has db xref: FAO:0000038

Axiom
annotated source: macroconidium
annotated property: IAO_0000115
annotated target: The larger of two types of asexual spores formed by some fungi; usually round or oblong.
has db xref: GOC:tfm
has db xref: ISBN:0471940526
has db xref: SGD:clt

ascospore
type: Class
subclass of: sexual spore
IAO_0000115: A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete.
has db xref: BTO:0000097
has db xref: FAO:0000020

Axiom
annotated source: ascospore
annotated property: IAO_0000115
annotated target: A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete.
has db xref: GOC:tfm
has db xref: ISBN:08199377X
has db xref: SGD:clt

zygospore
type: Class
subclass of: sexual spore
IAO_0000115: A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium.
has db xref: FAO:0000040

Axiom
annotated source: zygospore
annotated property: IAO_0000115
annotated target: A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium.
has db xref: ISBN:0471940526
has db xref: ISBN:08199377X
has db xref: SGD:clt

vestibular hair cell
type: Class
subclass of: CL_0002374
IAO_0000115: A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem.
has db xref: FMA:62351
has exact synonym: vestibular receptor cell

Axiom
annotated source: vestibular hair cell
annotated property: IAO_0000115
annotated target: A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem.
has db xref: GOC:tfm
has db xref: MESH:D018069

eosinophil progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002191
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001944
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000005307
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007857
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001865
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001867
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030222
subclass of: myeloid cell
subclass of: CL_0002191
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001944
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000005307
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007857
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001865
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001867
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0002202
  some values from: granulocyte monocyte progenitor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030222
IAO_0000115: Any granulocytopoietic cell that has part some transcription factor PU.1 and has part some CCAAT/enhancer-binding protein alpha and has part some erythroid transcription factor and lacks plasma membrane part some CD19 molecule and lacks plasma membrane part some CD4 molecule and lacks plasma membrane part some integrin alpha-M and lacks plasma membrane part some CD3 epsilon and lacks plasma membrane part some neural cell adhesion molecule 1 and lacks plasma membrane part some CD2 molecule and lacks plasma membrane part some T-cell surface glycoprotein CD8 alpha chain and lacks plasma membrane part some membrane-spanning 4-domains subfamily A member 1 and lacks plasma membrane part some T-cell surface glycoprotein CD5 and lacks plasma membrane part some CD14 molecule and lacks plasma membrane part some lymphocyte antigen 6G and lacks plasma membrane part some lymphocyte antigen 76 (mouse) and has plasma membrane part some CD34 molecule and has plasma membrane part some ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 and has plasma membrane part some interleukin-3 receptor class 2 alpha chain and has plasma membrane part some interleukin-5 receptor subunit alpha and has plasma membrane part some mast/stem cell growth factor receptor and is capable of some eosinophil differentiation.
has related synonym: CFU-Eo
has related synonym: EoP
has related synonym: colony forming unit eosinophil
has related synonym: eosinophil stem cell
comment: These cells are CD34-positive, CD45RA-negative, CD71-negative, and lineage-negative (CD2, CD3 epsilon, CD4, CD5, CD8a, CD14, CD19, CD20, integrin alpha-M, NCAM-1, SCA-1, Ly6G, Ly76).

Axiom
annotated source: eosinophil progenitor cell
annotated property: subClassOf
annotated target: CL_0002191
is inferred: true

Axiom
annotated source: eosinophil progenitor cell
annotated property: IAO_0000115
annotated target: Any granulocytopoietic cell that has part some transcription factor PU.1 and has part some CCAAT/enhancer-binding protein alpha and has part some erythroid transcription factor and lacks plasma membrane part some CD19 molecule and lacks plasma membrane part some CD4 molecule and lacks plasma membrane part some integrin alpha-M and lacks plasma membrane part some CD3 epsilon and lacks plasma membrane part some neural cell adhesion molecule 1 and lacks plasma membrane part some CD2 molecule and lacks plasma membrane part some T-cell surface glycoprotein CD8 alpha chain and lacks plasma membrane part some membrane-spanning 4-domains subfamily A member 1 and lacks plasma membrane part some T-cell surface glycoprotein CD5 and lacks plasma membrane part some CD14 molecule and lacks plasma membrane part some lymphocyte antigen 6G and lacks plasma membrane part some lymphocyte antigen 76 (mouse) and has plasma membrane part some CD34 molecule and has plasma membrane part some ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 and has plasma membrane part some interleukin-3 receptor class 2 alpha chain and has plasma membrane part some interleukin-5 receptor subunit alpha and has plasma membrane part some mast/stem cell growth factor receptor and is capable of some eosinophil differentiation.
has db xref: FBC:Autogenerated

Axiom
annotated source: eosinophil progenitor cell
annotated property: hasRelatedSynonym
annotated target: CFU-Eo
has synonym type: OMO_0003000

Axiom
annotated source: eosinophil progenitor cell
annotated property: hasRelatedSynonym
annotated target: EoP
has db xref: PMCID:PMC2212039
has db xref: PMCID:PMC2626675
has synonym type: OMO_0003000

eosinophilic myelocyte
type: Class
equivalent class: Class
  intersection of: immature eosinophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042582
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0070820
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001483
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001456
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001892
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001932
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002031
subclass of: immature eosinophil
subclass of: CL_0002087
subclass of: CL_0002193
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042582
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0070820
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001483
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001456
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001892
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001932
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002031
IAO_0000115: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive.
has db xref: BTO:0003454
has db xref: FMA:83542

Axiom
annotated source: eosinophilic myelocyte
annotated property: subClassOf
annotated target: immature eosinophil
is inferred: true

Axiom
annotated source: eosinophilic myelocyte
annotated property: IAO_0000115
annotated target: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: ISBN:0721601464
has db xref: PMID:19622087
has db xref: http://www.cap.org

basophil progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002191
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000005307
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007857
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007858
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002065
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030221
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000007431
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000016401
subclass of: myeloid cell
subclass of: CL_0002191
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000005307
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007857
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007858
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002065
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002028
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030221
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000007431
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000016401
IAO_0000115: A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa.
has exact synonym: BaP
has related synonym: CFU-Bas
has related synonym: basophilic stem cell
has related synonym: colony forming unit basophil
comment: BaP are also CD13-low and integrin beta-7-low. They are lin-negative (CD2, CD3e, CD4, CD5, CD8, CD11b, CD14, CD19, CD20, ly6g, ly76, and NCAM-1). They also lack expression of mast cell protease 1 (MCP-1) and microphthalmia-associated transcription factor (mitf).

Axiom
annotated source: basophil progenitor cell
annotated property: subClassOf
annotated target: CL_0002191
is inferred: true

Axiom
annotated source: basophil progenitor cell
annotated property: IAO_0000115
annotated target: A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: PMCID:PMC1312421
has db xref: http://www.copewithcytokines.de

basophilic myelocyte
type: Class
equivalent class: Class
  intersection of: immature basophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042582
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0005730
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0070820
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001483
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001456
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001892
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001932
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002031
subclass of: immature basophil
subclass of: CL_0002087
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042582
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0005730
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0070820
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001483
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001456
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001892
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001932
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002031
IAO_0000115: A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive.
has db xref: BTO:0003456
has db xref: FMA:83543

Axiom
annotated source: basophilic myelocyte
annotated property: subClassOf
annotated target: immature basophil
is inferred: true

Axiom
annotated source: basophilic myelocyte
annotated property: IAO_0000115
annotated target: A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: PMID:18466030
has db xref: http://www.cap.org

basidiospore
type: Class
subclass of: sexual spore
IAO_0000115: A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium.
has db xref: BTO:0002166
has db xref: FAO:0000021

Axiom
annotated source: basidiospore
annotated property: IAO_0000115
annotated target: A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium.
has db xref: GOC:clt
has db xref: ISBN:0471940526
has db xref: ISBN:08199377X

GABAergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0061534
subclass of: secretory cell
subclass of: neuron
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0061534
IAO_0000115: A neuron that uses GABA as a vesicular neurotransmitter
has db xref: FBbt:00007228
has db xref: FMA:84788
has db xref: MESH:D059330
has db xref: WBbt:0005190
has db xref: ZFA:0009276
has exact synonym: GABA-ergic neuron
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: GABAergic neuron
annotated property: IAO_0000115
annotated target: A neuron that uses GABA as a vesicular neurotransmitter
has db xref: GOC:tfm

Axiom
annotated source: GABAergic neuron
annotated property: hasDbXref
annotated target: FBbt:00007228
mapping justification: ManualMappingCuration

Axiom
annotated source: GABAergic neuron
annotated property: hasDbXref
annotated target: ZFA:0009276
mapping justification: UnspecifiedMatching

acinar cell
type: Class
equivalent class: Class
  intersection of: glandular secretory epithelial cell
  intersection of: protein secreting cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0009842
subclass of: glandular secretory epithelial cell
subclass of: protein secreting cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0009842
IAO_0000115: A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
description: Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:83625
has db xref: MESH:D061354
has db xref: ZFA:0009277
has exact synonym: acinic cell
has exact synonym: acinous cell
in subset: cellxgene subset

Axiom
annotated source: acinar cell
annotated property: IAO_0000115
annotated target: A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
has db xref: GOC:tfm
has db xref: http://www.copewithcytokines.de

Axiom
annotated source: acinar cell
annotated property: description
annotated target: Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/BF00710764
has db xref: DOI:10.1038/nrgastro.2013.36
has db xref: DOI:10.1097/MOG.0b013e32832ebfac
has db xref: DOI:10.1111/prd.12116
has db xref: DOI:10.1152/physrev.00011.2011

Axiom
annotated source: acinar cell
annotated property: hasDbXref
annotated target: ZFA:0009277
mapping justification: UnspecifiedMatching

acinar cell on CELLxGENE CellGuide
type: Axiom
annotated source: acinar cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000622

natural killer cell
type: Class
equivalent class: Class
  intersection of: CL_0001067
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002228
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050776
subclass of: CL_0001067
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: RO_0002202
  some values from: pro-NK cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002228
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050776
IAO_0000115: A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
has broad synonym: large granular lymphocyte
has broad synonym: null cell
has db xref: BTO:0000914
has db xref: BTO:0004716
has db xref: CALOHA:TS-0664
has db xref: FMA:63147
has db xref: FMA:83601
has db xref: MESH:D007694
has db xref: VHOG:0001697
has db xref: ZFA:0009278
has exact synonym: NK cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: natural killer cell
annotated property: IAO_0000115
annotated target: A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
has db xref: GOC:add
has db xref: ISBN:0781735149
has db xref: PMID:15771571

Axiom
annotated source: natural killer cell
annotated property: hasDbXref
annotated target: ZFA:0009278
mapping justification: UnspecifiedMatching

CD4-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001004
subclass of: mature alpha-beta T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000025402
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001004
disjoint with: CD8-positive, alpha-beta T cell
IAO_0000115: A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
has exact synonym: CD4-positive, alpha-beta T lymphocyte
has exact synonym: CD4-positive, alpha-beta T-cell
has exact synonym: CD4-positive, alpha-beta T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD4-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, alpha-beta T cell
annotated property: IAO_0000115
annotated target: A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
has db xref: GOC:add
has db xref: ISBN:0781735149

CD8-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000025402
subclass of: mature alpha-beta T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000025402
IAO_0000115: A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
description: CD8-positive, alpha-beta T cells, also referred to as CD8+ T cells, are integral components of the body's adaptive immune system. They are characterized by the presence of the CD8 glycoprotein on their cell surface and the alpha and beta chains in their T cell receptors (TCRs). CD8+ T cells primarily function as cytotoxic T cells (CTLs), their specialized role in the immune response being to detect and eliminate cells presenting foreign or abnormal antigens on their surfaces. Naïve CD8+ T cells patrol the central lymphoid organs, checking peptide– MHC class I molecule complexes for the presence of their cognate antigen on antigen-presenting cells. Recognition of the foreign antigen by the TCR and interaction with MHC class I molecules triggers a series of events leading to the activation of the CD8+ T cell. Once activated, the CD8+ T cell divides, matures, and differentiates into effector T cells capable of destroying the target cells. This cytotoxic function is carried out by the release of substances like perforin and granzymes, which induce apoptosis, or programmed cell death, in the target cells. In addition to their cytotoxic function, CD8+ T cells are known to release various cytokines, including interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α). These are potent mediators of the immune response and have roles in shaping the immune response and the inflammatory reaction. Following the resolution of an immune response, a small subset of activated CD8+ T cells persists as memory T cells, providing a quicker and more vigorous response upon subsequent encounters with the same antigen. These capabilities make CD8-positive, alpha-beta T cells indispensable for the body's defense against infections and malignant transformations. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subt…
has exact synonym: CD8-positive, alpha-beta T lymphocyte
has exact synonym: CD8-positive, alpha-beta T-cell
has exact synonym: CD8-positive, alpha-beta T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD8-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta T cell
annotated property: IAO_0000115
annotated target: A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: CD8-positive, alpha-beta T cell
annotated property: description
annotated target: CD8-positive, alpha-beta T cells, also referred to as CD8+ T cells, are integral components of the body's adaptive immune system. They are characterized by the presence of the CD8 glycoprotein on their cell surface and the alpha and beta chains in their T cell receptors (TCRs). CD8+ T cells primarily function as cytotoxic T cells (CTLs), their specialized role in the immune response being to detect and eliminate cells presenting foreign or abnormal antigens on their surfaces. Naïve CD8+ T cells patrol the central lymphoid organs, checking peptide– MHC class I molecule complexes for the presence of their cognate antigen on antigen-presenting cells. Recognition of the foreign antigen by the TCR and interaction with MHC class I molecules triggers a series of events leading to the activation of the CD8+ T cell. Once activated, the CD8+ T cell divides, matures, and differentiates into effector T cells capable of destroying the target cells. This cytotoxic function is carried out by the release of substances like perforin and granzymes, which induce apoptosis, or programmed cell death, in the target cells. In addition to their cytotoxic function, CD8+ T cells are known to release various cytokines, including interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α). These are potent mediators of the immune response and have roles in shaping the immune response and the inflammatory reaction. Following the resolution of an immune response, a small subset of activated CD8+ T cells persists as memory T cells, providing a quicker and more vigorous response upon subsequent encounters with the same antigen. These capabilities make CD8-positive, alpha-beta T cells indispensable for the body's defense against infections and malignant transformations. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subt…
has db xref: DOI:10.1016/j.immuni.2011.07.010
has db xref: DOI:10.1038/s41577-021-00574-3
has db xref: DOI:10.3389/fimmu.2018.02692
has db xref: DOI:10.3389/fimmu.2018.02826

CD8-positive, alpha-beta T cell on CELLxGENE CellGuide
type: Axiom
annotated source: CD8-positive, alpha-beta T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000625

supporting cell
type: Class
subclass of: cell
IAO_0000115: A cell whose primary function is to support other cell types.
has db xref: BTO:0002315
has db xref: ZFA:0009387
has exact synonym: supportive cell
in subset: cellxgene subset

Axiom
annotated source: supporting cell
annotated property: IAO_0000115
annotated target: A cell whose primary function is to support other cell types.
has db xref: FB:ma
has db xref: GOC:tfm

Axiom
annotated source: supporting cell
annotated property: hasDbXref
annotated target: ZFA:0009387
mapping justification: UnspecifiedMatching

hepatic stellate cell
type: Class
equivalent class: Class
  intersection of: CL_0002320
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002107
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000007939
subclass of: fibroblast
subclass of: extracellular matrix secreting cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002107
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000007939
IAO_0000115: A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver.
description: Hepatic stellate cells (HSCs) are a unique cell type found in the liver, residing in the space between the sinusoidal endothelial cells and the hepatocytes, known as the space of Disse. Despite constituting only 5-8% of the total number of liver cells, they play a significant role in the maintenance of liver health. They have a star-shaped (stellate) structure, hence their name and their principal function is the storage of vitamin A in their cytoplasm as retinyl esters. HSCs become highly active when the liver is damaged or diseased. They play a crucial role in the liver's response to injury and wound-healing process, converging into myofibroblasts, the cells responsible for scar tissue formation (fibrosis). They are also involved in maintaining the extracellular matrix balance by producing matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs), which break down and inhibit the breakdown of collagen respectively. HSCs also play a part in regulating blood flow through the liver’s blood vessels, help fight infections, and are involved in interactions among different types of liver cells. Recent research has implicated them in regulating liver regeneration and in the development of liver cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0002741
has db xref: CALOHA:TS-0452
has db xref: FMA:67763
has db xref: ZFA:0009279
has exact synonym: Ito cell
has exact synonym: hepatic perisinusoidal cell
has exact synonym: perisinusoidal cell
has related synonym: fat-storing cell
has related synonym: lipocyte
has related synonym: vitamin A-storing cells
in subset: cellxgene subset
in subset: human reference atlas
comment: Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen.

Axiom
annotated source: hepatic stellate cell
annotated property: IAO_0000115
annotated target: A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver.
has db xref: GOC:dsd
has db xref: MESH:D055166
has db xref: PMID:12808230
has db xref: PMID:17239632
has db xref: PMID:18222966
has db xref: PMID:9302568
has db xref: http://en.wikipedia.org/wiki/Hepatic_stellate_cell

Axiom
annotated source: hepatic stellate cell
annotated property: description
annotated target: Hepatic stellate cells (HSCs) are a unique cell type found in the liver, residing in the space between the sinusoidal endothelial cells and the hepatocytes, known as the space of Disse. Despite constituting only 5-8% of the total number of liver cells, they play a significant role in the maintenance of liver health. They have a star-shaped (stellate) structure, hence their name and their principal function is the storage of vitamin A in their cytoplasm as retinyl esters. HSCs become highly active when the liver is damaged or diseased. They play a crucial role in the liver's response to injury and wound-healing process, converging into myofibroblasts, the cells responsible for scar tissue formation (fibrosis). They are also involved in maintaining the extracellular matrix balance by producing matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs), which break down and inhibit the breakdown of collagen respectively. HSCs also play a part in regulating blood flow through the liver’s blood vessels, help fight infections, and are involved in interactions among different types of liver cells. Recent research has implicated them in regulating liver regeneration and in the development of liver cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/hep4.1628
has db xref: DOI:10.1016/S0083-6729(06)75006-3
has db xref: DOI:10.1038/s41598-019-43759-6
has db xref: DOI:10.1172/JCI66369

Axiom
annotated source: hepatic stellate cell
annotated property: hasDbXref
annotated target: ZFA:0009279
mapping justification: UnspecifiedMatching

Axiom
annotated source: hepatic stellate cell
annotated property: hasRelatedSynonym
annotated target: vitamin A-storing cells
has db xref: PMID:12808230

hepatic stellate cell on CELLxGENE CellGuide
type: Axiom
annotated source: hepatic stellate cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000632

Axiom
annotated source: hepatic stellate cell
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM889.CJPK.447

chromophil cell of anterior pituitary gland
type: Class
equivalent class: Class
  intersection of: chromaffin cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002196
subclass of: glandular secretory epithelial cell
subclass of: chromaffin cell
subclass of: peptide hormone secreting cell
subclass of: CL_0012001
subclass of: CL_2000004
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002196
IAO_0000115: A cell that stains readily in the anterior pituitary gland.
has db xref: FMA:83089

Axiom
annotated source: chromophil cell of anterior pituitary gland
annotated property: IAO_0000115
annotated target: A cell that stains readily in the anterior pituitary gland.
has db xref: GOC:tfm
has db xref: ISBN:0618947256

basophil cell of pars distalis of adenohypophysis
type: Class
subclass of: chromophil cell of anterior pituitary gland
IAO_0000115: A basophilic chromophil cell that of the anterior pituitary gland.
has db xref: FMA:83094
has exact synonym: basophil cell of anterior lobe of hypophysis
has related synonym: beta cell
has related synonym: pituitary beta cell

Axiom
annotated source: basophil cell of pars distalis of adenohypophysis
annotated property: IAO_0000115
annotated target: A basophilic chromophil cell that of the anterior pituitary gland.
has db xref: GOC:tfm

Bergmann glial cell
type: Class
subclass of: CL_0002603
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002979
IAO_0000115: Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses.
description: Bergmann glial cells, also known as Bergmann glia or Bergmann astrocytes, are specialized astrocytes located in the cerebellum, specifically in the Purkinje cell layer. They were discovered and named after the German histologist Karl Bergmann and are known for their characteristic morphology. Unique to Bergmann glial cells is their long, fibrous processes, which extend through the molecular layer to the cerebellar surface, aligning parallel to the Purkinje cells' dendrites. These extensions play a detailed role in the structural organization and function of the cerebellum. The primary function of Bergmann glial cells is to support and nourish the adjacent neuronal cells, especially the Purkinje cells. Their strategic arrangements around synapses or nerve junctions also indicate their role in facilitating communication between neurons and in modulating synaptic plasticity. The glial cells remove excess neurotransmitters from the synaptic clefts and thus help maintain homeostasis. An additional important role of Bergmann glia is in the guided migration of granule cells during cerebellar development. This guidance is critical for the proper formation and arrangement of the cerebellar circuitry. In addition to these roles, recent studies have revealed a vital function of Bergmann glial cells in maintaining the overall health and functioning of the cerebellum. In instances of cerebellar injury or disease, these cells respond proactively and change their morphology and activity, a process known as reactive gliosis. This response seems to protect and restore the neural circuits. However, aberrant activation of Bergmann glial cells has been associated with several neurodegenerative diseases and disorders, such as spinocerebellar ataxia, underscoring their significance in the pathobiology of the nervous system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in …
has db xref: FMA:54559
has db xref: ZFA:0009282
has exact synonym: Bergmann astrocyte
has exact synonym: Bergmann glial cell of cerebellum
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: Bergmann glial cell
annotated property: IAO_0000115
annotated target: Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses.
has db xref: GOC:tfm
has db xref: http://www.neurolex.org/wiki/Category:Bergmann_Glial_Cell

Axiom
annotated source: Bergmann glial cell
annotated property: description
annotated target: Bergmann glial cells, also known as Bergmann glia or Bergmann astrocytes, are specialized astrocytes located in the cerebellum, specifically in the Purkinje cell layer. They were discovered and named after the German histologist Karl Bergmann and are known for their characteristic morphology. Unique to Bergmann glial cells is their long, fibrous processes, which extend through the molecular layer to the cerebellar surface, aligning parallel to the Purkinje cells' dendrites. These extensions play a detailed role in the structural organization and function of the cerebellum. The primary function of Bergmann glial cells is to support and nourish the adjacent neuronal cells, especially the Purkinje cells. Their strategic arrangements around synapses or nerve junctions also indicate their role in facilitating communication between neurons and in modulating synaptic plasticity. The glial cells remove excess neurotransmitters from the synaptic clefts and thus help maintain homeostasis. An additional important role of Bergmann glia is in the guided migration of granule cells during cerebellar development. This guidance is critical for the proper formation and arrangement of the cerebellar circuitry. In addition to these roles, recent studies have revealed a vital function of Bergmann glial cells in maintaining the overall health and functioning of the cerebellum. In instances of cerebellar injury or disease, these cells respond proactively and change their morphology and activity, a process known as reactive gliosis. This response seems to protect and restore the neural circuits. However, aberrant activation of Bergmann glial cells has been associated with several neurodegenerative diseases and disorders, such as spinocerebellar ataxia, underscoring their significance in the pathobiology of the nervous system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in …
has db xref: DOI:10.1002/jnr.10197
has db xref: DOI:10.1007/s12035-013-8405-y
has db xref: DOI:10.1016/S0074-7742(08)60530-9
has db xref: DOI:10.1038/nn1750
has db xref: DOI:10.1080/14734220600724569

Axiom
annotated source: Bergmann glial cell
annotated property: hasDbXref
annotated target: ZFA:0009282
mapping justification: UnspecifiedMatching

Bergmann glial cell on CELLxGENE CellGuide
type: Axiom
annotated source: Bergmann glial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000644

Axiom
annotated source: Bergmann glial cell
annotated property: depiction
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
has db xref: doi:10.3389/fnins.2020.00293

basal cell
type: Class
subclass of: epithelial fate stem cell
IAO_0000115: Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament.
has db xref: BTO:0000939
has db xref: FMA:62516
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: basal cell
annotated property: IAO_0000115
annotated target: Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament.
has db xref: GOC:tfm
has db xref: ISBN:0517223651

multinucleated giant cell
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001908
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0002432
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0002544
subclass of: myeloid leukocyte
subclass of: CL_4052002
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0002432
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0002544
subclass of: Restriction
  on property: RO_0002202
  some values from: macrophage
IAO_0000115: A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.
has db xref: BTO:0003107
has db xref: FMA:83035
has db xref: MESH:D015726
has exact synonym: Langerhans giant cell
has exact synonym: foreign body giant cell
has exact synonym: macrophage polykaryon
has exact synonym: multinucleate giant cell
has exact synonym: syncytial giant cell
has related synonym: MGC
in subset: blood and immune upper slim
comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this.

Axiom
annotated source: multinucleated giant cell
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: multinucleated giant cell
annotated property: IAO_0000115
annotated target: A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0702022918
has db xref: ISBN:0702024783
has db xref: PMID:33348900
has db xref: Wikipedia:Giant_cell

Axiom
annotated source: multinucleated giant cell
annotated property: hasExactSynonym
annotated target: Langerhans giant cell
has db xref: ISBN:0702022918
has db xref: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: hasExactSynonym
annotated target: foreign body giant cell
has db xref: ISBN:0702022918
has db xref: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: hasExactSynonym
annotated target: macrophage polykaryon
has db xref: ISBN:0702022918
has db xref: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: hasExactSynonym
annotated target: multinucleate giant cell
has db xref: ISBN:0702022918
has db xref: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: hasExactSynonym
annotated target: syncytial giant cell
has db xref: ISBN:0702022918
has db xref: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: hasRelatedSynonym
annotated target: MGC
has db xref: PMID:33348900
has synonym type: OMO_0003000

kidney granular cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002113
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002001
subclass of: protein secreting cell
subclass of: smooth muscle cell
subclass of: CL_1000618
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002001
IAO_0000115: A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.
has broad synonym: juxtaglomerular cell
has db xref: FMA:84138
has db xref: ZFA:0005238
has exact synonym: JG cell
has exact synonym: renin secreting cell
in subset: human reference atlas

Axiom
annotated source: kidney granular cell
annotated property: IAO_0000115
annotated target: A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.
has db xref: GOC:cvs
has db xref: GOC:tfm
has db xref: PMID:11457727

Axiom
annotated source: kidney granular cell
annotated property: hasDbXref
annotated target: ZFA:0005238
mapping justification: UnspecifiedMatching

mesangial cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0002681
subclass of: CL_1001318
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002319
subclass of: Restriction
  on property: RO_0002202
  some values from: mesenchymal stem cell
IAO_0000115: A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries.
description: Mesangial cells are specialized cells that primarily reside in the middle layer, or mesangium, of the renal glomerulus within the kidney. The primary function of mesangial cells is to maintain the structural stability and function of the glomerular capillary tuft. They achieve this by providing structural support to the capillary loops, controlling the surface area available for filtration in response to physiological alterations in blood pressure, and removing trapped material and proteins from the basement membrane, which otherwise could cause damage. Moreover, mesangial cells regulate the glomerular blood flow by contracting and relaxing, similar to smooth muscle cells. They also synthesize extracellular matrix components, including collagen and fibronectin, that form the structural framework of the glomerulus. Beyond their structural and regulatory roles, mesangial cells are involved in several immunologic functions. They express a variety of receptors that can recognize immune complexes and subsequently mediate an inflammatory reaction. Their role in the immune response includes the production of a variety of cytokines and growth factors, which make them a key cellular component in the progression of several renal diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0000853
has db xref: CALOHA:TS-0617
has db xref: FMA:70972
has db xref: MESH:D050527
has db xref: ZFA:0009283
has exact synonym: kidney mesangial cell
in subset: cellxgene subset
comment: Do all of these cells really develop from some mesenchymal stem cell?

Axiom
annotated source: mesangial cell
annotated property: IAO_0000115
annotated target: A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries.
has db xref: GOC:tfm
has db xref: http://www.copewithcytokines.de/cope.cgi

Axiom
annotated source: mesangial cell
annotated property: description
annotated target: Mesangial cells are specialized cells that primarily reside in the middle layer, or mesangium, of the renal glomerulus within the kidney. The primary function of mesangial cells is to maintain the structural stability and function of the glomerular capillary tuft. They achieve this by providing structural support to the capillary loops, controlling the surface area available for filtration in response to physiological alterations in blood pressure, and removing trapped material and proteins from the basement membrane, which otherwise could cause damage. Moreover, mesangial cells regulate the glomerular blood flow by contracting and relaxing, similar to smooth muscle cells. They also synthesize extracellular matrix components, including collagen and fibronectin, that form the structural framework of the glomerulus. Beyond their structural and regulatory roles, mesangial cells are involved in several immunologic functions. They express a variety of receptors that can recognize immune complexes and subsequently mediate an inflammatory reaction. Their role in the immune response includes the production of a variety of cytokines and growth factors, which make them a key cellular component in the progression of several renal diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/BF00180754
has db xref: DOI:10.1038/s41581-021-00474-8
has db xref: DOI:10.1681/ASN.2019070724
has db xref: DOI:10.3389/fimmu.2022.1063497
has db xref: DOI:10.3389/fmed.2021.740527

Axiom
annotated source: mesangial cell
annotated property: hasDbXref
annotated target: ZFA:0009283
mapping justification: UnspecifiedMatching

mesangial cell on CELLxGENE CellGuide
type: Axiom
annotated source: mesangial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000650

podocyte
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0005751
subclass of: CL_0002522
subclass of: CL_1000450
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0005751
IAO_0000115: A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes.
description: Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approve…
has broad synonym: epithelial cell of visceral layer of glomerular capsule
has db xref: BTO:0002295
has db xref: FMA:70967
has db xref: ZFA:0009285
has exact synonym: glomerular podocyte
has exact synonym: glomerular visceral epithelial cell
has exact synonym: kidney podocyte
has exact synonym: renal podocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: podocyte
annotated property: IAO_0000115
annotated target: A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes.
has db xref: GOC:tfm
has db xref: https://doi.org/10.1101/2021.10.10.463829

Axiom
annotated source: podocyte
annotated property: description
annotated target: Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approve…
has db xref: DOI:10.1038/s41467-022-33748-1
has db xref: DOI:10.1038/s41572-020-0196-7
has db xref: DOI:10.1146/annurev-physiol-020911-153238
has db xref: DOI:10.1159/000481633
has db xref: DOI:10.3389/fcell.2021.771931

Axiom
annotated source: podocyte
annotated property: hasBroadSynonym
annotated target: epithelial cell of visceral layer of glomerular capsule
has db xref: FMA:70967

Axiom
annotated source: podocyte
annotated property: hasDbXref
annotated target: ZFA:0009285
mapping justification: UnspecifiedMatching

Axiom
annotated source: podocyte
annotated property: hasExactSynonym
annotated target: glomerular podocyte
has db xref: FMA:70967

podocyte on CELLxGENE CellGuide
type: Axiom
annotated source: podocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000653

Axiom
annotated source: podocyte
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM778.SHGJ.294

primary oocyte
type: Class
equivalent class: Class
  intersection of: oocyte
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0051321
subclass of: oocyte
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0051321
subclass of: Restriction
  on property: RO_0002202
  some values from: oogonial cell
IAO_0000115: A primary oocyte is an oocyte that has not completed female meosis I.
has db xref: BTO:0000512
has db xref: FMA:18645
has related synonym: primary oogonium
in subset: human reference atlas

Axiom
annotated source: primary oocyte
annotated property: subClassOf
annotated target: oocyte
is inferred: true

Axiom
annotated source: primary oocyte
annotated property: IAO_0000115
annotated target: A primary oocyte is an oocyte that has not completed female meosis I.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

secondary oocyte
type: Class
equivalent class: Class
  intersection of: oocyte
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0007147
subclass of: oocyte
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0007147
subclass of: Restriction
  on property: RO_0002202
  some values from: primary oocyte
IAO_0000115: A secondary oocyte is an oocyte that has not completed meiosis II.
has db xref: BTO:0003094
has db xref: FMA:18646
has related synonym: primary oogonium

Axiom
annotated source: secondary oocyte
annotated property: subClassOf
annotated target: oocyte
is inferred: true

Axiom
annotated source: secondary oocyte
annotated property: IAO_0000115
annotated target: A secondary oocyte is an oocyte that has not completed meiosis II.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

primary spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001394
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007140
subclass of: spermatocyte
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001394
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007140
IAO_0000115: A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes.
has db xref: BTO:0001115
has db xref: CALOHA:TS-2194
has db xref: FMA:72292

Axiom
annotated source: primary spermatocyte
annotated property: IAO_0000115
annotated target: A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

secondary spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001375
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007142
subclass of: spermatocyte
subclass of: eukaryotic cell
subclass of: haploid cell
subclass of: Restriction
  on property: RO_0002202
  some values from: primary spermatocyte
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007142
IAO_0000115: One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids.
has db xref: BTO:0000709
has db xref: CALOHA:TS-2195
has db xref: FBbt:00004941
has db xref: FMA:72293

Axiom
annotated source: secondary spermatocyte
annotated property: IAO_0000115
annotated target: One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: secondary spermatocyte
annotated property: hasDbXref
annotated target: FBbt:00004941
mapping justification: ManualMappingCuration

distal tip cell (sensu Nematoda)
type: Class
subclass of: mitogenic signaling cell

fenestrated endothelial cell
type: Class
equivalent class: Class
  intersection of: endothelial cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002064
subclass of: endothelial cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0002064
IAO_0000115: An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.
description: Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. Overa…
has db xref: ZFA:0009286
has exact synonym: window cell
in subset: cellxgene subset

Axiom
annotated source: fenestrated endothelial cell
annotated property: IAO_0000115
annotated target: An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.
has db xref: DOI:10.1007/978-3-211-99390-3_133

Axiom
annotated source: fenestrated endothelial cell
annotated property: description
annotated target: Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. Overa…
has db xref: DOI:10.1002/ar.1092200109
has db xref: DOI:10.1016/0306-4522(86)90162-4
has db xref: DOI:10.1016/j.devcel.2012.11.003
has db xref: DOI:10.1038/s41467-022-31571-2
has db xref: DOI:10.1152/ajprenal.90601.2008

Axiom
annotated source: fenestrated endothelial cell
annotated property: hasDbXref
annotated target: ZFA:0009286
mapping justification: UnspecifiedMatching

fenestrated endothelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: fenestrated endothelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000666

collagen secreting cell
type: Class
subclass of: extracellular matrix secreting cell
IAO_0000115: An extracellular matrix secreting cell that secretes collagen.
has db xref: ZFA:0009287
in subset: cellxgene subset

Axiom
annotated source: collagen secreting cell
annotated property: IAO_0000115
annotated target: An extracellular matrix secreting cell that secretes collagen.
has db xref: GOC:tfm

Axiom
annotated source: collagen secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009287
mapping justification: UnspecifiedMatching

pericyte
type: Class
subclass of: contractile cell
subclass of: supporting cell
subclass of: CL_0002320
subclass of: CL_0008034
IAO_0000115: An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells.
description: Pericytes, also known as Rouget cells, are a type of cell embedded in the wall of small blood vessels such as capillaries and venules. Not only do these cells share a basement membrane with endothelial cells, but they also have a direct physical contact with them, forming the blood-brain and blood-retinal barrier. They are an essential component of the neurovascular unit, a structure critical for maintaining brain homeostasis and a consistent neural microenvironment. Pericytes play a crucial role in the regulation of microvascular blood flow and permeability. They dynamically respond to changes in blood flow and can relax or contract like smooth muscle cells, thereby controlling capillary diameter and blood flow to the tissues. Moreover, pericytes contribute significantly to the regulation of endothelial cell proliferation and migration, implying their vital role in angiogenesis and the stability of blood vessels. Their ability to differentiate into multiple cell types, including fibroblasts, macrophages, and smooth muscle cells, reveals their importance in tissue repair and remodeling. Furthermore, pericytes have demonstrated functions in regulating immune and inflammatory responses. Pericytes also collaborate with endothelial cells in preserving the integrity of the blood-brain barrier, thus protecting the central nervous system from potential damage due to harmful substances and pathogens. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0002441
has db xref: FMA:63174
has db xref: ZFA:0009112
has exact synonym: ARC
has exact synonym: adventitial reticular cell
has exact synonym: cell of Rouget
has exact synonym: pericyte cell
has exact synonym: pericyte of Rouget
has related synonym: adventitial cell
in subset: cellxgene subset
in subset: human reference atlas
comment: Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A.

Axiom
annotated source: pericyte
annotated property: IAO_0000115
annotated target: An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells.
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0721662544
has db xref: MESH:D020286
has db xref: PMID:16807374
has db xref: PMID:17986482
has db xref: PMID:20024907

Axiom
annotated source: pericyte
annotated property: description
annotated target: Pericytes, also known as Rouget cells, are a type of cell embedded in the wall of small blood vessels such as capillaries and venules. Not only do these cells share a basement membrane with endothelial cells, but they also have a direct physical contact with them, forming the blood-brain and blood-retinal barrier. They are an essential component of the neurovascular unit, a structure critical for maintaining brain homeostasis and a consistent neural microenvironment. Pericytes play a crucial role in the regulation of microvascular blood flow and permeability. They dynamically respond to changes in blood flow and can relax or contract like smooth muscle cells, thereby controlling capillary diameter and blood flow to the tissues. Moreover, pericytes contribute significantly to the regulation of endothelial cell proliferation and migration, implying their vital role in angiogenesis and the stability of blood vessels. Their ability to differentiate into multiple cell types, including fibroblasts, macrophages, and smooth muscle cells, reveals their importance in tissue repair and remodeling. Furthermore, pericytes have demonstrated functions in regulating immune and inflammatory responses. Pericytes also collaborate with endothelial cells in preserving the integrity of the blood-brain barrier, thus protecting the central nervous system from potential damage due to harmful substances and pathogens. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/978-1-60761-938-3_2
has db xref: DOI:10.1016/j.cjtee.2020.02.006
has db xref: DOI:10.1177/0271678X15610340
has db xref: DOI:10.3389/fncel.2019.00282
has db xref: DOI:10.3390/biomedicines11020600

Axiom
annotated source: pericyte
annotated property: hasDbXref
annotated target: ZFA:0009112
mapping justification: UnspecifiedMatching

Axiom
annotated source: pericyte
annotated property: hasExactSynonym
annotated target: ARC
has db xref: PMID:17986482

pericyte on CELLxGENE CellGuide
type: Axiom
annotated source: pericyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000669

primordial germ cell
type: Class
equivalent class: Class
  intersection of: germ line cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000922
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048870
subclass of: germ line cell
subclass of: motile cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000922
IAO_0000115: A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
has db xref: FMA:70567
has db xref: ZFA:0009288
has exact synonym: gonocyte
has exact synonym: primitive germ cell
in subset: cellxgene subset

Axiom
annotated source: primordial germ cell
annotated property: subClassOf
annotated target: germ line cell
is inferred: true

Axiom
annotated source: primordial germ cell
annotated property: subClassOf
annotated target: motile cell
is inferred: true

Axiom
annotated source: primordial germ cell
annotated property: IAO_0000115
annotated target: A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
has db xref: GOC:tfm
has db xref: PMID:1381289

Axiom
annotated source: primordial germ cell
annotated property: hasDbXref
annotated target: ZFA:0009288
mapping justification: UnspecifiedMatching

centripetally migrating follicle cell
type: Class
subclass of: follicle cell of egg chamber
IAO_0000115: A follicle cell that migrates from the dorso-anterior part of the oocyte associated follicular epithelium, in between the nurse cells and the oocyte, and participates in the formation of the operculum.
has db xref: FBbt:00004906
has exact synonym: centripetal follicle cell

Axiom
annotated source: centripetally migrating follicle cell
annotated property: IAO_0000115
annotated target: A follicle cell that migrates from the dorso-anterior part of the oocyte associated follicular epithelium, in between the nurse cells and the oocyte, and participates in the formation of the operculum.
has db xref: PMID:36807509

Axiom
annotated source: centripetally migrating follicle cell
annotated property: hasDbXref
annotated target: FBbt:00004906
mapping justification: ManualMappingCuration

female gamete
type: Class
subclass of: female germ cell
subclass of: gamete
IAO_0000115: A mature sexual reproductive cell of the female germline.

Axiom
annotated source: female gamete
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

Axiom
annotated source: female gamete
annotated property: IAO_0000115
annotated target: A mature sexual reproductive cell of the female germline.
has db xref: GOC:tfm

gut absorptive cell
type: Class
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001277
IAO_0000115: Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.
has db xref: ZFA:0009289
in subset: cellxgene subset

Axiom
annotated source: gut absorptive cell
annotated property: IAO_0000115
annotated target: Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.
has db xref: JB:jb

Axiom
annotated source: gut absorptive cell
annotated property: hasDbXref
annotated target: ZFA:0009289
mapping justification: UnspecifiedMatching

commissural neuron
type: Class
subclass of: CL_2000029
IAO_0000115: A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates.
comment: Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development.

Axiom
annotated source: commissural neuron
annotated property: IAO_0000115
annotated target: A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates.
has db xref: PMID:17560562
has db xref: PMID:31693445

Axiom
annotated source: commissural neuron
annotated property: comment
annotated target: Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development.
has db xref: PMID:25960414
has db xref: PMID:27532244
has db xref: PMID:31514748
has db xref: PMID:33438755

glutamatergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0061535
subclass of: secretory cell
subclass of: neuron
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0061535
IAO_0000115: A neuron that is capable of some neurotansmission by glutamate secretion.
has db xref: FBbt:00100291
has db xref: WBbt:0006829
has db xref: ZFA:0009290
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: glutamatergic neuron
annotated property: hasDbXref
annotated target: FBbt:00100291
mapping justification: ManualMappingCuration

Axiom
annotated source: glutamatergic neuron
annotated property: hasDbXref
annotated target: ZFA:0009290
mapping justification: UnspecifiedMatching

muscle precursor cell
type: Class
equivalent class: Class
  intersection of: CL_0011115
  intersection of: Restriction
    on property: RO_0002203
    some values from: muscle cell
subclass of: eukaryotic cell
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002202
  some values from: mesodermal cell
subclass of: Restriction
  on property: RO_0002203
  some values from: muscle cell
IAO_0000115: A non-terminally differentiated cell that is capable of developing into a muscle cell.
description: Muscle precursor cells, commonly referred to as myogenic progenitor cells or myoblasts, play a pivotal role in the intricate processes of muscle regeneration and development. As undifferentiated cells, they harbor the potential to evolve into distinct specialized cells, specifically the muscle cell or myocyte. Their crucial contribution lies in guiding the transformation of the mesodermal layer, one of the three primary germ cell layers in the early embryo, into fully developed skeletal muscle tissues during embryonic development. Muscle precursor cells are characterized by their proliferative capacity and rapid differentiation into mature myocytes. They fuse into myotubes, culminating in the formation of muscle fibers. Their responsiveness to signals such as insulin-like growth factors, transforming growth factor-β, and neural inputs enables precise control over their proliferation and differentiation. This regenerative capacity equips them with the ability to repair injured or damaged muscle tissue, a critical function in preserving muscle homeostasis and overall function. These cells also actively contribute to adaptive responses, such as muscle growth and strengthening, in reaction to factors like training or aging. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009291
in subset: cellxgene subset

Axiom
annotated source: muscle precursor cell
annotated property: IAO_0000115
annotated target: A non-terminally differentiated cell that is capable of developing into a muscle cell.
has db xref: GOC:add

Axiom
annotated source: muscle precursor cell
annotated property: description
annotated target: Muscle precursor cells, commonly referred to as myogenic progenitor cells or myoblasts, play a pivotal role in the intricate processes of muscle regeneration and development. As undifferentiated cells, they harbor the potential to evolve into distinct specialized cells, specifically the muscle cell or myocyte. Their crucial contribution lies in guiding the transformation of the mesodermal layer, one of the three primary germ cell layers in the early embryo, into fully developed skeletal muscle tissues during embryonic development. Muscle precursor cells are characterized by their proliferative capacity and rapid differentiation into mature myocytes. They fuse into myotubes, culminating in the formation of muscle fibers. Their responsiveness to signals such as insulin-like growth factors, transforming growth factor-β, and neural inputs enables precise control over their proliferation and differentiation. This regenerative capacity equips them with the ability to repair injured or damaged muscle tissue, a critical function in preserving muscle homeostasis and overall function. These cells also actively contribute to adaptive responses, such as muscle growth and strengthening, in reaction to factors like training or aging. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1089/ars.2007.1792
has db xref: DOI:10.1152/physrev.00061.2017
has db xref: https://www.sciencedirect.com/topics/engineering/muscle-precursor-cell

Axiom
annotated source: muscle precursor cell
annotated property: hasDbXref
annotated target: ZFA:0009291
mapping justification: UnspecifiedMatching

muscle precursor cell on CELLxGENE CellGuide
type: Axiom
annotated source: muscle precursor cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000680

radial glial cell
type: Class
subclass of: glial cell
subclass of: Restriction
  on property: RO_0002202
  some values from: neurecto-epithelial cell
IAO_0000115: A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration.
has db xref: ZFA:0009292
has narrow synonym: forebrain radial glial cell
in subset: cellxgene subset
comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of radial glial cells acting as neural progenitors throughout life.

Axiom
annotated source: radial glial cell
annotated property: IAO_0000115
annotated target: A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration.
has db xref: GOC:dph

Axiom
annotated source: radial glial cell
annotated property: hasDbXref
annotated target: ZFA:0009292
mapping justification: UnspecifiedMatching

cerebrospinal fluid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0033326
subclass of: neurecto-epithelial cell
subclass of: CL_1100001
subclass of: Restriction
  on property: RO_0002202
  some values from: migratory neural crest cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0033326
IAO_0000115: A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid.
has db xref: ZFA:0009295

Axiom
annotated source: cerebrospinal fluid secreting cell
annotated property: IAO_0000115
annotated target: A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid.
has db xref: GOC:tfm

Axiom
annotated source: cerebrospinal fluid secreting cell
annotated property: hasDbXref
annotated target: ZFA:0009295
mapping justification: UnspecifiedMatching

stellate interneuron
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0070010
subclass of: interneuron
subclass of: stellate neuron
IAO_0000115: Any interneuron that has characteristic some stellate morphology.
has db xref: ZFA:0009297
in subset: BDS subset

Axiom
annotated source: stellate interneuron
annotated property: IAO_0000115
annotated target: Any interneuron that has characteristic some stellate morphology.
has db xref: FBC:Autogenerated

Axiom
annotated source: stellate interneuron
annotated property: hasDbXref
annotated target: ZFA:0009297
mapping justification: UnspecifiedMatching

Cajal-Retzius cell
type: Class
subclass of: glutamatergic neuron
subclass of: CL_0012001
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0070006
IAO_0000115: A type of transient, early-born glutamatergic neuron located primarily in the marginal zone (future layer I) of the developing cerebral cortex and hippocampus in vertebrates. it is characterized by a bipolar morphology with an elongated soma, a single thick dendrite oriented toward the pial surface, and a long, thin axon that extends tangentially to form horizontal plexuses across the cortical surface. It is important for the multiple developmental processes including migration, dendritogenesis and synaptogenesis. It typically undergoes programmed cell death following cortical maturation with species- and region specific patterns of survival. In mice, it is predominantly observed in the hippocampal formation, particularly in the stratum lacunosum-moleculare and outer molecular layer of the dentate gyrus (van Bruggen et al., 2023). In contrast, in humans, a second morphologically distinct subpopulation emerges mid-gestation and persists postnatally, with surviving cells observed in the cortical sulci and the hippocampus.
contributor: https://orcid.org/0000-0001-7258-9596
description: Cajal-Retzius cells are unique, early-born neurons found within the developing cerebral cortex and hippocampus. They are named after Santiago Ramon y Cajal and Gustaf Retzius, who first discovered them independently in the late 19th century. These neurons are characterized by horizontally oriented bipolar or multipolar cell bodies, facilitating their function in structuring the architecture of the cortex. The primary role of Cajal-Retzius cells is to mediate the correct formation of the cortical layers in the developing brain. They accomplish this chiefly through the secretion of the extracellular matrix protein Reelin, which interacts with receptors on migrating neurons to control neuronal migration and position. The Reelin signal provided by Cajal-Retzius cells is essential to establish the cortical plate, where new neurons arising from the ventricular zone accumulate and form the recognizable layered structure of the cortical region. Disruptions in Reelin signaling can lead to reeler-like phenotypes characterized by inversion of cortical layers, demonstrating the importance of these cells during normal brain development. In addition to layer formation, Cajal-Retzius cells also play a role in synaptic plasticity, which is a key aspect of learning, memory, and cognitive function. It has been suggested that these cells are involved in establishing the first functional synapses in the developing cortex, providing initial neural network activity. Furthermore, they have been linked to the modulation of gamma-aminobutyric acid (GABA) trafficking, excitatory-inhibitory balance, and thus, the fine-tune of the neural network activity during early postnatal life. Despite their disappearance shortly after birth in rodents and during early adolescence in humans, Cajal-Retzius cells lay the groundwork for the structure and functionality of the brain's cortical region. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, …
has db xref: ZFA:0009300
has exact synonym: CR cells
has exact synonym: Horizontal cells of Cajal
in subset: cellxgene subset
comment: While previously called 'pioneer neurons' of the marginal zone, Cajal-Retzius cells are differentiated from pioneer neurons (which are Reln-negative) by their Reln-immunoreactivity.

Axiom
annotated source: Cajal-Retzius cell
annotated property: IAO_0000115
annotated target: A type of transient, early-born glutamatergic neuron located primarily in the marginal zone (future layer I) of the developing cerebral cortex and hippocampus in vertebrates. it is characterized by a bipolar morphology with an elongated soma, a single thick dendrite oriented toward the pial surface, and a long, thin axon that extends tangentially to form horizontal plexuses across the cortical surface. It is important for the multiple developmental processes including migration, dendritogenesis and synaptogenesis. It typically undergoes programmed cell death following cortical maturation with species- and region specific patterns of survival. In mice, it is predominantly observed in the hippocampal formation, particularly in the stratum lacunosum-moleculare and outer molecular layer of the dentate gyrus (van Bruggen et al., 2023). In contrast, in humans, a second morphologically distinct subpopulation emerges mid-gestation and persists postnatally, with surviving cells observed in the cortical sulci and the hippocampus.
has db xref: PMID:10600995
has db xref: PMID:34047341
has db xref: PMID:36774666
has db xref: PMID:37775311
has db xref: PMID:9728912

Axiom
annotated source: Cajal-Retzius cell
annotated property: description
annotated target: Cajal-Retzius cells are unique, early-born neurons found within the developing cerebral cortex and hippocampus. They are named after Santiago Ramon y Cajal and Gustaf Retzius, who first discovered them independently in the late 19th century. These neurons are characterized by horizontally oriented bipolar or multipolar cell bodies, facilitating their function in structuring the architecture of the cortex. The primary role of Cajal-Retzius cells is to mediate the correct formation of the cortical layers in the developing brain. They accomplish this chiefly through the secretion of the extracellular matrix protein Reelin, which interacts with receptors on migrating neurons to control neuronal migration and position. The Reelin signal provided by Cajal-Retzius cells is essential to establish the cortical plate, where new neurons arising from the ventricular zone accumulate and form the recognizable layered structure of the cortical region. Disruptions in Reelin signaling can lead to reeler-like phenotypes characterized by inversion of cortical layers, demonstrating the importance of these cells during normal brain development. In addition to layer formation, Cajal-Retzius cells also play a role in synaptic plasticity, which is a key aspect of learning, memory, and cognitive function. It has been suggested that these cells are involved in establishing the first functional synapses in the developing cortex, providing initial neural network activity. Furthermore, they have been linked to the modulation of gamma-aminobutyric acid (GABA) trafficking, excitatory-inhibitory balance, and thus, the fine-tune of the neural network activity during early postnatal life. Despite their disappearance shortly after birth in rodents and during early adolescence in humans, Cajal-Retzius cells lay the groundwork for the structure and functionality of the brain's cortical region. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, …
has db xref: DOI:10.1016/S0166-2236(97)01164-8
has db xref: DOI:10.1038/nrn2009
has db xref: DOI:10.1111/j.1440-169X.2009.01102.x
has db xref: DOI:10.1155/2014/597395
has db xref: DOI:10.1523/JNEUROSCI.1407-14.2014

Axiom
annotated source: Cajal-Retzius cell
annotated property: hasDbXref
annotated target: ZFA:0009300
mapping justification: UnspecifiedMatching

Axiom
annotated source: Cajal-Retzius cell
annotated property: hasExactSynonym
annotated target: CR cells
has db xref: WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753

Axiom
annotated source: Cajal-Retzius cell
annotated property: hasExactSynonym
annotated target: Horizontal cells of Cajal
has db xref: WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753

Axiom
annotated source: Cajal-Retzius cell
annotated property: comment
annotated target: While previously called 'pioneer neurons' of the marginal zone, Cajal-Retzius cells are differentiated from pioneer neurons (which are Reln-negative) by their Reln-immunoreactivity.
has db xref: PMID:10600995

Cajal-Retzius cell on CELLxGENE CellGuide
type: Axiom
annotated source: Cajal-Retzius cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000695

PP cell
type: Class
subclass of: enteroendocrine cell
subclass of: peptide hormone secreting cell
IAO_0000115: A cell that stores and secretes pancreatic polypeptide hormone.
description: PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:62938
has db xref: FMA:83409
has exact synonym: type F enteroendocrine cell
in subset: cellxgene subset

Axiom
annotated source: PP cell
annotated property: IAO_0000115
annotated target: A cell that stores and secretes pancreatic polypeptide hormone.
has db xref: GOC:tfm
has db xref: JB:jb
has db xref: PMID:15153415

Axiom
annotated source: PP cell
annotated property: description
annotated target: PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.febslet.2014.07.005
has db xref: DOI:10.1016/j.mce.2015.06.028
has db xref: DOI:10.1038/s41580-020-00317-7
has db xref: DOI:10.1210/jc.2003-030630
has db xref: DOI:10.1369/00221554155835

PP cell on CELLxGENE CellGuide
type: Axiom
annotated source: PP cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000696

dopaminergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0061527
subclass of: CL_4033050
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0061527
IAO_0000115: A neuron that releases dopamine as a neurotransmitter.
has db xref: BTO:0004032
has db xref: FBbt:00005131
has db xref: FMA:84787
has db xref: MESH:D059290
has db xref: WBbt:0006746
has db xref: ZFA:0009301
has exact synonym: dopaminergic cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: dopaminergic neuron
annotated property: IAO_0000115
annotated target: A neuron that releases dopamine as a neurotransmitter.
has db xref: GOC:dhill

Axiom
annotated source: dopaminergic neuron
annotated property: hasDbXref
annotated target: FBbt:00005131
mapping justification: ManualMappingCuration

Axiom
annotated source: dopaminergic neuron
annotated property: hasDbXref
annotated target: ZFA:0009301
mapping justification: UnspecifiedMatching

endothelial tip cell
type: Class
subclass of: blood vessel endothelial cell
IAO_0000115: A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels.
description: Endothelial tip cells are a specialized type of cell that play a crucial role in angiogenesis, the formation of new blood vessels from the existing vasculature. These cells are located at the ends of growing capillary sprouts, their position giving them the term "tip" cells. Endothelial tip cells are characterized by a number of attributes which facilitate them to lead the way in angiogenesis: They have a highly dynamic, large, and polarized shape, and they extend numerous long and mobile filopodia, or finger-like projections, which continuously probe the extracellular microenvironment for cues that control the growth and movement of the cells. The filopodia are equipped with several receptors, including Vascular Endothelial Growth Factor Receptor (VEGFR) -2 and -3, which respond to guidance signals during angiogenesis. Their distinctive morphology with a broad leading edge and small cell body trailing behind helps in efficiently moving in the right direction responding to cues. The function of endothelial tip cells is fundamental to the angiogenesis process. Guiding the sprouting vessel, they direct the subsequent proliferation and migration of the stalk cells, which follow the tip cells and form the body of the sprout. These tip cells do not proliferate, but instead, dictate the division of stalk cells, leading to the elongation of the sprout. They also help in lumen formation. The guidance and sprouting decisions of endothelial tip cells are critical for creating a functional and efficient network of vessels that can appropriately supply oxygen and nutrients to tissues. Notably, tip cells play a role in pathological conditions such as tumor angiogenesis and eye diseases, making them an important area of research in cell biology and medicine. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some su…
has db xref: ZFA:0009303
in subset: cellxgene subset

Axiom
annotated source: endothelial tip cell
annotated property: IAO_0000115
annotated target: A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels.
has db xref: PMID:15376331

Axiom
annotated source: endothelial tip cell
annotated property: description
annotated target: Endothelial tip cells are a specialized type of cell that play a crucial role in angiogenesis, the formation of new blood vessels from the existing vasculature. These cells are located at the ends of growing capillary sprouts, their position giving them the term "tip" cells. Endothelial tip cells are characterized by a number of attributes which facilitate them to lead the way in angiogenesis: They have a highly dynamic, large, and polarized shape, and they extend numerous long and mobile filopodia, or finger-like projections, which continuously probe the extracellular microenvironment for cues that control the growth and movement of the cells. The filopodia are equipped with several receptors, including Vascular Endothelial Growth Factor Receptor (VEGFR) -2 and -3, which respond to guidance signals during angiogenesis. Their distinctive morphology with a broad leading edge and small cell body trailing behind helps in efficiently moving in the right direction responding to cues. The function of endothelial tip cells is fundamental to the angiogenesis process. Guiding the sprouting vessel, they direct the subsequent proliferation and migration of the stalk cells, which follow the tip cells and form the body of the sprout. These tip cells do not proliferate, but instead, dictate the division of stalk cells, leading to the elongation of the sprout. They also help in lumen formation. The guidance and sprouting decisions of endothelial tip cells are critical for creating a functional and efficient network of vessels that can appropriately supply oxygen and nutrients to tissues. Notably, tip cells play a role in pathological conditions such as tumor angiogenesis and eye diseases, making them an important area of research in cell biology and medicine. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some su…
has db xref: DOI:10.1016/j.devcel.2021.06.021
has db xref: DOI:10.1016/j.semcdb.2014.04.009
has db xref: DOI:10.1038/nrclinonc.2009.64
has db xref: DOI:10.1101/cshperspect.a006569

Axiom
annotated source: endothelial tip cell
annotated property: hasDbXref
annotated target: ZFA:0009303
mapping justification: UnspecifiedMatching

endothelial tip cell on CELLxGENE CellGuide
type: Axiom
annotated source: endothelial tip cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000704

R7 photoreceptor cell
type: Class
subclass of: UV sensitive photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000971
has db xref: FBbt:00004225
has exact synonym: R7 cell

Axiom
annotated source: R7 photoreceptor cell
annotated property: hasDbXref
annotated target: FBbt:00004225
mapping justification: ManualMappingCuration

leptomeningeal cell
type: Class
equivalent class: Class
  intersection of: extracellular matrix secreting cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0003210
subclass of: extracellular matrix secreting cell
subclass of: CL_0002319
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0003210
IAO_0000115: Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus.
has db xref: ZFA:0009305
has related synonym: leptomemingeal cell
in subset: cellxgene subset

Axiom
annotated source: leptomeningeal cell
annotated property: subClassOf
annotated target: extracellular matrix secreting cell
is inferred: true

Axiom
annotated source: leptomeningeal cell
annotated property: IAO_0000115
annotated target: Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus.
has db xref: JB:jb

Axiom
annotated source: leptomeningeal cell
annotated property: hasDbXref
annotated target: ZFA:0009305
mapping justification: UnspecifiedMatching

R8 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000971
has db xref: FBbt:00004227
has exact synonym: R8 cell

Axiom
annotated source: R8 photoreceptor cell
annotated property: hasDbXref
annotated target: FBbt:00004227
mapping justification: ManualMappingCuration

neurecto-epithelial cell
type: Class
equivalent class: Class
  intersection of: CL_0002077
  intersection of: Restriction
    on property: RO_0002202
    some values from: neurectodermal cell
subclass of: columnar/cuboidal epithelial cell
subclass of: CL_0002077
subclass of: Restriction
  on property: RO_0002202
  some values from: neurectodermal cell
IAO_0000115: Epithelial cells derived from neural plate and neural crest.
has broad synonym: neuroepithelial cell
has db xref: BTO:0004301
has db xref: FMA:70557
comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).

Axiom
annotated source: neurecto-epithelial cell
annotated property: IAO_0000115
annotated target: Epithelial cells derived from neural plate and neural crest.
has db xref: GOC:tfm

cumulus granulosa cell
type: Class
subclass of: protein secreting cell
subclass of: granulosa cell
subclass of: UBERON_0004120
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_4033084
IAO_0000115: Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle.
has db xref: BTO:0002236
has db xref: MESH:D054885
has exact synonym: cumulus cell
in subset: human reference atlas

Axiom
annotated source: cumulus granulosa cell
annotated property: IAO_0000115
annotated target: Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle.
has db xref: GOC:tfm
has db xref: http://www.copewithcytokines.org/cope.cgi

embryonic crystal cell
type: Class
subclass of: crystal cell
subclass of: CL_0011008
IAO_0000115: A crystal cell that derives from the embryonic head mesoderm.
has db xref: FBbt:00001690

Axiom
annotated source: embryonic crystal cell
annotated property: hasDbXref
annotated target: FBbt:00001690
mapping justification: ManualMappingCuration

lymph gland crystal cell
type: Class
subclass of: crystal cell
subclass of: lymph gland hemocyte
IAO_0000115: A crystal cell that derives from the larval lymph gland.

compound eye cone cell
type: Class
subclass of: crystallin accumulating cell
subclass of: CL_0002319
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000971
IAO_0000115: A cell of an ommatidium that secretes lens materials.
has db xref: FBbt:00004193
has exact synonym: Semper cell
has related synonym: cone cell (sensu Endopterygota)
comment: Not to be confused with the Semper cells of the Semper organ found in gastropods.

Axiom
annotated source: compound eye cone cell
annotated property: IAO_0000115
annotated target: A cell of an ommatidium that secretes lens materials.
has db xref: PMID:34343526
has db xref: doi:10.1017/CBO9780511818202.023

Axiom
annotated source: compound eye cone cell
annotated property: hasDbXref
annotated target: FBbt:00004193
mapping justification: ManualMappingCuration

Axiom
annotated source: compound eye cone cell
annotated property: comment
annotated target: Not to be confused with the Semper cells of the Semper organ found in gastropods.
has db xref: doi:10.1242/jcs.s3-105.71.331

cystoblast
type: Class
subclass of: eukaryotic cell
subclass of: germ cell
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 6656

somatic stem cell
type: Class
equivalent class: Class
  intersection of: stem cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048103
subclass of: stem cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048103
IAO_0000115: A stem cell that can give rise to cell types of the body other than those of the germ-line.
description: Somatic stem cells, also known as adult stem cells, are undifferentiated cells found throughout the body post-embryonic development. They reside in specialized niches within tissues such as the bone marrow, brain, muscles, skin, and liver. Fundamentally, these cells possess the ability to self-renew, maintaining their numbers, and to generate differentiated cells that replace dying cells and repair damaged tissues. The potency of somatic stem cells varies based on their tissue of origin. For instance, hematopoietic stem cells in the bone marrow exhibit multipotency, giving rise to all blood cell types. Conversely, muscle stem cells display unipotency, generating only muscle cells. Somatic stem cells respond to environmental signals that regulate their quiescence, activation, and differentiation states. In response to tissue injury, they proliferate and differentiate into specific mature cell types to replace lost or damaged cells. Intricate mechanisms ensure a delicate balance between self-renewal and differentiation, guiding tissue maintenance and repair without risking aberrant cell proliferation leading to tumor formation. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: CALOHA:TS-2086
has db xref: MESH:D053687
has db xref: ZFA:0009307
in subset: cellxgene subset

Axiom
annotated source: somatic stem cell
annotated property: IAO_0000115
annotated target: A stem cell that can give rise to cell types of the body other than those of the germ-line.
has db xref: GO:0048103

Axiom
annotated source: somatic stem cell
annotated property: description
annotated target: Somatic stem cells, also known as adult stem cells, are undifferentiated cells found throughout the body post-embryonic development. They reside in specialized niches within tissues such as the bone marrow, brain, muscles, skin, and liver. Fundamentally, these cells possess the ability to self-renew, maintaining their numbers, and to generate differentiated cells that replace dying cells and repair damaged tissues. The potency of somatic stem cells varies based on their tissue of origin. For instance, hematopoietic stem cells in the bone marrow exhibit multipotency, giving rise to all blood cell types. Conversely, muscle stem cells display unipotency, generating only muscle cells. Somatic stem cells respond to environmental signals that regulate their quiescence, activation, and differentiation states. In response to tissue injury, they proliferate and differentiate into specific mature cell types to replace lost or damaged cells. Intricate mechanisms ensure a delicate balance between self-renewal and differentiation, guiding tissue maintenance and repair without risking aberrant cell proliferation leading to tumor formation. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.stem.2011.10.004
has db xref: DOI:10.1159/000345615
has db xref: DOI:10.1186/s13287-019-1165-5
has db xref: DOI:10.15283/ijsc19127
has db xref: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/adult-stem-cell

Axiom
annotated source: somatic stem cell
annotated property: hasDbXref
annotated target: ZFA:0009307
mapping justification: UnspecifiedMatching

somatic stem cell on CELLxGENE CellGuide
type: Axiom
annotated source: somatic stem cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000723

heterocyst
type: Class
subclass of: prokaryotic cell
subclass of: nitrogen fixing cell
IAO_0000115: A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions.
has db xref: BTO:0000600

Axiom
annotated source: heterocyst
annotated property: IAO_0000115
annotated target: A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions.
has db xref: MA:ma

nitrogen fixing cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0009399
subclass of: cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0009399
IAO_0000115: Any cell that is capable of some nitrogen fixation.

Axiom
annotated source: nitrogen fixing cell
annotated property: IAO_0000115
annotated target: Any cell that is capable of some nitrogen fixation.
has db xref: FBC:Autogenerated

chlamydospore
type: Class
subclass of: fungal asexual spore
IAO_0000115: An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material.
comment: Considering obsoleting as sometimes used to refer to protozoans too. But reference indicates term was intended for fungus.

Axiom
annotated source: chlamydospore
annotated property: IAO_0000115
annotated target: An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material.
has db xref: GOC:tfm
has db xref: ISBN:085199377X

leading edge cell
type: Class
subclass of: epithelial cell
IAO_0000115: A cell at the front of a migrating epithelial sheet.

Axiom
annotated source: leading edge cell
annotated property: IAO_0000115
annotated target: A cell at the front of a migrating epithelial sheet.
has db xref: MA:ma

urothelial cell
type: Class
equivalent class: Class
  intersection of: transitional epithelial cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000365
subclass of: stratified epithelial cell
subclass of: transitional epithelial cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000365
IAO_0000115: A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria.
description: Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis. (This extended descripti…
has db xref: FMA:84127
has db xref: ZFA:0009308
has narrow synonym: urinary tract transitional epithelial cell
in subset: cellxgene subset

Axiom
annotated source: urothelial cell
annotated property: IAO_0000115
annotated target: A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria.
has db xref: GOC:tfm
has db xref: MA:ma
has db xref: doi:10.1038/s41385-022-00565-0

Axiom
annotated source: urothelial cell
annotated property: description
annotated target: Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis. (This extended descripti…
has db xref: DOI:10.1002/nau.22195
has db xref: DOI:10.1038/ki.2009.73
has db xref: DOI:10.1038/ncpuro0672
has db xref: DOI:10.1038/s41579-020-0324-0
has db xref: DOI:10.1152/physrev.00041.2019

Axiom
annotated source: urothelial cell
annotated property: hasDbXref
annotated target: ZFA:0009308
mapping justification: UnspecifiedMatching

urothelial cell on CELLxGENE CellGuide
type: Axiom
annotated source: urothelial cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000731

lymph gland plasmatocyte
type: Class
subclass of: plasmatocyte
subclass of: lymph gland hemocyte
IAO_0000115: A plasmatocyte that derives from the larval lymph gland.

lymph gland hemocyte
type: Class
subclass of: hemocyte (sensu Arthropoda)
IAO_0000115: A hemocyte that derives from the larval lymph gland.
has db xref: FBbt:00005917

Axiom
annotated source: lymph gland hemocyte
annotated property: IAO_0000115
annotated target: A hemocyte that derives from the larval lymph gland.
has db xref: doi:10.1242/dev.00702

Axiom
annotated source: lymph gland hemocyte
annotated property: hasDbXref
annotated target: FBbt:00005917
mapping justification: ManualMappingCuration

striated muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0030017
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001410
subclass of: muscle cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0030017
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001410
disjoint with: CL_0008000
IAO_0000115: Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
has db xref: BTO:0002916
has db xref: CALOHA:TS-2157
has db xref: FMA:86936
has db xref: ZFA:0005784

Axiom
annotated source: striated muscle cell
annotated property: IAO_0000115
annotated target: Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
has db xref: GOC:tfm
has db xref: ISBN:0721662544

Axiom
annotated source: striated muscle cell
annotated property: hasDbXref
annotated target: ZFA:0005784
mapping justification: UnspecifiedMatching

leukocyte
type: Class
equivalent class: Class
  intersection of: hematopoietic cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002505
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001667
subclass of: BFO_0000002
subclass of: motile cell
subclass of: eukaryotic cell
subclass of: hematopoietic cell
subclass of: CL_0002242
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002405
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: RO_0002202
  some values from: hematopoietic stem cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001667
IAO_0000115: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
has db xref: BTO:0000751
has db xref: CALOHA:TS-0549
has db xref: FMA:62852
has db xref: MESH:D007962
has db xref: NCIT:C12529
has db xref: ZFA:0009309
has exact synonym: WBC
has exact synonym: leucocyte
has exact synonym: white blood cell
has related synonym: immune cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: leukocyte
annotated property: subClassOf
annotated target: hematopoietic cell
is inferred: true

Axiom
annotated source: leukocyte
annotated property: IAO_0000115
annotated target: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:978-0-323-05290-0

Axiom
annotated source: leukocyte
annotated property: hasDbXref
annotated target: ZFA:0009309
mapping justification: UnspecifiedMatching

Axiom
annotated source: leukocyte
annotated property: hasExactSynonym
annotated target: WBC
has db xref: PMID:40794848
has synonym type: OMO_0003000

retinal ganglion cell
type: Class
subclass of: BFO_0000002
subclass of: neuron
subclass of: Restriction
  on property: RO_0002100
  some values from: UBERON_0000966
IAO_0000115: The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.
description: Retinal ganglion cells (RGCs) are a type of neuron located near the inner surface of the retina, playing a critical role in the visual pathway. There are approximately 1 million RGCs in a typical human eye, each receiving inputs from multiple photoreceptor cells. As the only neurons in the retina that send information to the brain, they are the final output neurons of the vertebrate retina, and their axons constitute the majority of fibers in the optic nerve. The primary function of RGCs is to receive visual information from photoreceptors via intermediary bipolar and amacrine cells, process it, and transmit it to the brain through their axons. The information that RGCs relay encompasses various aspects of the visual field, including color, contrast, brightness, and motion. A diverse population of RGCs, up to 30 distinct subtypes, each contributes to a specific aspect of vision, such as object motion, edge detection, or color contrast, illustrating the complexity of visual data processing that occurs already at the retinal level. RGCs also play a role in the regulation of circadian rhythms and the pupillary light reflex. Some RGCs contain the photopigment melanopsin and respond directly to light, separately from the retinal rod and cone cells found in the outer retina. These photosensitive RGCs are primarily involved in subconscious vision, particularly the regulation of circadian rhythms and the pupillary light reflex in response to changes in ambient light intensity. Hence, RGCs serve a highly specialized and diverse role in transmitting visual information and regulating light-dependent responses, view modalities, and key physiological processes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0001800
has db xref: FMA:67765
has db xref: MESH:D012165
has db xref: ZFA:0009310
has exact synonym: gangliocyte
has exact synonym: ganglion cell of retina
has related synonym: RGC
has related synonym: RGCs
in subset: cellxgene subset
in subset: eye upper slim
in subset: human reference atlas

Axiom
annotated source: retinal ganglion cell
annotated property: IAO_0000115
annotated target: The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.
has db xref: GOC:dph

Axiom
annotated source: retinal ganglion cell
annotated property: description
annotated target: Retinal ganglion cells (RGCs) are a type of neuron located near the inner surface of the retina, playing a critical role in the visual pathway. There are approximately 1 million RGCs in a typical human eye, each receiving inputs from multiple photoreceptor cells. As the only neurons in the retina that send information to the brain, they are the final output neurons of the vertebrate retina, and their axons constitute the majority of fibers in the optic nerve. The primary function of RGCs is to receive visual information from photoreceptors via intermediary bipolar and amacrine cells, process it, and transmit it to the brain through their axons. The information that RGCs relay encompasses various aspects of the visual field, including color, contrast, brightness, and motion. A diverse population of RGCs, up to 30 distinct subtypes, each contributes to a specific aspect of vision, such as object motion, edge detection, or color contrast, illustrating the complexity of visual data processing that occurs already at the retinal level. RGCs also play a role in the regulation of circadian rhythms and the pupillary light reflex. Some RGCs contain the photopigment melanopsin and respond directly to light, separately from the retinal rod and cone cells found in the outer retina. These photosensitive RGCs are primarily involved in subconscious vision, particularly the regulation of circadian rhythms and the pupillary light reflex in response to changes in ambient light intensity. Hence, RGCs serve a highly specialized and diverse role in transmitting visual information and regulating light-dependent responses, view modalities, and key physiological processes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/cne.10652
has db xref: DOI:10.1016/j.neuron.2019.07.016
has db xref: DOI:10.1038/nature16468
has db xref: DOI:10.1111/j.1444-0938.2010.00479.x
has db xref: DOI:10.1146/annurev-neuro-071714-034120

Axiom
annotated source: retinal ganglion cell
annotated property: hasDbXref
annotated target: ZFA:0009310
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal ganglion cell
annotated property: hasRelatedSynonym
annotated target: RGC
has db xref: doi:10.1038/s41598-020-66092-9
has synonym type: OMO_0003000

Axiom
annotated source: retinal ganglion cell
annotated property: hasRelatedSynonym
annotated target: RGCs
has db xref: doi:10.1038/s41598-020-66092-9
has synonym type: OMO_0003000
has synonym type: OMO_0003004

retinal ganglion cell on CELLxGENE CellGuide
type: Axiom
annotated source: retinal ganglion cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000740

cardiac muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0007100
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0030017
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0002478
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0060047
subclass of: striated muscle cell
subclass of: CL_0002494
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0002478
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0060047
subclass of: Restriction
  on property: RO_0002202
  some values from: cardiac muscle myoblast
IAO_0000115: Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
description: Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to…
has broad synonym: cardiocyte
has db xref: BTO:0001539
has db xref: CALOHA:TS-0115
has db xref: FMA:14067
has db xref: MESH:D032383
has db xref: ZFA:0009316
has exact synonym: cardiac muscle fiber
has exact synonym: cardiac myocyte
has exact synonym: cardiomyocyte
has exact synonym: heart muscle cell
in subset: cellxgene subset
in subset: human reference atlas
comment: This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.

Axiom
annotated source: cardiac muscle cell
annotated property: IAO_0000115
annotated target: Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
has db xref: GOC:mtg_cardiacconduct_nov11
has db xref: GOC:tfm
has db xref: ISBN:0323052908
has db xref: PMID:22426062
has db xref: PMID:4711263

Axiom
annotated source: cardiac muscle cell
annotated property: description
annotated target: Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to…
has db xref: DOI:10.1016/j.ccep.2010.10.012
has db xref: DOI:10.1038/nrcardio.2016.203
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK572070
has db xref: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle

Axiom
annotated source: cardiac muscle cell
annotated property: hasDbXref
annotated target: ZFA:0009316
mapping justification: UnspecifiedMatching

Axiom
annotated source: cardiac muscle cell
annotated property: hasExactSynonym
annotated target: cardiac muscle fiber
has db xref: GO:0048739

cardiac muscle cell on CELLxGENE CellGuide
type: Axiom
annotated source: cardiac muscle cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000746

cyanophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0005005
IAO_0000115: A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance.
has db xref: ZFA:0009317
has related synonym: blue chromatophore

Axiom
annotated source: cyanophore
annotated property: IAO_0000115
annotated target: A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance.
has db xref: SANBI:mhl

Axiom
annotated source: cyanophore
annotated property: hasDbXref
annotated target: ZFA:0009317
mapping justification: UnspecifiedMatching

retinal bipolar neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002100
    some values from: UBERON_0001791
subclass of: BFO_0000002
subclass of: glutamatergic neuron
subclass of: CL_0008028
subclass of: CL_0009004
subclass of: Restriction
  on property: RO_0002100
  some values from: UBERON_0001791
subclass of: Restriction
  on property: RO_0002215
  some values from: Class
    intersection of: GO_0061535
    intersection of: Restriction
      on property: BFO_0000050
      some values from: GO_0098976
IAO_0000115: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer.
description: The retinal bipolar neuron is an integral part of the eye, specifically located within the retina. They are secondary neurons in the visual pathway and primarily serve to transmit information from photoreceptor cells, which respond to light, to retinal ganglion cells, which carry the signal to the brain. As such, these cells play a pivotal role in our ability to interpret and perceive visual information. The structure of retinal bipolar neurons is unique and significant to their function. They are termed "bipolar" due to their morphology, having two poles: a single dendrite on one end and an axon on the other. The dendrite end connects to photoreceptor cells (rods or cones), while the axon end synapses with retinal ganglion cells. In the center of the dendrite and axon lies the cell body, which houses the cell's nucleus and other vital organelles. At the functional level, retinal bipolar neurons can be categorized into ON and OFF types based on their response to light. 'ON' bipolar cells are depolarized (electrical potential across the cell membrane decreases) under light conditions, thereby increasing their rate of neurotransmitter release onto the downstream ganglion cells. In contrast, 'OFF' bipolar cells are hyperpolarized (electrical potential increases) in light conditions, decreasing their rate of neurotransmitter release. This dual system allows for a fine-tuned response and the ability to perceive differences in light intensity and contrast, thus creating a nuanced and detailed visual world. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009318
has related synonym: BC
has related synonym: BCs
has related synonym: BPs
in subset: cellxgene subset
in subset: eye upper slim
in subset: human reference atlas

Axiom
annotated source: retinal bipolar neuron
annotated property: IAO_0000115
annotated target: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer.
has db xref: PMID:14689473

Axiom
annotated source: retinal bipolar neuron
annotated property: description
annotated target: The retinal bipolar neuron is an integral part of the eye, specifically located within the retina. They are secondary neurons in the visual pathway and primarily serve to transmit information from photoreceptor cells, which respond to light, to retinal ganglion cells, which carry the signal to the brain. As such, these cells play a pivotal role in our ability to interpret and perceive visual information. The structure of retinal bipolar neurons is unique and significant to their function. They are termed "bipolar" due to their morphology, having two poles: a single dendrite on one end and an axon on the other. The dendrite end connects to photoreceptor cells (rods or cones), while the axon end synapses with retinal ganglion cells. In the center of the dendrite and axon lies the cell body, which houses the cell's nucleus and other vital organelles. At the functional level, retinal bipolar neurons can be categorized into ON and OFF types based on their response to light. 'ON' bipolar cells are depolarized (electrical potential across the cell membrane decreases) under light conditions, thereby increasing their rate of neurotransmitter release onto the downstream ganglion cells. In contrast, 'OFF' bipolar cells are hyperpolarized (electrical potential increases) in light conditions, decreasing their rate of neurotransmitter release. This dual system allows for a fine-tuned response and the ability to perceive differences in light intensity and contrast, thus creating a nuanced and detailed visual world. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.preteyeres.2008.03.003
has db xref: DOI:10.1016/j.ydbio.2021.09.005
has db xref: DOI:10.1017/S0952523810000209
has db xref: DOI:10.1038/nrn3783
has db xref: DOI:10.1126/science.201028

Axiom
annotated source: retinal bipolar neuron
annotated property: hasDbXref
annotated target: ZFA:0009318
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal bipolar neuron
annotated property: hasRelatedSynonym
annotated target: BC
has db xref: doi:10.1038/s41598-020-66092-9
has synonym type: OMO_0003000

Axiom
annotated source: retinal bipolar neuron
annotated property: hasRelatedSynonym
annotated target: BCs
has db xref: doi:10.1038/s41598-020-66092-9
has synonym type: OMO_0003000
has synonym type: OMO_0003004

Axiom
annotated source: retinal bipolar neuron
annotated property: hasRelatedSynonym
annotated target: BPs
has db xref: geo:GSE137537
has synonym type: OMO_0003000
has synonym type: OMO_0003004

reference transcriptomic data on Cell Annotation Platform
type: Axiom
annotated source: retinal bipolar neuron
annotated property: seeAlso
annotated target: https://celltype.info/project/544/dataset/1157

retinal bipolar neuron on CELLxGENE CellGuide
type: Axiom
annotated source: retinal bipolar neuron
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000748

ON-bipolar cell
type: Class
subclass of: retinal bipolar neuron
IAO_0000115: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors.
has db xref: ZFA:0009319
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: ON-bipolar cell
annotated property: IAO_0000115
annotated target: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors.
has db xref: PMID:14689473

Axiom
annotated source: ON-bipolar cell
annotated property: hasDbXref
annotated target: ZFA:0009319
mapping justification: UnspecifiedMatching

rod bipolar cell
type: Class
subclass of: ON-bipolar cell
subclass of: Restriction
  on property: RO_0002102
  some values from: UBERON_0008925
subclass of: Restriction
  on property: RO_0002102
  some values from: UBERON_0008926
subclass of: Restriction
  on property: RO_0002103
  some values from: retinal rod cell
subclass of: Restriction
  on property: RO_0015004
  some values from: CLM_1001251
subclass of: Restriction
  on property: RO_0015004
  some values from: CLM_1001266
IAO_0000115: A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light.
RO_0002175: NCBITaxon_32443
RO_0002175: NCBITaxon 9606
description: Rod bipolar cells constitute a significant component of the retinal neural network and play a pivotal role in signal transmission from rod photoreceptor cells to the other subsequent neuronal cells within the vision system. They belong to the category of interneurons, or connector cells, effectively conveying visual information under low light conditions. Non-mammalian and mammalian visual systems feature these cells serving as the primary conduit for scotopic (night vision) signals. These cells harness their strategic position in the retina's inner nuclear layer to receive information from the rod photoreceptor cells and transmit it to amacrine and ganglion cells. Structurally, they are named bipolar due to their distinctive shape, with dendrites extending towards the outer retina to connect with rod cells, while their axons lead inwards to form synapses with ganglion and amacrine cells in the inner plexiform layer. Each rod bipolar cell tends to interface with several rod cells and several downstream neurons, forming intricate networks. Bearing intricate dendritic trees, these cells can integrate responses from multiple rod cells efficiently, amplifying the retinal signal's strength. They employ glutamate, a type of neurotransmitter, to govern synaptic communication between photoreceptor cells and downstream neurons. This stratified arrangement of rod bipolar cells endows them with the capability to translate light signals into neural signals, predominantly maintaining the spatial and temporal resolution of our visual perception in dim lighting. They are key to our night vision and our ability to detect changes in our light environment. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:67750
has db xref: ZFA:0009321
in subset: cellxgene subset
comment: The marker set CDHR3, PRKCA-AS1 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000751 in the retina with a confidence of 0.929575519 (NS-Forest FBeta value).
comment: The marker set ENSG00000227681, C16orf74 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000751 in the retina with a confidence of 0.907779697 (NS-Forest FBeta value).

Axiom
annotated source: rod bipolar cell
annotated property: IAO_0000115
annotated target: A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light.
has db xref: GOC:tfm
has db xref: PMID:14689473

Axiom
annotated source: rod bipolar cell
annotated property: RO_0002175
annotated target: NCBITaxon_32443
has db xref: PMID:38627529

Axiom
annotated source: rod bipolar cell
annotated property: description
annotated target: Rod bipolar cells constitute a significant component of the retinal neural network and play a pivotal role in signal transmission from rod photoreceptor cells to the other subsequent neuronal cells within the vision system. They belong to the category of interneurons, or connector cells, effectively conveying visual information under low light conditions. Non-mammalian and mammalian visual systems feature these cells serving as the primary conduit for scotopic (night vision) signals. These cells harness their strategic position in the retina's inner nuclear layer to receive information from the rod photoreceptor cells and transmit it to amacrine and ganglion cells. Structurally, they are named bipolar due to their distinctive shape, with dendrites extending towards the outer retina to connect with rod cells, while their axons lead inwards to form synapses with ganglion and amacrine cells in the inner plexiform layer. Each rod bipolar cell tends to interface with several rod cells and several downstream neurons, forming intricate networks. Bearing intricate dendritic trees, these cells can integrate responses from multiple rod cells efficiently, amplifying the retinal signal's strength. They employ glutamate, a type of neurotransmitter, to govern synaptic communication between photoreceptor cells and downstream neurons. This stratified arrangement of rod bipolar cells endows them with the capability to translate light signals into neural signals, predominantly maintaining the spatial and temporal resolution of our visual perception in dim lighting. They are key to our night vision and our ability to detect changes in our light environment. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/cne.23370
has db xref: DOI:10.1007/s004410000304
has db xref: DOI:10.1016/j.visres.2004.07.043
has db xref: DOI:10.1038/294592a0
has db xref: DOI:10.1038/nrn3783

Axiom
annotated source: rod bipolar cell
annotated property: hasDbXref
annotated target: ZFA:0009321
mapping justification: UnspecifiedMatching

Axiom
annotated source: rod bipolar cell
annotated property: comment
annotated target: The marker set CDHR3, PRKCA-AS1 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000751 in the retina with a confidence of 0.929575519 (NS-Forest FBeta value).
has db xref: https://doi.org/10.5281/zenodo.11165918

Axiom
annotated source: rod bipolar cell
annotated property: comment
annotated target: The marker set ENSG00000227681, C16orf74 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000751 in the retina with a confidence of 0.907779697 (NS-Forest FBeta value).
has db xref: https://doi.org/10.5281/zenodo.11165918

reference transcriptomic data on Cell Annotation Platform
type: Axiom
annotated source: rod bipolar cell
annotated property: seeAlso
annotated target: https://celltype.info/project/544/dataset/1157

rod bipolar cell on CELLxGENE CellGuide
type: Axiom
annotated source: rod bipolar cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000751

cone retinal bipolar cell
type: Class
equivalent class: Class
  intersection of: retinal bipolar neuron
  intersection of: Restriction
    on property: RO_0002103
    some values from: retinal cone cell
subclass of: retinal bipolar neuron
subclass of: Restriction
  on property: RO_0002103
  some values from: retinal cone cell
subclass of: Restriction
  on property: RO_0015004
  some values from: CLM_1001241
subclass of: Restriction
  on property: RO_0015004
  some values from: CLM_1001261
IAO_0000115: A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer.
RO_0002175: NCBITaxon 9606
has db xref: ZFA:0009322
in subset: cellxgene subset
comment: The marker set COL19A1, DOK5 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000752 in the retina with a confidence of 0.843060252 (NS-Forest FBeta value).
comment: The marker set DOK5, ST6GALNAC3 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000752 in the retina with a confidence of 0.782434709 (NS-Forest FBeta value).

Axiom
annotated source: cone retinal bipolar cell
annotated property: IAO_0000115
annotated target: A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer.
has db xref: PMID:14689473

Axiom
annotated source: cone retinal bipolar cell
annotated property: hasDbXref
annotated target: ZFA:0009322
mapping justification: UnspecifiedMatching

Axiom
annotated source: cone retinal bipolar cell
annotated property: comment
annotated target: The marker set COL19A1, DOK5 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000752 in the retina with a confidence of 0.843060252 (NS-Forest FBeta value).
has db xref: https://doi.org/10.5281/zenodo.11165918

Axiom
annotated source: cone retinal bipolar cell
annotated property: comment
annotated target: The marker set DOK5, ST6GALNAC3 can identify the Human cell type http://purl.obolibrary.org/obo/CL_0000752 in the retina with a confidence of 0.782434709 (NS-Forest FBeta value).
has db xref: https://doi.org/10.5281/zenodo.11165918

nucleated thrombocyte
type: Class
equivalent class: Class
  intersection of: myeloid cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0007596
subclass of: single nucleate cell
subclass of: myeloid cell
subclass of: Restriction
  on property: RO_0002202
  some values from: thromboblast
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0007596
IAO_0000115: A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates.
has db xref: ZFA:0009323
in subset: blood and immune upper slim
comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals.

Axiom
annotated source: nucleated thrombocyte
annotated property: subClassOf
annotated target: myeloid cell
is inferred: true

Axiom
annotated source: nucleated thrombocyte
annotated property: IAO_0000115
annotated target: A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:16360205

Axiom
annotated source: nucleated thrombocyte
annotated property: hasDbXref
annotated target: ZFA:0009323
mapping justification: UnspecifiedMatching

myeloid cell
type: Class
equivalent class: Class
  intersection of: hematopoietic cell
  intersection of: Restriction
    on property: RO_0002202
    some values from: common myeloid progenitor
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: hematopoietic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: common myeloid progenitor
IAO_0000115: A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
has db xref: BTO:0001441
has db xref: CALOHA:TS-0647
has db xref: MESH:D022423
has db xref: ZFA:0009324
in subset: cellxgene subset

Axiom
annotated source: myeloid cell
annotated property: subClassOf
annotated target: hematopoietic cell
is inferred: true

Axiom
annotated source: myeloid cell
annotated property: IAO_0000115
annotated target: A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
has db xref: GOC:add

Axiom
annotated source: myeloid cell
annotated property: hasDbXref
annotated target: ZFA:0009324
mapping justification: UnspecifiedMatching

erythroid lineage cell
type: Class
subclass of: myeloid cell
IAO_0000115: A immature or mature cell in the lineage leading to and including erythrocytes.
has db xref: CALOHA:TS-0290
has db xref: FMA:62845
has db xref: FMA:83516
has db xref: ZFA:0009325
has exact synonym: erythropoietic cell
in subset: cellxgene subset
in subset: human reference atlas
comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.

Axiom
annotated source: erythroid lineage cell
annotated property: IAO_0000115
annotated target: A immature or mature cell in the lineage leading to and including erythrocytes.
has db xref: GOC:add
has db xref: GOC:tfm

Axiom
annotated source: erythroid lineage cell
annotated property: hasDbXref
annotated target: ZFA:0009325
mapping justification: UnspecifiedMatching

erythroblast
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005634
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0005730
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030218
subclass of: erythroid lineage cell
subclass of: CL_0011026
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005634
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0005730
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: RO_0002202
  some values from: proerythroblast
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030218
IAO_0000115: A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
has db xref: BTO:0001571
has db xref: CALOHA:TS-0289
has db xref: FMA:83504
has db xref: MESH:D004900
has db xref: ZFA:0005237
has exact synonym: normoblast
in subset: blood and immune upper slim
in subset: cellxgene subset

Axiom
annotated source: erythroblast
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: erythroblast
annotated property: IAO_0000115
annotated target: A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
has db xref: GOC:add
has db xref: ISBN:0721601464
has db xref: PMID:18174176

Axiom
annotated source: erythroblast
annotated property: hasDbXref
annotated target: ZFA:0005237
mapping justification: UnspecifiedMatching

myeloid leukocyte
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: RO_0002202
    some values from: common myeloid progenitor
subclass of: leukocyte
subclass of: myeloid cell
IAO_0000115: A cell of the monocyte, granulocyte, or mast cell lineage.
description: Myeloid leukocytes are a group of immune cells descended from the myeloid lineage. The myeloid lineage constitutes a significant portion of the body's defense system, particularly against microbial pathogens and foreign substances. Myeloid leukocytes originate from hematopoietic stem cells located in the bone marrow. The commitment of a pluripotent hematopoietic stem cell into a myeloid progenitor cell represents the initiation step towards the development of myeloid leukocytes. Once differentiated, these cells contribute diversely to both the innate and adaptive immune responses in the body. Myeloid leukocytes include several distinct cell types based on functionality and structure, encompassing monocytes, macrophages, granulocytes (neutrophils, eosinophils, and basophils), and dendritic cells. Each cell type has specialized functions, occupying a unique role in the body's immune response. For instance, neutrophils are prolific phagocytes—cells that engulf and destroy pathogens—while eosinophils are instrumental in combating multicellular parasites and modulating allergic inflammatory responses. Monocytes, in addition to their phagocytic activities, can enter peripheral tissues and differentiate into macrophages or dendritic cells which are crucial for antigen presentation to T cells. Another critical function of myeloid leukocytes is their involvement in tissue remodeling and repair. For example, macrophages not only play a key role in defending the body but also perform duties essential for wound healing, such as removing dead cells and stimulating tissue repair. In general, myeloid leukocytes participate in the removal of old and damaged cells, an essential process for maintaining good health and homeostasis. Through the orchestration of complex interactions and signal transductions, myeloid leukocytes provide the body with a robust defense system against foreign invaders and participate in maintaining the body's overall balance and function. (This extended desc…
has db xref: ZFA:0009326
in subset: cellxgene subset

Axiom
annotated source: myeloid leukocyte
annotated property: subClassOf
annotated target: leukocyte
is inferred: true

Axiom
annotated source: myeloid leukocyte
annotated property: IAO_0000115
annotated target: A cell of the monocyte, granulocyte, or mast cell lineage.
has db xref: GOC:add

Axiom
annotated source: myeloid leukocyte
annotated property: description
annotated target: Myeloid leukocytes are a group of immune cells descended from the myeloid lineage. The myeloid lineage constitutes a significant portion of the body's defense system, particularly against microbial pathogens and foreign substances. Myeloid leukocytes originate from hematopoietic stem cells located in the bone marrow. The commitment of a pluripotent hematopoietic stem cell into a myeloid progenitor cell represents the initiation step towards the development of myeloid leukocytes. Once differentiated, these cells contribute diversely to both the innate and adaptive immune responses in the body. Myeloid leukocytes include several distinct cell types based on functionality and structure, encompassing monocytes, macrophages, granulocytes (neutrophils, eosinophils, and basophils), and dendritic cells. Each cell type has specialized functions, occupying a unique role in the body's immune response. For instance, neutrophils are prolific phagocytes—cells that engulf and destroy pathogens—while eosinophils are instrumental in combating multicellular parasites and modulating allergic inflammatory responses. Monocytes, in addition to their phagocytic activities, can enter peripheral tissues and differentiate into macrophages or dendritic cells which are crucial for antigen presentation to T cells. Another critical function of myeloid leukocytes is their involvement in tissue remodeling and repair. For example, macrophages not only play a key role in defending the body but also perform duties essential for wound healing, such as removing dead cells and stimulating tissue repair. In general, myeloid leukocytes participate in the removal of old and damaged cells, an essential process for maintaining good health and homeostasis. Through the orchestration of complex interactions and signal transductions, myeloid leukocytes provide the body with a robust defense system against foreign invaders and participate in maintaining the body's overall balance and function. (This extended desc…
has db xref: DOI:10.1016/j.biocel.2004.01.020
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK563148/

Axiom
annotated source: myeloid leukocyte
annotated property: hasDbXref
annotated target: ZFA:0009326
mapping justification: UnspecifiedMatching

myeloid leukocyte on CELLxGENE CellGuide
type: Axiom
annotated source: myeloid leukocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000766

basophil
type: Class
equivalent class: Class
  intersection of: granulocyte
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001344
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001950
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001255
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001865
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000007431
subclass of: granulocyte
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001344
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001950
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001255
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001865
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000007431
IAO_0000115: Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
has broad synonym: polymorphonuclear leucocyte
has broad synonym: polymorphonuclear leukocyte
has db xref: BTO:0000129
has db xref: CALOHA:TS-0073
has db xref: FMA:62862
has exact synonym: basophilic leucocyte
has exact synonym: basophilic leukocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive.

Axiom
annotated source: basophil
annotated property: subClassOf
annotated target: granulocyte
is inferred: true

Axiom
annotated source: basophil
annotated property: IAO_0000115
annotated target: Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: MESH:D001491
has db xref: PMCID:PMC2626675
has db xref: PMID:11927641
has db xref: PMID:19741522
has db xref: PMID:21236338
has db xref: PMID:9933081

immature basophil
type: Class
equivalent class: Class
  intersection of: basophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017509
subclass of: basophil
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017509
subclass of: Restriction
  on property: RO_0002202
  some values from: basophilic promyelocyte
IAO_0000115: Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking.
has exact synonym: immature basophilic leucocyte
has exact synonym: immature basophilic leukocyte

Axiom
annotated source: immature basophil
annotated property: subClassOf
annotated target: basophil
is inferred: true

Axiom
annotated source: immature basophil
annotated property: IAO_0000115
annotated target: Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking.
has db xref: GOC:add
has db xref: ISBN:0721601464

basophilic metamyelocyte
type: Class
equivalent class: Class
  intersection of: immature basophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017507
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000792
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042582
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0070820
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001456
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001483
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001892
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001932
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002031
subclass of: immature basophil
subclass of: CL_0002192
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017507
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000792
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042582
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0070820
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001456
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001483
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001892
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001932
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002031
subclass of: Restriction
  on property: RO_0002202
  some values from: basophilic myelocyte
IAO_0000115: A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive.
has db xref: FMA:84198

Axiom
annotated source: basophilic metamyelocyte
annotated property: subClassOf
annotated target: immature basophil
is inferred: true

Axiom
annotated source: basophilic metamyelocyte
annotated property: IAO_0000115
annotated target: A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive.
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: PMID:18466030

band form basophil
type: Class
equivalent class: Class
  intersection of: immature basophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017506
subclass of: immature basophil
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017506
subclass of: Restriction
  on property: RO_0002202
  some values from: basophilic metamyelocyte
IAO_0000115: A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil.

Axiom
annotated source: band form basophil
annotated property: subClassOf
annotated target: immature basophil
is inferred: true

Axiom
annotated source: band form basophil
annotated property: IAO_0000115
annotated target: A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil.
has db xref: GOC:add
has db xref: ISBN:0721601464
has db xref: PMID:18466030
has db xref: http://www.cap.org

eosinophil
type: Class
equivalent class: Class
  intersection of: granulocyte
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001254
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001255
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001307
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000005178
subclass of: granulocyte
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001254
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001255
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001307
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000005178
IAO_0000115: Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive.
description: Eosinophils are a type of granulocyte derived from myeloid progenitors in the bone marrow; they are a part of the body's immune system. Named for their affinity to eosin, a red acidic dye used in staining procedures, eosinophils contribute to the immune system's response by migrating to inflammation sites, particularly those produced by allergic reactions and infections due to multicellular parasites. They comprise ~1-5% of the white blood cells in circulation. Eosinophils play crucial roles in mediating inflammatory responses. They carry granules containing a variety of enzymes and proteins, including major basic protein (MBP), eosinophil peroxidase (EPO), eosinophil cationic protein (ECP), and eosinophil-derived neurotoxin (EDN). These enzymes and proteins are effective in killing bacteria, parasites, and some cancer cells. When exposed to an antigen, eosinophils degranulate and release these mediators to the site of infection, resulting in the destruction of invading microorganisms. Specifically, in parasitic infections, eosinophils attach themselves to the parasites and release these cytotoxic granules, causing a lethal rupture in the parasite's surface. Eosinphils may also release cytokines to attract other immune cells to sites of infection and to skew the response towards type 2 immunity. Eosinophils are also involved in conditions such as asthma and allergic reactions. They secrete chemical mediators such as leukotrienes and prostaglandins that trigger contraction of smooth muscles, causing symptoms such as bronchoconstriction observed in asthma. However, these multifunctional cells, while useful in defending the body, may also inadvertently cause tissue damage if excessively activated. Increased numbers of eosinophils, a condition known as eosinophilia, can indicate a variety of diseases including allergies, skin disorders, parasitic and fungal infections, autoimmune diseases, certain types of cancer, and asthma. (This extended description was generated by …
has broad synonym: polymorphonuclear leucocyte
has broad synonym: polymorphonuclear leukocyte
has db xref: BTO:0000399
has db xref: CALOHA:TS-0279
has db xref: FMA:62861
has db xref: MESH:D004804
has exact synonym: eosinocyte
has exact synonym: eosinophilic granulocyte
has exact synonym: eosinophilic leucocyte
has exact synonym: eosinophilic leukocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte.

Axiom
annotated source: eosinophil
annotated property: subClassOf
annotated target: granulocyte
is inferred: true

Axiom
annotated source: eosinophil
annotated property: IAO_0000115
annotated target: Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: PMCID:PMC2626675
has db xref: PMID:10914487
has db xref: PMID:1662676

Axiom
annotated source: eosinophil
annotated property: description
annotated target: Eosinophils are a type of granulocyte derived from myeloid progenitors in the bone marrow; they are a part of the body's immune system. Named for their affinity to eosin, a red acidic dye used in staining procedures, eosinophils contribute to the immune system's response by migrating to inflammation sites, particularly those produced by allergic reactions and infections due to multicellular parasites. They comprise ~1-5% of the white blood cells in circulation. Eosinophils play crucial roles in mediating inflammatory responses. They carry granules containing a variety of enzymes and proteins, including major basic protein (MBP), eosinophil peroxidase (EPO), eosinophil cationic protein (ECP), and eosinophil-derived neurotoxin (EDN). These enzymes and proteins are effective in killing bacteria, parasites, and some cancer cells. When exposed to an antigen, eosinophils degranulate and release these mediators to the site of infection, resulting in the destruction of invading microorganisms. Specifically, in parasitic infections, eosinophils attach themselves to the parasites and release these cytotoxic granules, causing a lethal rupture in the parasite's surface. Eosinphils may also release cytokines to attract other immune cells to sites of infection and to skew the response towards type 2 immunity. Eosinophils are also involved in conditions such as asthma and allergic reactions. They secrete chemical mediators such as leukotrienes and prostaglandins that trigger contraction of smooth muscles, causing symptoms such as bronchoconstriction observed in asthma. However, these multifunctional cells, while useful in defending the body, may also inadvertently cause tissue damage if excessively activated. Increased numbers of eosinophils, a condition known as eosinophilia, can indicate a variety of diseases including allergies, skin disorders, parasitic and fungal infections, autoimmune diseases, certain types of cancer, and asthma. (This extended description was generated by …
has db xref: DOI:10.1016/j.mayocp.2021.04.025
has db xref: DOI:10.1038/nri3341
has db xref: DOI:10.1128/microbiolspec.mchd-0020-2015
has db xref: DOI:10.1146/annurev-pathmechdis-012419-032756
has db xref: DOI:10.1182/blood-2012-06-330845

eosinophil on CELLxGENE CellGuide
type: Axiom
annotated source: eosinophil
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000771

immature eosinophil
type: Class
equivalent class: Class
  intersection of: eosinophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017509
subclass of: eosinophil
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017509
subclass of: Restriction
  on property: RO_0002202
  some values from: eosinophilic promyelocyte
IAO_0000115: Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking.
has exact synonym: immature eosinocyte
has exact synonym: immature eosinophilic leucocyte
has exact synonym: immature eosinophilic leukocyte

Axiom
annotated source: immature eosinophil
annotated property: subClassOf
annotated target: eosinophil
is inferred: true

Axiom
annotated source: immature eosinophil
annotated property: IAO_0000115
annotated target: Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking.
has db xref: GOC:add
has db xref: ISBN:0721601464

eosinophilic metamyelocyte
type: Class
equivalent class: Class
  intersection of: immature eosinophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017502
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017507
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000792
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042582
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0070820
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001456
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001483
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001892
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001932
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002031
subclass of: immature eosinophil
subclass of: CL_0002192
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017502
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017507
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000792
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042582
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0070820
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001456
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001483
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001892
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001932
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002031
subclass of: Restriction
  on property: RO_0002202
  some values from: eosinophilic myelocyte
IAO_0000115: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative.

Axiom
annotated source: eosinophilic metamyelocyte
annotated property: subClassOf
annotated target: immature eosinophil
is inferred: true

Axiom
annotated source: eosinophilic metamyelocyte
annotated property: IAO_0000115
annotated target: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: PMID:19622087

band form eosinophil
type: Class
equivalent class: Class
  intersection of: immature eosinophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017506
subclass of: immature eosinophil
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017506
subclass of: Restriction
  on property: RO_0002202
  some values from: eosinophilic metamyelocyte
IAO_0000115: A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil.

Axiom
annotated source: band form eosinophil
annotated property: subClassOf
annotated target: immature eosinophil
is inferred: true

Axiom
annotated source: band form eosinophil
annotated property: IAO_0000115
annotated target: A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: PMID:19622087
has db xref: http://www.cap.org

neutrophil
type: Class
equivalent class: Class
  intersection of: granulocyte
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001479
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001879
subclass of: granulocyte
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001479
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001879
IAO_0000115: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
description: Neutrophils are an essential component of the human immune system and belong to the category of white blood cells known as granulocytes. They constitute approximately 50-70% of all white blood cells, making them the most abundant type of immune cells in mammals. Neutrophils develop in the bone marrow from hematopoietic stem cells before being released into the bloodstream where they circulate before migration into tissues, thereby exhibiting a multi-step process that includes margination, rolling, adhesion, and transmigration. Phenotypically and functionally, neutrophils represent a heterogeneous cell population. They are the immune system’s immediate responders and are the first cells to migrate towards the site of an infection. They play a critical role in defending the body from potential pathogenic bacteria and fungi. Their primary mechanism of action involves phagocytosis, where they engulf and destroy these microbes. Neutrophils are characterized by the presence of large quantities of granules containing antimicrobial proteins and enzymes, including defensins and myeloperoxidase, which are released once the cell has recognized and attached to the microbes. The enzymes and other antimicrobial agents can also be released into the surrounding environment, a process known as degranulation. Neutrophils also possess the unique biological ability to eliminate pathogens through a process called neutrophil extracellular trap (NET) formation, or NETosis. In this process, neutrophils release a mixture of DNA, histones, and granule proteins that form a web-like structure which traps and kills microbes. Notably, this process usually leads to the death of the neutrophil itself, referred to as cell suicide or programmed cell death. Neutrophils play a crucial role in the immune system by rapidly responding to infections and inflammation, excessive or dysregulated neutrophil activity can contribute to tissue damage and chronic inflammation, exacerbating various diseases such a…
has broad synonym: PMN
has broad synonym: poly
has broad synonym: polymorphonuclear leucocyte
has broad synonym: polymorphonuclear leukocyte
has broad synonym: polymorphonuclear neutrophil
has broad synonym: polynuclear neutrophilic leucocyte
has broad synonym: polynuclear neutrophilic leukocyte
has db xref: BTO:0000130
has db xref: CALOHA:TS-0688
has db xref: FMA:62860
has db xref: MESH:D009504
has db xref: ZFA:0009327
has exact synonym: neutrocyte
has exact synonym: neutrophil leucocyte
has exact synonym: neutrophil leukocyte
has exact synonym: neutrophilic leucocyte
has exact synonym: neutrophilic leukocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: neutrophil
annotated property: subClassOf
annotated target: granulocyte
is inferred: true

Axiom
annotated source: neutrophil
annotated property: IAO_0000115
annotated target: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: ISBN:0721601464

Axiom
annotated source: neutrophil
annotated property: description
annotated target: Neutrophils are an essential component of the human immune system and belong to the category of white blood cells known as granulocytes. They constitute approximately 50-70% of all white blood cells, making them the most abundant type of immune cells in mammals. Neutrophils develop in the bone marrow from hematopoietic stem cells before being released into the bloodstream where they circulate before migration into tissues, thereby exhibiting a multi-step process that includes margination, rolling, adhesion, and transmigration. Phenotypically and functionally, neutrophils represent a heterogeneous cell population. They are the immune system’s immediate responders and are the first cells to migrate towards the site of an infection. They play a critical role in defending the body from potential pathogenic bacteria and fungi. Their primary mechanism of action involves phagocytosis, where they engulf and destroy these microbes. Neutrophils are characterized by the presence of large quantities of granules containing antimicrobial proteins and enzymes, including defensins and myeloperoxidase, which are released once the cell has recognized and attached to the microbes. The enzymes and other antimicrobial agents can also be released into the surrounding environment, a process known as degranulation. Neutrophils also possess the unique biological ability to eliminate pathogens through a process called neutrophil extracellular trap (NET) formation, or NETosis. In this process, neutrophils release a mixture of DNA, histones, and granule proteins that form a web-like structure which traps and kills microbes. Notably, this process usually leads to the death of the neutrophil itself, referred to as cell suicide or programmed cell death. Neutrophils play a crucial role in the immune system by rapidly responding to infections and inflammation, excessive or dysregulated neutrophil activity can contribute to tissue damage and chronic inflammation, exacerbating various diseases such a…
has db xref: DOI:10.1007/s10753-016-0458-4
has db xref: DOI:10.1038/s41577-019-0141-8
has db xref: DOI:10.1038/s41577-021-00571-6
has db xref: DOI:10.1111/febs.15803
has db xref: DOI:10.3389/fphys.2018.00113

Axiom
annotated source: neutrophil
annotated property: hasDbXref
annotated target: ZFA:0009327
mapping justification: UnspecifiedMatching

neutrophil on CELLxGENE CellGuide
type: Axiom
annotated source: neutrophil
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000775

immature neutrophil
type: Class
equivalent class: Class
  intersection of: neutrophil
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017509
subclass of: neutrophil
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017509
subclass of: Restriction
  on property: RO_0002202
  some values from: neutrophilic promyelocyte
IAO_0000115: Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking.
description: An immature neutrophil, also known as a band neutrophil or band cell, is an intermediary stage in neutrophilic granulocyte development. Immature neutrophils are formed in the bone marrow then released into the bloodstream where they eventually mature into functional, mature segmented neutrophils. They are characterized by an unsegmented, curved nucleus, a distinguishing factor that differentiates them from mature neutrophils, which possess a multi-lobed nucleus. Immature neutrophils can be found in circulation, but their numbers may increase drastically during infection. These cells are released from the bone marrow as a result of emergency granulopoiesis. The role of these cells in infection and acute inflammation remains controversial, and it has been suggested that these cells could possess immunosuppressive or proinflammatory activity. An increase of immature neutrophils in the bloodstream, a condition referred to as bandemia or a left shift, can be an important clinical indicator. While low-level presence is typical, an abnormally high count can signal severe or systemic bacterial infection, inflammation, or less commonly, diseases that affect bone marrow function such as leukemia. However, not all bacterial infections will result in a left shift. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009328
has exact synonym: immatuer neutrophilic leukocyte
has exact synonym: immature neutrocyte
has exact synonym: immature neutrophil leucocyte
has exact synonym: immature neutrophil leukocyte
has exact synonym: immature neutrophilic leucocyte
in subset: cellxgene subset

Axiom
annotated source: immature neutrophil
annotated property: subClassOf
annotated target: neutrophil
is inferred: true

Axiom
annotated source: immature neutrophil
annotated property: IAO_0000115
annotated target: Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking.
has db xref: GOC:add
has db xref: ISBN:0721601464

Axiom
annotated source: immature neutrophil
annotated property: description
annotated target: An immature neutrophil, also known as a band neutrophil or band cell, is an intermediary stage in neutrophilic granulocyte development. Immature neutrophils are formed in the bone marrow then released into the bloodstream where they eventually mature into functional, mature segmented neutrophils. They are characterized by an unsegmented, curved nucleus, a distinguishing factor that differentiates them from mature neutrophils, which possess a multi-lobed nucleus. Immature neutrophils can be found in circulation, but their numbers may increase drastically during infection. These cells are released from the bone marrow as a result of emergency granulopoiesis. The role of these cells in infection and acute inflammation remains controversial, and it has been suggested that these cells could possess immunosuppressive or proinflammatory activity. An increase of immature neutrophils in the bloodstream, a condition referred to as bandemia or a left shift, can be an important clinical indicator. While low-level presence is typical, an abnormally high count can signal severe or systemic bacterial infection, inflammation, or less commonly, diseases that affect bone marrow function such as leukemia. However, not all bacterial infections will result in a left shift. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.cca.2016.03.017
has db xref: DOI:10.1016/j.it.2019.04.012
has db xref: DOI:10.1016/j.it.2019.04.013
has db xref: DOI:10.3389/fimmu.2020.01259/full

Axiom
annotated source: immature neutrophil
annotated property: hasDbXref
annotated target: ZFA:0009328
mapping justification: UnspecifiedMatching

immature neutrophil on CELLxGENE CellGuide
type: Axiom
annotated source: immature neutrophil
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000776

mesangial phagocyte
type: Class
equivalent class: Class
  intersection of: tissue-resident macrophage
  intersection of: Restriction
    on property: RO_0001025
    some values from: UBERON_0002320
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0019882
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0048771
subclass of: tissue-resident macrophage
subclass of: Restriction
  on property: RO_0001025
  some values from: UBERON_0002320
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0048771
IAO_0000115: A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling.
has broad synonym: mesangial cell

Axiom
annotated source: mesangial phagocyte
annotated property: subClassOf
annotated target: tissue-resident macrophage
is inferred: true

Axiom
annotated source: mesangial phagocyte
annotated property: IAO_0000115
annotated target: A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0702022918
has db xref: ISBN:3540536663
has db xref: PMID:1600140
has db xref: PMID:16146841

mononuclear osteoclast
type: Class
equivalent class: Class
  intersection of: osteoclast
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
subclass of: osteoclast
subclass of: mononuclear phagocyte
IAO_0000115: A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts.
has db xref: ZFA:0009329
comment: Morphology: mononuclear, highly vesicular.

Axiom
annotated source: mononuclear osteoclast
annotated property: subClassOf
annotated target: osteoclast
is inferred: true

Axiom
annotated source: mononuclear osteoclast
annotated property: IAO_0000115
annotated target: A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:12713016
has db xref: PMID:15055519
has db xref: PMID:17380158
has db xref: PMID:9415452

Axiom
annotated source: mononuclear osteoclast
annotated property: hasDbXref
annotated target: ZFA:0009329
mapping justification: UnspecifiedMatching

multinuclear osteoclast
type: Class
equivalent class: Class
  intersection of: osteoclast
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001908
subclass of: osteoclast
subclass of: multinucleated phagocyte
subclass of: CL_4052002
subclass of: Restriction
  on property: RO_0002202
  some values from: mononuclear osteoclast
IAO_0000115: A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone.
has exact synonym: multinucleated osteoclast
comment: Morphology: multinucleated, highly vesicular.

Axiom
annotated source: multinuclear osteoclast
annotated property: subClassOf
annotated target: osteoclast
is inferred: true

Axiom
annotated source: multinuclear osteoclast
annotated property: IAO_0000115
annotated target: A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone.
has db xref: GOC:add
has db xref: PMID:12713016
has db xref: PMID:29379067
has db xref: PMID:38903088
has db xref: PMID:9415452

multinuclear odontoclast
type: Class
equivalent class: Class
  intersection of: odontoclast
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001908
subclass of: odontoclast
subclass of: multinuclear osteoclast
subclass of: Restriction
  on property: RO_0002202
  some values from: mononuclear odontoclast
IAO_0000115: A specialized multinuclear osteoclast associated with the absorption and removal of cementum.
has exact synonym: multinucleated odontoclast
comment: Morphology: multinucleated, highly vesicular; location: roots of deciduous (milk) teeth.

Axiom
annotated source: multinuclear odontoclast
annotated property: subClassOf
annotated target: odontoclast
is inferred: true

Axiom
annotated source: multinuclear odontoclast
annotated property: IAO_0000115
annotated target: A specialized multinuclear osteoclast associated with the absorption and removal of cementum.
has db xref: GOC:add
has db xref: PMID:9415452

mononuclear odontoclast
type: Class
equivalent class: Class
  intersection of: odontoclast
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
subclass of: odontoclast
subclass of: mononuclear osteoclast
IAO_0000115: A specialized mononuclear osteoclast associated with the absorption and removal of cementum.
has db xref: ZFA:0009330
comment: Morphology: Mononuclear, highly vesicular; location: roots of deciduous (milk) teeth.

Axiom
annotated source: mononuclear odontoclast
annotated property: subClassOf
annotated target: odontoclast
is inferred: true

Axiom
annotated source: mononuclear odontoclast
annotated property: subClassOf
annotated target: mononuclear osteoclast
is inferred: true

Axiom
annotated source: mononuclear odontoclast
annotated property: IAO_0000115
annotated target: A specialized mononuclear osteoclast associated with the absorption and removal of cementum.
has db xref: GOC:add
has db xref: PMID:9415452

Axiom
annotated source: mononuclear odontoclast
annotated property: hasDbXref
annotated target: ZFA:0009330
mapping justification: UnspecifiedMatching

myeloid dendritic cell
type: Class
equivalent class: Class
  intersection of: conventional dendritic cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001865
  intersection of: Restriction
    on property: RO_0002202
    some values from: myeloid cell
subclass of: myeloid leukocyte
subclass of: conventional dendritic cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001865
subclass of: Restriction
  on property: RO_0002202
  some values from: myeloid cell
IAO_0000115: A dendritic cell of the myeloid lineage.
description: Myeloid dendritic cells are a subset of dendritic cells derived from the common myeloid progenitor cell. "Conventional" and "myeloid" DCs are often used interchangeably. In contrast, dendritic cells may also arise from the common lymphoid progenitor. Monocyte-derived dendritic cells may also be induced by inflammatory states. Dendritic cells function as antigen-presenting cells and are able to activate naïve T cells to induce the adaptive immune response. Dendritic cells capture, process, and present antigens derived from pathogens to mount a specific immune response against the invading antigen. Dendritic cells also produce a range of cytokines that help in modulating and recruiting other immune cells during an immune response. Dendritic cells can contribute to immune tolerance by deleting self-reactive T cells or by inducing regulatory T-cells, thereby preventing autoimmunity. Dendritic cells thus are important in orchestrating the adaptive immune response and are pivotal in combating infections and maintaining tolerance to self. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has broad synonym: interdigitating cell
has broad synonym: veiled cell
has db xref: BTO:0004721
has exact synonym: CD11c+CD123- DC
has exact synonym: mDC
in subset: cellxgene subset
comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8).

Axiom
annotated source: myeloid dendritic cell
annotated property: subClassOf
annotated target: conventional dendritic cell
is inferred: true

Axiom
annotated source: myeloid dendritic cell
annotated property: IAO_0000115
annotated target: A dendritic cell of the myeloid lineage.
has db xref: GOC:add
has db xref: PMID:10449155
has db xref: PMID:17332250
has db xref: PMID:9521319

Axiom
annotated source: myeloid dendritic cell
annotated property: description
annotated target: Myeloid dendritic cells are a subset of dendritic cells derived from the common myeloid progenitor cell. "Conventional" and "myeloid" DCs are often used interchangeably. In contrast, dendritic cells may also arise from the common lymphoid progenitor. Monocyte-derived dendritic cells may also be induced by inflammatory states. Dendritic cells function as antigen-presenting cells and are able to activate naïve T cells to induce the adaptive immune response. Dendritic cells capture, process, and present antigens derived from pathogens to mount a specific immune response against the invading antigen. Dendritic cells also produce a range of cytokines that help in modulating and recruiting other immune cells during an immune response. Dendritic cells can contribute to immune tolerance by deleting self-reactive T cells or by inducing regulatory T-cells, thereby preventing autoimmunity. Dendritic cells thus are important in orchestrating the adaptive immune response and are pivotal in combating infections and maintaining tolerance to self. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/jlb.66.2.205
has db xref: DOI:10.1016/j.imbio.2014.12.010
has db xref: DOI:10.1016/j.immuni.2007.06.006
has db xref: DOI:10.1111/imm.12888
has db xref: DOI:10.3389/fimmu.2018.03176

myeloid dendritic cell on CELLxGENE CellGuide
type: Axiom
annotated source: myeloid dendritic cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000782

multinucleated phagocyte
type: Class
equivalent class: Class
  intersection of: phagocyte (sensu Vertebrata)
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001908
subclass of: multinucleate cell
subclass of: phagocyte (sensu Vertebrata)
IAO_0000115: A phagocyte formed by the fusion of mononuclear phagocytes.

Axiom
annotated source: multinucleated phagocyte
annotated property: subClassOf
annotated target: phagocyte (sensu Vertebrata)
is inferred: true

Axiom
annotated source: multinucleated phagocyte
annotated property: IAO_0000115
annotated target: A phagocyte formed by the fusion of mononuclear phagocytes.
has db xref: GOC:add
has db xref: GOC:tfm

plasmacytoid dendritic cell
type: Class
equivalent class: Class
  intersection of: dendritic cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032606
subclass of: dendritic cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032606
IAO_0000115: A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.
description: Plasmacytoid dendritic cells (pDCs), initially known as interferon-producing cells, are a unique subpopulation of dendritic cells. Unlike conventional dendritic cells (cDCs), plasmacytoid dendritic cells are characterized by their distinctive plasma cell-like morphology. These cells play vital roles in the innate and adaptive immune response, particularly in the antiviral response. Highly prevalent in the blood and lymphoid organs, pDCs are rare in non-lymphoid tissues, with the exception of inflamed tissues and tumors where they are often recruited. A key role of plasmacytoid dendritic cells is their rapid and robust production of type 1 interferons in response to viral infections. This is crucial for antiviral defense as interferon signals to other immune cells to increase their antiviral defenses. pDCs achieve this by detecting viral nucleic acids in the cytosol through Toll-like receptors (TLRs), specifically TLR7 and TLR9. Upon recognition, these cells quickly produce substantial amounts of interferons, which plays a significant role in the containment of viral replication and the development of acquired antiviral immunity. The potential of plasmacytoid dendritic cells for antigen presentations to naive T cells is relatively low under steady-state conditions. Upon activation by certain stimuli, such as viruses or CpG oligodeoxynucleotides, they have the ability to differentiate into efficient antigen-presenting cells. This transition to activated cells involves an upregulation of major histocompatibility complex (MHC) class II molecules and co-stimulatory molecules, thus allowing them to effectively present antigenic peptides to naive T cells. This crucial function in linking innate and adaptive immunity underlines the importance of pDCs to the overall immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain informatio…
has db xref: BTO:0004625
has exact synonym: DC2
has exact synonym: IPC
has exact synonym: T-associated plasma cell
has exact synonym: interferon-producing cell
has exact synonym: lymphoid dendritic cell
has exact synonym: pDC
has exact synonym: plasmacytoid T cell
has exact synonym: plasmacytoid monocyte
has exact synonym: type 2 DC
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: plasmacytoid dendritic cell
annotated property: subClassOf
annotated target: dendritic cell
is inferred: true

Axiom
annotated source: plasmacytoid dendritic cell
annotated property: IAO_0000115
annotated target: A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: PMCID:PMC2118448
has db xref: PMCID:PMC538703
has db xref: PMID:15549123
has db xref: PMID:17332250
has db xref: PMID:17850486
has db xref: PMID:20304825

Axiom
annotated source: plasmacytoid dendritic cell
annotated property: description
annotated target: Plasmacytoid dendritic cells (pDCs), initially known as interferon-producing cells, are a unique subpopulation of dendritic cells. Unlike conventional dendritic cells (cDCs), plasmacytoid dendritic cells are characterized by their distinctive plasma cell-like morphology. These cells play vital roles in the innate and adaptive immune response, particularly in the antiviral response. Highly prevalent in the blood and lymphoid organs, pDCs are rare in non-lymphoid tissues, with the exception of inflamed tissues and tumors where they are often recruited. A key role of plasmacytoid dendritic cells is their rapid and robust production of type 1 interferons in response to viral infections. This is crucial for antiviral defense as interferon signals to other immune cells to increase their antiviral defenses. pDCs achieve this by detecting viral nucleic acids in the cytosol through Toll-like receptors (TLRs), specifically TLR7 and TLR9. Upon recognition, these cells quickly produce substantial amounts of interferons, which plays a significant role in the containment of viral replication and the development of acquired antiviral immunity. The potential of plasmacytoid dendritic cells for antigen presentations to naive T cells is relatively low under steady-state conditions. Upon activation by certain stimuli, such as viruses or CpG oligodeoxynucleotides, they have the ability to differentiate into efficient antigen-presenting cells. This transition to activated cells involves an upregulation of major histocompatibility complex (MHC) class II molecules and co-stimulatory molecules, thus allowing them to effectively present antigenic peptides to naive T cells. This crucial function in linking innate and adaptive immunity underlines the importance of pDCs to the overall immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain informatio…
has db xref: DOI:10.1016/bs.ircmb.2019.07.004
has db xref: DOI:10.1016/j.immuni.2007.06.006
has db xref: DOI:10.1016/j.immuni.2018.12.027
has db xref: DOI:10.1038/nri3865

plasmacytoid dendritic cell on CELLxGENE CellGuide
type: Axiom
annotated source: plasmacytoid dendritic cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000784

mature B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002504
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0042113
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0002335
subclass of: professional antigen presenting cell
subclass of: CL_0001201
subclass of: Restriction
  on property: RO_0002202
  some values from: transitional stage B cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042113
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0002335
disjoint with: immature B cell
disjoint with: precursor B cell
disjoint with: transitional stage B cell
IAO_0000115: A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen.
description: A mature B cell is a critical component of the body's immune system, with different mature B cell subsets providing distinct functions in both adaptive and innate humoral immune responses. The primary role of these cells in the immune function is to produce antibodies or immunoglobulins which serve to neutralize or aid in the destruction of pathogens – microbes, viruses or any toxin that is harmful to the body. Mature B cells develop from immature B cells that have migrated from the bone marrow to the spleen where they differentiate through transitional B cell stages (called T1 and T2). Following antigen activation, mature B cells then undergo further developmental stages. Before encountering a specific antigen, mature B cells are called ‘naïve’ B cells. Due to the high variability of B cell receptors (BCR) even within the same individual, each naive B cell is capable of recognizing a unique molecular structure, leading to an immensely diverse repertoire of these cells ready to react against a wide array of pathogenic threats. Mature B cell subsets include follicular and marginal zone B cells, so named because they are enriched in the follicles and marginal zones of the spleen, respectively, although they are not confined to these compartments. Follicular B cells depend upon T cells for activation against specific antigens, and this reaction forms germinal centers in which the follicular B cells differentiate into germinal center B cells. Following class switch recombination and somatic hypermutation, these cells can differentiate into plasma cells, which secrete high-affinity antibodies, or memory B cells, which contribute to immunological memory when re-challenged by the same antigen. Marginal zone B cells can function as antigen-presenting cells and can also rapidly respond to blood-borne antigens by differentiating into antibody-secreting plasma cells with short half-lives. In addition to follicular and marginal zone B cells, there is a third population of matur…
has db xref: ZFA:0009331
has exact synonym: mature B lymphocyte
has exact synonym: mature B-cell
has exact synonym: mature B-lymphocyte
in subset: cellxgene subset
comment: Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive.

Axiom
annotated source: mature B cell
annotated property: subClassOf
annotated target: CL_0001201
is inferred: true

Axiom
annotated source: mature B cell
annotated property: IAO_0000115
annotated target: A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: ISBN:0781735149

Axiom
annotated source: mature B cell
annotated property: description
annotated target: A mature B cell is a critical component of the body's immune system, with different mature B cell subsets providing distinct functions in both adaptive and innate humoral immune responses. The primary role of these cells in the immune function is to produce antibodies or immunoglobulins which serve to neutralize or aid in the destruction of pathogens – microbes, viruses or any toxin that is harmful to the body. Mature B cells develop from immature B cells that have migrated from the bone marrow to the spleen where they differentiate through transitional B cell stages (called T1 and T2). Following antigen activation, mature B cells then undergo further developmental stages. Before encountering a specific antigen, mature B cells are called ‘naïve’ B cells. Due to the high variability of B cell receptors (BCR) even within the same individual, each naive B cell is capable of recognizing a unique molecular structure, leading to an immensely diverse repertoire of these cells ready to react against a wide array of pathogenic threats. Mature B cell subsets include follicular and marginal zone B cells, so named because they are enriched in the follicles and marginal zones of the spleen, respectively, although they are not confined to these compartments. Follicular B cells depend upon T cells for activation against specific antigens, and this reaction forms germinal centers in which the follicular B cells differentiate into germinal center B cells. Following class switch recombination and somatic hypermutation, these cells can differentiate into plasma cells, which secrete high-affinity antibodies, or memory B cells, which contribute to immunological memory when re-challenged by the same antigen. Marginal zone B cells can function as antigen-presenting cells and can also rapidly respond to blood-borne antigens by differentiating into antibody-secreting plasma cells with short half-lives. In addition to follicular and marginal zone B cells, there is a third population of matur…
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1016/B978-0-12-397933-9.00007-2
has db xref: DOI:10.1186/s12967-020-02289-w

Axiom
annotated source: mature B cell
annotated property: hasDbXref
annotated target: ZFA:0009331
mapping justification: UnspecifiedMatching

mature B cell on CELLxGENE CellGuide
type: Axiom
annotated source: mature B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000785

plasma cell
type: Class
equivalent class: Class
  intersection of: antibody secreting cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017508
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005794
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0019814
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0042613
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001935
subclass of: antibody secreting cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017508
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005794
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0019814
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0042613
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001935
subclass of: Restriction
  on property: RO_0002202
  some values from: plasmablast
IAO_0000115: A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
has db xref: BTO:0000392
has db xref: FMA:70574
has db xref: MESH:D010950
has db xref: ZFA:0009332
has exact synonym: plasma B cell
has exact synonym: plasma B-cell
has exact synonym: plasmacyte
has exact synonym: plasmocyte
has related synonym: effector B cell
has related synonym: effector B-cell
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive.

Axiom
annotated source: plasma cell
annotated property: subClassOf
annotated target: antibody secreting cell
is inferred: true

Axiom
annotated source: plasma cell
annotated property: IAO_0000115
annotated target: A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GO_REF:0000031
has db xref: ISBN:0721601464
has db xref: ISBN:0781735149
has db xref: PMID:19447676
has db xref: PMID:20081059
has db xref: PMID:20839338
has db xref: PMID:20951740
has db xref: http://en.wikipedia.org/wiki/Plasma_cell

Axiom
annotated source: plasma cell
annotated property: hasDbXref
annotated target: ZFA:0009332
mapping justification: UnspecifiedMatching

memory B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001935
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0042613
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0002344
subclass of: mature B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001935
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0042613
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0002344
IAO_0000115: A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative.
description: Memory B cells are a subtype of B cells that play a significant role in the adaptive immune response. They originate as part of B lymphocytes lineage and differentiate into memory B cells after activation by an antigen. The primary function of memory B cells is to respond rapidly to preexposure of the same antigen which originally activated it. Upon re-encountering the antigen, memory B cells can quickly differentiate into plasmablasts to generate antibodies or seed germinal centers to generate a robust immune response. Memory B cells can derive from mature B cells that undergo the germinal center reaction or those that differentiate in extrafollicular clusters. It is generally thought that memory B cells activated via the extrafollicular pathway are shorter-lived and produce lower-affinity antibodies, while those activated in germinal centers are longer-lived and produce high-affinity antibodies, having undergone somatic hypermutation. Memory B cells have a prolonged lifespan, lasting for years or even decades, enabling them to provide sustained protection against repeated or persistent infections. These cells are therefore a fundamental component of humoral immunological memory. As such, these cells are also important factors in the response to immunization/ (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009333
has exact synonym: memory B lymphocyte
has exact synonym: memory B-cell
has exact synonym: memory B-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Memory B-cells are also reportedly CD5-negative, CD10-negative, CD21-positive, CD22-positive, CD23-negative, CD24-positive, CD25-positive, CD27-positive, CD34-negative, CD38-negative, CD40-positive, CD43-negative, CD44-positive, CD45-positive, CD53-positive, CD80-negative, CD81-negative, CD86-positive, and CD196/CCR6-positive.

Axiom
annotated source: memory B cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: memory B cell
annotated property: IAO_0000115
annotated target: A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: PMID:20081059
has db xref: PMID:20839338
has db xref: http://en.wikipedia.org/wiki/Memory_B_cell

Axiom
annotated source: memory B cell
annotated property: description
annotated target: Memory B cells are a subtype of B cells that play a significant role in the adaptive immune response. They originate as part of B lymphocytes lineage and differentiate into memory B cells after activation by an antigen. The primary function of memory B cells is to respond rapidly to preexposure of the same antigen which originally activated it. Upon re-encountering the antigen, memory B cells can quickly differentiate into plasmablasts to generate antibodies or seed germinal centers to generate a robust immune response. Memory B cells can derive from mature B cells that undergo the germinal center reaction or those that differentiate in extrafollicular clusters. It is generally thought that memory B cells activated via the extrafollicular pathway are shorter-lived and produce lower-affinity antibodies, while those activated in germinal centers are longer-lived and produce high-affinity antibodies, having undergone somatic hypermutation. Memory B cells have a prolonged lifespan, lasting for years or even decades, enabling them to provide sustained protection against repeated or persistent infections. These cells are therefore a fundamental component of humoral immunological memory. As such, these cells are also important factors in the response to immunization/ (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/B978-0-12-397933-9.00007-2
has db xref: DOI:10.1038/leu.2016.226
has db xref: DOI:10.1111/imr.13016
has db xref: DOI:10.1111/sji.12336
has db xref: DOI:10.3389/fimmu.2019.01787/full

Axiom
annotated source: memory B cell
annotated property: hasDbXref
annotated target: ZFA:0009333
mapping justification: UnspecifiedMatching

memory B cell on CELLxGENE CellGuide
type: Axiom
annotated source: memory B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000787

naive B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0002344
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001963
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
subclass of: mature B cell
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0002344
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001963
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
IAO_0000115: A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery.
description: Naïve B cells are mature B lymphocytes that have not previously encountered a specific antigen, implying that they are "naïve" or "inexperienced". They express B-cell receptors (BCRs) on the cell surface that enable them to detect specific foreign antigens. Due to the high variability of BCRs even within the same individual, each naïve B cell is capable of recognizing a unique molecular structure, leading to an immensely diverse repertoire of these cells ready to react against a wide array of pathogenic threats. They are critical for humoral immunity as they are the precursors of antigen-specific B cells, giving rise to effector cells or memory B cells after antigen encounter and activation. The primary function of naïve B cells involves recognizing foreign antigens and initiating the immune response. If the B-cell receptor-engaged naïve B cell receives a proper activation signal from a helper T cell, it begins to proliferate and differentiate into plasma cells and memory B cells. Plasma cells secrete antibodies that neutralize the antigen, whereas memory B cells provide long-term immunity by remembering the specific pathogen for quicker attack upon any future invasions by the same entity. Furthermore, naïve B cells play a crucial role in the establishment of germinal centers (GCs), which are special zones within secondary lymphoid organs where mature B cells undergo clonal expansion, antibody class switching, and somatic hypermutation for the production of high-affinity antibodies. The maturation and changes within these GCs not only enhance the body's defense mechanisms against ongoing infections, but also promise a more rapid and effective response during subsequent encounters with the same pathogen. In summary, naïve B cells represent a stage in B cell development and serve as foundations for the adaptive humoral immune response, playing pivotal roles in antigen recognition, initiation of immune response, and long-term immunological memory. (This extended descri…
has db xref: ZFA:0009334
has exact synonym: naive B lymphocyte
has exact synonym: naive B-cell
has exact synonym: naive B-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'naive B cell'. Per DSD: Naive B cells are also reportedly CD10-negative, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD25-negative, CD27-negative, CD34-negative, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD80-negative, CD81-positive, CD84-positive, CD86-negative, CD95-negative, CD138-negative, CD150-positive, CD184/CXCR4-positive, CD185/CXCR5-positive, CD196/CCR6-positive, CD200-positive, CD229-positive, CD243-positive, CD289-positive, CD290-positive, CD352-positive, MHCII/HLA-DR-positive, cadherin 9-positive, and sIgH-positive, Transcription factors: Pax5-positive, ETS1-positive, FOXO1A-positive, KLF4-positive, KLF9-positive, MiTF-positive, OBF1-positive, PLZF-positive, and SpiB-positive.

Axiom
annotated source: naive B cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: naive B cell
annotated property: IAO_0000115
annotated target: A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: ISBN:0781765196
has db xref: PMID:19447676
has db xref: PMID:20081059
has db xref: PMID:20839338
has db xref: PMID:20933013
has db xref: PMID:22343568

Axiom
annotated source: naive B cell
annotated property: description
annotated target: Naïve B cells are mature B lymphocytes that have not previously encountered a specific antigen, implying that they are "naïve" or "inexperienced". They express B-cell receptors (BCRs) on the cell surface that enable them to detect specific foreign antigens. Due to the high variability of BCRs even within the same individual, each naïve B cell is capable of recognizing a unique molecular structure, leading to an immensely diverse repertoire of these cells ready to react against a wide array of pathogenic threats. They are critical for humoral immunity as they are the precursors of antigen-specific B cells, giving rise to effector cells or memory B cells after antigen encounter and activation. The primary function of naïve B cells involves recognizing foreign antigens and initiating the immune response. If the B-cell receptor-engaged naïve B cell receives a proper activation signal from a helper T cell, it begins to proliferate and differentiate into plasma cells and memory B cells. Plasma cells secrete antibodies that neutralize the antigen, whereas memory B cells provide long-term immunity by remembering the specific pathogen for quicker attack upon any future invasions by the same entity. Furthermore, naïve B cells play a crucial role in the establishment of germinal centers (GCs), which are special zones within secondary lymphoid organs where mature B cells undergo clonal expansion, antibody class switching, and somatic hypermutation for the production of high-affinity antibodies. The maturation and changes within these GCs not only enhance the body's defense mechanisms against ongoing infections, but also promise a more rapid and effective response during subsequent encounters with the same pathogen. In summary, naïve B cells represent a stage in B cell development and serve as foundations for the adaptive humoral immune response, playing pivotal roles in antigen recognition, initiation of immune response, and long-term immunological memory. (This extended descri…
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1016/B978-0-12-397933-9.00007-2
has db xref: DOI:10.1186/s12967-020-02289-w

Axiom
annotated source: naive B cell
annotated property: hasDbXref
annotated target: ZFA:0009334
mapping justification: UnspecifiedMatching

naive B cell on CELLxGENE CellGuide
type: Axiom
annotated source: naive B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000788

alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0042105
subclass of: T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0042105
disjoint with: gamma-delta T cell
IAO_0000115: A T cell that expresses an alpha-beta T cell receptor complex.
has db xref: ZFA:0009335
has exact synonym: alpha-beta T lymphocyte
has exact synonym: alpha-beta T-cell
has exact synonym: alpha-beta T-lymphocyte
in subset: blood and immune upper slim
in subset: cellxgene subset

Axiom
annotated source: alpha-beta T cell
annotated property: subClassOf
annotated target: T cell
is inferred: true

Axiom
annotated source: alpha-beta T cell
annotated property: IAO_0000115
annotated target: A T cell that expresses an alpha-beta T cell receptor complex.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: alpha-beta T cell
annotated property: hasDbXref
annotated target: ZFA:0009335
mapping justification: UnspecifiedMatching

immature alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: alpha-beta T cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0045058
subclass of: alpha-beta T cell
subclass of: CL_0002420
IAO_0000115: An alpha-beta T cell that has an immature phenotype and has not completed T cell selection.
description: Immature alpha-beta T cells represent a subpopulation of T cells in the thymus that are at a development stage in which they are yet to attain full functional status. The term 'alpha-beta' refers to the two distinct types of chains, alpha (α) and beta (β), which form the T cell receptor (TCR) located on the cell's surface. This T cell receptor enables the cell to identify and bind to specific antigens in order to initiate an immune response. Immature alpha-beta T cells arise from lymphoid progenitor cells in the bone marrow and migrate to the thymus, where the maturation of T cells takes place. In the thymus, immature cells (thymocytes) undergo a series of division and differentiation events characterized by the rearrangement of their TCR genes. Upon successful recombination, the cells express a functional alpha-beta TCR on their surface and can then be subjected to a process of selection based on the specificity of the newly expressed receptors. These stages of development are critical to ensuring that only cells with a suitable TCR repertoire survive, ready to be deployed within the immune system. Multiple subsets of immature alpha-beta T cells can be distinguished, depending on the developmental and differentiation stage, including CD4+CD8+ double positive thymocytes, CD4+ or CD8+ single positive thymocytes and immature NK T cells. Immature alpha-beta T cells are critically important to immune function. They constitute the foundation for the adaptive immune system - a fundamental component in combating pathological agents. Once fully matured, these cells can differentiate further into effector T cell types (like helper, cytotoxic, and regulatory T cells), each having unique functional roles in an immune response. The proper development of immature alpha-beta T cells is fundamental to the overall health and efficacy of the immune system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL edit…
has exact synonym: immature alpha-beta T lymphocyte
has exact synonym: immature alpha-beta T-cell
has exact synonym: immature alpha-beta T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: immature alpha-beta T cell
annotated property: subClassOf
annotated target: alpha-beta T cell
is inferred: true

Axiom
annotated source: immature alpha-beta T cell
annotated property: IAO_0000115
annotated target: An alpha-beta T cell that has an immature phenotype and has not completed T cell selection.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: immature alpha-beta T cell
annotated property: description
annotated target: Immature alpha-beta T cells represent a subpopulation of T cells in the thymus that are at a development stage in which they are yet to attain full functional status. The term 'alpha-beta' refers to the two distinct types of chains, alpha (α) and beta (β), which form the T cell receptor (TCR) located on the cell's surface. This T cell receptor enables the cell to identify and bind to specific antigens in order to initiate an immune response. Immature alpha-beta T cells arise from lymphoid progenitor cells in the bone marrow and migrate to the thymus, where the maturation of T cells takes place. In the thymus, immature cells (thymocytes) undergo a series of division and differentiation events characterized by the rearrangement of their TCR genes. Upon successful recombination, the cells express a functional alpha-beta TCR on their surface and can then be subjected to a process of selection based on the specificity of the newly expressed receptors. These stages of development are critical to ensuring that only cells with a suitable TCR repertoire survive, ready to be deployed within the immune system. Multiple subsets of immature alpha-beta T cells can be distinguished, depending on the developmental and differentiation stage, including CD4+CD8+ double positive thymocytes, CD4+ or CD8+ single positive thymocytes and immature NK T cells. Immature alpha-beta T cells are critically important to immune function. They constitute the foundation for the adaptive immune system - a fundamental component in combating pathological agents. Once fully matured, these cells can differentiate further into effector T cell types (like helper, cytotoxic, and regulatory T cells), each having unique functional roles in an immune response. The proper development of immature alpha-beta T cells is fundamental to the overall health and efficacy of the immune system. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL edit…
has db xref: DOI:10.1016/j.immuni.2018.01.007
has db xref: DOI:10.1016/j.immuni.2020.03.019
has db xref: DOI:10.1038/s41392-023-01471-y
has db xref: DOI:10.3389/fimmu.2022.884569
has db xref: https://www.sciencedirect.com/topics/immunology-and-microbiology/alpha-beta-t-cell

immature alpha-beta T cell on CELLxGENE CellGuide
type: Axiom
annotated source: immature alpha-beta T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000790

mature alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0045058
subclass of: alpha-beta T cell
subclass of: CL_0002419
subclass of: Restriction
  on property: RO_0002202
  some values from: immature alpha-beta T cell
IAO_0000115: A alpha-beta T cell that has a mature phenotype.
description: Mature alpha-beta T cells, also known as αβ T cells, are critical components of the adaptive immune system, responsible for a mediated immune response to pathogens and infected body cells. They derive their name from the alpha and beta chains that make up their characteristic T-cell receptor (TCR), a protein complex that binds to antigens. These cells undergo a maturation process in the thymus, where they learn to recognize self-antigens, thus achieving self-tolerance. Maturation of alpha-beta T cells takes place in the thymus and is tightly controlled by various transcriptional and epigenetic regulators. They develop through several stages from progenitors to mature T cells, from CD4-CD8- double negative cells to CD4+CD8+ double positive cells, until they eventually become CD4+ or CD8+ single positive cells. Once matured, alpha-beta T cells primarily serve as regulators and effectors in an immune response. They are adept at recognizing fragments of antigens, often viruses or bacteria, presented on the surface of other cells via major histocompatibility complex (MHC) molecules. Once they encounter and recognize an antigen, they become activated, proliferate and differentiate into distinct subsets of effector T cells, such as cytotoxic T cells, helper T cells, and Natural Killer (NK) cells, each with a specific role in immune response. Cytotoxic T cells, the effector cells for cell-mediated immunity, are adept at killing cells that have been infected, particularly with viruses. They do this by binding to infected cells and releasing cytotoxic substances which induce apoptosis, or cell death, thus eliminating the infected cells. The main function of NK cells is to kill virally infected cells, and to detect early signs of cancer. Helper T cells do not kill infected cells directly but play a key role in modulating or orchestrating the immune response by releasing cytokines that recruit and regulate other immunity cells such as B cells and macrophages. Therefore, the ver…
has exact synonym: mature alpha-beta T lymphocyte
has exact synonym: mature alpha-beta T-cell
has exact synonym: mature alpha-beta T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: mature alpha-beta T cell
annotated property: subClassOf
annotated target: alpha-beta T cell
is inferred: true

Axiom
annotated source: mature alpha-beta T cell
annotated property: IAO_0000115
annotated target: A alpha-beta T cell that has a mature phenotype.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: mature alpha-beta T cell
annotated property: description
annotated target: Mature alpha-beta T cells, also known as αβ T cells, are critical components of the adaptive immune system, responsible for a mediated immune response to pathogens and infected body cells. They derive their name from the alpha and beta chains that make up their characteristic T-cell receptor (TCR), a protein complex that binds to antigens. These cells undergo a maturation process in the thymus, where they learn to recognize self-antigens, thus achieving self-tolerance. Maturation of alpha-beta T cells takes place in the thymus and is tightly controlled by various transcriptional and epigenetic regulators. They develop through several stages from progenitors to mature T cells, from CD4-CD8- double negative cells to CD4+CD8+ double positive cells, until they eventually become CD4+ or CD8+ single positive cells. Once matured, alpha-beta T cells primarily serve as regulators and effectors in an immune response. They are adept at recognizing fragments of antigens, often viruses or bacteria, presented on the surface of other cells via major histocompatibility complex (MHC) molecules. Once they encounter and recognize an antigen, they become activated, proliferate and differentiate into distinct subsets of effector T cells, such as cytotoxic T cells, helper T cells, and Natural Killer (NK) cells, each with a specific role in immune response. Cytotoxic T cells, the effector cells for cell-mediated immunity, are adept at killing cells that have been infected, particularly with viruses. They do this by binding to infected cells and releasing cytotoxic substances which induce apoptosis, or cell death, thus eliminating the infected cells. The main function of NK cells is to kill virally infected cells, and to detect early signs of cancer. Helper T cells do not kill infected cells directly but play a key role in modulating or orchestrating the immune response by releasing cytokines that recruit and regulate other immunity cells such as B cells and macrophages. Therefore, the ver…
has db xref: DOI:10.1016/j.immuni.2018.01.007
has db xref: DOI:10.1038/s41392-023-01471-y
has db xref: DOI:10.3389/fimmu.2022.884569
has db xref: https://www.sciencedirect.com/topics/immunology-and-microbiology/alpha-beta-t-cell

mature alpha-beta T cell on CELLxGENE CellGuide
type: Axiom
annotated source: mature alpha-beta T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000791

CD4-positive, CD25-positive, alpha-beta regulatory T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001380
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050777
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001869
subclass of: CD4-positive, alpha-beta T cell
subclass of: regulatory T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001869
IAO_0000115: A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
description: The CD4-positive, CD25-positive, alpha-beta regulatory T (Treg) cell serves as a vital element in the mammalian immune system, playing a pivotal role in maintaining immune homeostasis and preventing autoimmunity. This particular T regulatory cell is characterized by CD4 proteins and a high level of CD25 (the alpha chain of the interleukin-2 receptor) on its cell surface. The T-cell receptor (TCR) of these Treg cells is composed of alpha and beta protein chains, making them a subtype of the alpha-beta T cell population that recognize and bind to antigens presented by MHC class II molecules. The primary function of CD4-positive, CD25-positive, alpha-beta Treg cells is regulating immune responses, ensuring that the immune response is proportionate and preventing autoimmunity, maintaining peripheral immune tolerance, and limiting chronic inflammation. They achieve this regulation by suppressing or downregulating the proliferation of effector immune cells, which are activated in response to antigens, to prevent their excessive or uncontrolled activity. CD4-positive, CD25-positive, alpha-beta Treg cells can suppress immune responses via a variety of mechanisms, including the release of inhibitory cytokines, in particular IL-10 and TGFβ, or through cytolysis of effector immune cells (e.g. antibody-producing B cells) involving perforin and granzymes. They can also modulate the maturation or function of dendritic cells, which are key antigen-presenting cells, and thereby reduce their ability to stimulate effector T cells. This downregulation also suppresses effector T cell functions against self-antigens—proteins that are innate to the body—to prevent autoimmunity. In essence, Treg cells act as a policing force within the immune system to maintain balance and prevent overreaction which can potentially lead to damaging effects. Besides their crucial role in preventing autoimmunity, CD4-positive, CD25-positive, alpha-beta Treg cells contribute to other functions such as tumor …
has broad synonym: Treg
has broad synonym: suppressor T cell
has broad synonym: suppressor T lymphocyte
has broad synonym: suppressor T-cell
has broad synonym: suppressor T-lymphocyte
has exact synonym: CD4-positive, CD25-positive, alpha-beta regulatory T lymphocyte
has exact synonym: CD4-positive, CD25-positive, alpha-beta regulatory T-cell
has exact synonym: CD4-positive, CD25-positive, alpha-beta regulatory T-lymphocyte
in subset: cellxgene subset
comment: This cell type is compatible with the HIPC Lyoplate markers for 'Treg'. The inclusion of CD127lo in the logical definition is compatible with both human and mouse T cells of this subtype.

Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: IAO_0000115
annotated target: A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149
has db xref: PMID:19464985
has db xref: PMID:22343568

Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: description
annotated target: The CD4-positive, CD25-positive, alpha-beta regulatory T (Treg) cell serves as a vital element in the mammalian immune system, playing a pivotal role in maintaining immune homeostasis and preventing autoimmunity. This particular T regulatory cell is characterized by CD4 proteins and a high level of CD25 (the alpha chain of the interleukin-2 receptor) on its cell surface. The T-cell receptor (TCR) of these Treg cells is composed of alpha and beta protein chains, making them a subtype of the alpha-beta T cell population that recognize and bind to antigens presented by MHC class II molecules. The primary function of CD4-positive, CD25-positive, alpha-beta Treg cells is regulating immune responses, ensuring that the immune response is proportionate and preventing autoimmunity, maintaining peripheral immune tolerance, and limiting chronic inflammation. They achieve this regulation by suppressing or downregulating the proliferation of effector immune cells, which are activated in response to antigens, to prevent their excessive or uncontrolled activity. CD4-positive, CD25-positive, alpha-beta Treg cells can suppress immune responses via a variety of mechanisms, including the release of inhibitory cytokines, in particular IL-10 and TGFβ, or through cytolysis of effector immune cells (e.g. antibody-producing B cells) involving perforin and granzymes. They can also modulate the maturation or function of dendritic cells, which are key antigen-presenting cells, and thereby reduce their ability to stimulate effector T cells. This downregulation also suppresses effector T cell functions against self-antigens—proteins that are innate to the body—to prevent autoimmunity. In essence, Treg cells act as a policing force within the immune system to maintain balance and prevent overreaction which can potentially lead to damaging effects. Besides their crucial role in preventing autoimmunity, CD4-positive, CD25-positive, alpha-beta Treg cells contribute to other functions such as tumor …
has db xref: DOI:10.1016/j.immuni.2019.01.020
has db xref: DOI:10.1038/nri2343
has db xref: DOI:10.1146/annurev-immunol-042718-041717
has db xref: DOI:10.3389/fimmu.2019.03100
has db xref: DOI:10.3389/fimmu.2021.750542

Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: hasBroadSynonym
annotated target: Treg
has db xref: PMID:22343568

CD4-positive, CD25-positive, alpha-beta regulatory T cell on CELLxGENE CellGuide
type: Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000792

CD4-positive, alpha-beta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0001025
    some values from: UBERON_0001277
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002385
subclass of: CD4-positive, alpha-beta T cell
subclass of: alpha-beta intraepithelial T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: CD4-positive, alpha-beta thymocyte
IAO_0000115: A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract.
has broad synonym: IEL
has broad synonym: intraepithelial lymphocyte
has exact synonym: CD4-positive, alpha-beta intraepithelial T lymphocyte
has exact synonym: CD4-positive, alpha-beta intraepithelial T-cell
has exact synonym: CD4-positive, alpha-beta intraepithelial T-lymphocyte
in subset: human reference atlas

Axiom
annotated source: CD4-positive, alpha-beta intraepithelial T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, alpha-beta intraepithelial T cell
annotated property: IAO_0000115
annotated target: A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

CD8-positive, alpha-beta cytotoxic T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003466
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003499
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001913
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0033380
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0030217
subclass of: CD8-positive, alpha-beta T cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003466
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003499
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD8-positive, alpha-beta T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001913
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0033380
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030217
IAO_0000115: A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
description: The CD8-positive, alpha-beta cytotoxic T cell plays a crucial role in the immune response system of vertebrates. A key feature of these cells is the expression of CD8, a transmembrane glycoprotein that serves as a co-receptor for the T cell receptor (TCR). Notably, the alpha-beta refers to the TCR heterodimer on the T cell, utilized to recognize the antigens displayed by Major Histocompatibility Complex (MHC) class I molecules on antigen-presenting cells. Functioning primarily to combat intracellular pathogens, CD8+ T cells primarily seek and destroy cells infected by viruses or transformed by cancer. The TCR on the CD8+ T cell recognizes and binds to the antigen-MHC I complex displayed on the infected cell’s surface. Following this interaction, along with the engagement of co-stimulatory molecules, the T cell becomes activated. Upon activation, the CD8+ T cell proliferates and differentiates into cytotoxic T lymphocytes (CTL), ready to survey the body for the recognized antigen. CTLs employ two major cytotoxic mechanisms: the release of cytotoxic granules and the expression of death-inducing ligands on their surface. Cytotoxic granules contain perforin, a protein that forms pores in the targeted cell membrane, and granzymes, enzymes that trigger apoptosis inside the targeted cell through the activation of caspases. The Fas ligand and TRAIL death-inducing ligands on CTLs also bind to their respective receptors on the target cell and initiate a caspase cascade leading to cell death of the target. This cytotoxic function of the CD8+ alpha-beta T cell is critical in the control of infections and in cancer surveillance. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has broad synonym: cytotoxic T cell
has broad synonym: cytotoxic T lymphocyte
has broad synonym: cytotoxic T-cell
has broad synonym: cytotoxic T-lymphocyte
has broad synonym: killer T cell
has broad synonym: killer T lymphocyte
has broad synonym: killer T-cell
has broad synonym: killer T-lymphocyte
has db xref: CALOHA:TS-0190
has exact synonym: CD8-positive, alpha-beta cytotoxic T lymphocyte
has exact synonym: CD8-positive, alpha-beta cytotoxic T-cell
has exact synonym: CD8-positive, alpha-beta cytotoxic T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Note that while T cells of this subset are loosely referred to 'cytotoxic T cells,' as many other T cell types, including CD4-positive, alpha-beta T cells and gamma-delta T cells exhibit cytotoxicity in vitro and in vivo.

Axiom
annotated source: CD8-positive, alpha-beta cytotoxic T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta cytotoxic T cell
annotated property: IAO_0000115
annotated target: A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

Axiom
annotated source: CD8-positive, alpha-beta cytotoxic T cell
annotated property: description
annotated target: The CD8-positive, alpha-beta cytotoxic T cell plays a crucial role in the immune response system of vertebrates. A key feature of these cells is the expression of CD8, a transmembrane glycoprotein that serves as a co-receptor for the T cell receptor (TCR). Notably, the alpha-beta refers to the TCR heterodimer on the T cell, utilized to recognize the antigens displayed by Major Histocompatibility Complex (MHC) class I molecules on antigen-presenting cells. Functioning primarily to combat intracellular pathogens, CD8+ T cells primarily seek and destroy cells infected by viruses or transformed by cancer. The TCR on the CD8+ T cell recognizes and binds to the antigen-MHC I complex displayed on the infected cell’s surface. Following this interaction, along with the engagement of co-stimulatory molecules, the T cell becomes activated. Upon activation, the CD8+ T cell proliferates and differentiates into cytotoxic T lymphocytes (CTL), ready to survey the body for the recognized antigen. CTLs employ two major cytotoxic mechanisms: the release of cytotoxic granules and the expression of death-inducing ligands on their surface. Cytotoxic granules contain perforin, a protein that forms pores in the targeted cell membrane, and granzymes, enzymes that trigger apoptosis inside the targeted cell through the activation of caspases. The Fas ligand and TRAIL death-inducing ligands on CTLs also bind to their respective receptors on the target cell and initiate a caspase cascade leading to cell death of the target. This cytotoxic function of the CD8+ alpha-beta T cell is critical in the control of infections and in cancer surveillance. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/s12276-023-01105-x
has db xref: DOI:10.3389/fimmu.2022.883010
has db xref: DOI:10.3389/fmolb.2021.628332
has db xref: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cytotoxic-t-cell

CD8-positive, alpha-beta cytotoxic T cell on CELLxGENE CellGuide
type: Axiom
annotated source: CD8-positive, alpha-beta cytotoxic T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000794

CD8-positive, alpha-beta regulatory T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050777
subclass of: CD8-positive, alpha-beta T cell
subclass of: regulatory T cell
IAO_0000115: A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
has broad synonym: suppressor T cell
has broad synonym: suppressor T lymphocyte
has broad synonym: suppressor T-cell
has broad synonym: suppressor T-lymphocyte
has exact synonym: CD8+ T(reg)
has exact synonym: CD8+ Treg
has exact synonym: CD8+ regulatory T cell
has exact synonym: CD8-positive T(reg)
has exact synonym: CD8-positive Treg
has exact synonym: CD8-positive, alpha-beta Treg
has exact synonym: CD8-positive, alpha-beta regulatory T lymphocyte
has exact synonym: CD8-positive, alpha-beta regulatory T-cell
has exact synonym: CD8-positive, alpha-beta regulatory T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: CD8-positive, alpha-beta regulatory T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta regulatory T cell
annotated property: IAO_0000115
annotated target: A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: alpha-beta intraepithelial T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000025402
subclass of: alpha-beta intraepithelial T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000025402
IAO_0000115: A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
description: CD8-alpha-beta-positive, alpha-beta intraepithelial T cells are subpopulation of αβ intraepithelial lymphocytes (IELs) which are predominately found in the intraepithelial layer of the intestine, skin and lung. They are characterized by the cell surface expression of both αβ T cell receptors (TCRs) and the CD8 αβ co-receptors, which are responsible for recognizing specific antigens expressed on the surface of pathogenic cells. The primary function of CD8-alpha-beta-positive, alpha-beta intraepithelial T cells revolves around providing immune protection by targeting and eliminating cells infected with viruses or other pathogens. The TCR-CD8 complex on their surfaces recognizes major histocompatibility complex (MHC) class I molecules on infected cells. After recognition, the T cells bind to the infected cells and release cytotoxic agents that trigger apoptosis, leading to the death of the infected cells and effectively curbing the spread of the invading pathogen. This process also helps create a memory response for the same pathogens, enabling quicker responses in subsequent encounters. With a majority of pathogens entering the body through the epithelial surfaces like skin and mucous membranes, having these T cells strategically located in these layers enables an effective first line of defense. Apart from pathogen detection and removal, they also contribute to maintaining tissue integrity and providing a surveillance mechanism against tumorigenic cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has broad synonym: IEL
has broad synonym: intraepithelial lymphocyte
has exact synonym: CD8-positive, alpha-beta intraepithelial T lymphocyte
has exact synonym: CD8-positive, alpha-beta intraepithelial T-cell
has exact synonym: CD8-positive, alpha-beta intraepithelial T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
annotated property: subClassOf
annotated target: alpha-beta intraepithelial T cell
is inferred: true

Axiom
annotated source: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
annotated property: IAO_0000115
annotated target: A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
has db xref: GOC:add
has db xref: ISBN:0781735149

Axiom
annotated source: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
annotated property: description
annotated target: CD8-alpha-beta-positive, alpha-beta intraepithelial T cells are subpopulation of αβ intraepithelial lymphocytes (IELs) which are predominately found in the intraepithelial layer of the intestine, skin and lung. They are characterized by the cell surface expression of both αβ T cell receptors (TCRs) and the CD8 αβ co-receptors, which are responsible for recognizing specific antigens expressed on the surface of pathogenic cells. The primary function of CD8-alpha-beta-positive, alpha-beta intraepithelial T cells revolves around providing immune protection by targeting and eliminating cells infected with viruses or other pathogens. The TCR-CD8 complex on their surfaces recognizes major histocompatibility complex (MHC) class I molecules on infected cells. After recognition, the T cells bind to the infected cells and release cytotoxic agents that trigger apoptosis, leading to the death of the infected cells and effectively curbing the spread of the invading pathogen. This process also helps create a memory response for the same pathogens, enabling quicker responses in subsequent encounters. With a majority of pathogens entering the body through the epithelial surfaces like skin and mucous membranes, having these T cells strategically located in these layers enables an effective first line of defense. Apart from pathogen detection and removal, they also contribute to maintaining tissue integrity and providing a surveillance mechanism against tumorigenic cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/s41385-018-0016-5
has db xref: DOI:10.1038/s41385-020-0294-6
has db xref: DOI:10.3389/fimmu.2022.1059042

CD8-alpha-beta-positive, alpha-beta intraepithelial T cell on CELLxGENE CellGuide
type: Axiom
annotated source: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000796

alpha-beta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: RO_0001025
    some values from: UBERON_0001277
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002385
subclass of: mature alpha-beta T cell
subclass of: CL_0020035
IAO_0000115: A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
has broad synonym: IEL
has broad synonym: intraepithelial lymphocyte
has exact synonym: alpha-beta intraepithelial T lymphocyte
has exact synonym: alpha-beta intraepithelial T-cell
has exact synonym: alpha-beta intraepithelial T-lymphocyte

Axiom
annotated source: alpha-beta intraepithelial T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: alpha-beta intraepithelial T cell
annotated property: IAO_0000115
annotated target: A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

gamma-delta T cell
type: Class
equivalent class: Class
  intersection of: T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0042106
subclass of: T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0042106
IAO_0000115: A T cell that expresses a gamma-delta T cell receptor complex.
description: Gamma-delta T cells, also referred to as γδ T cells, are a distinct subset of T lymphocytes that play unique roles in the immune system. They are defined by expression of heterodimeric T-cell receptors (TCRs) comprised of γ and δ chains. They share characteristics with both innate and adaptive immune cells, and unlike alpha-beta (αβ) T cells, they do not require antigen processing and Major Histocompatibility Complex (MHC) presentation for the recognition of antigens. This unique response mechanism allows them to contribute to rapid immune responses, particularly in the context of tissue injury and infection. Depending on the γδ TCR and the context, different subsets of gamma-delta T cells perform a variety of functions which range from regulating thermogenesis in adipose tissue to controlling the plasticity of neuronal synapses in the central nervous system. A key function is in tissue homeostasis and surveillance against infectious agents and tumors. They can carry out their defense role through several mechanisms, such as cytokine production, killing of target cells, and regulation of other immune cell responses. In response to pathogens, these cells produce a wide range of cytokines, including interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and interleukin-17 (IL-17), which help recruit and activate other immune cells to the site of infection. Furthermore, gamma-delta T cells can directly kill infected cells or cancerous cells, which is instrumental in preventing the spread of infection or malignancy. Despite the broadly generalized role in immunity, the function of gamma-delta T cells can vastly vary depending on their tissue location. In the skin and mucosal tissues, they provide quick response to pathogens, while in secondary lymphoid organs, their regulatory functions shape the adaptive immune response. In recent years, their role in the context of autoimmunity and cancer has gained attention, with emerging studies suggesting their potential f…
has db xref: ZFA:0009336
has exact synonym: gamma-delta T lymphocyte
has exact synonym: gamma-delta T-cell
has exact synonym: gamma-delta T-lymphocyte
has exact synonym: gammadelta T cell
has related synonym: gd T cell
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways.

Axiom
annotated source: gamma-delta T cell
annotated property: subClassOf
annotated target: T cell
is inferred: true

Axiom
annotated source: gamma-delta T cell
annotated property: IAO_0000115
annotated target: A T cell that expresses a gamma-delta T cell receptor complex.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: gamma-delta T cell
annotated property: description
annotated target: Gamma-delta T cells, also referred to as γδ T cells, are a distinct subset of T lymphocytes that play unique roles in the immune system. They are defined by expression of heterodimeric T-cell receptors (TCRs) comprised of γ and δ chains. They share characteristics with both innate and adaptive immune cells, and unlike alpha-beta (αβ) T cells, they do not require antigen processing and Major Histocompatibility Complex (MHC) presentation for the recognition of antigens. This unique response mechanism allows them to contribute to rapid immune responses, particularly in the context of tissue injury and infection. Depending on the γδ TCR and the context, different subsets of gamma-delta T cells perform a variety of functions which range from regulating thermogenesis in adipose tissue to controlling the plasticity of neuronal synapses in the central nervous system. A key function is in tissue homeostasis and surveillance against infectious agents and tumors. They can carry out their defense role through several mechanisms, such as cytokine production, killing of target cells, and regulation of other immune cell responses. In response to pathogens, these cells produce a wide range of cytokines, including interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and interleukin-17 (IL-17), which help recruit and activate other immune cells to the site of infection. Furthermore, gamma-delta T cells can directly kill infected cells or cancerous cells, which is instrumental in preventing the spread of infection or malignancy. Despite the broadly generalized role in immunity, the function of gamma-delta T cells can vastly vary depending on their tissue location. In the skin and mucosal tissues, they provide quick response to pathogens, while in secondary lymphoid organs, their regulatory functions shape the adaptive immune response. In recent years, their role in the context of autoimmunity and cancer has gained attention, with emerging studies suggesting their potential f…
has db xref: DOI:10.1038/s41571-022-00722-1
has db xref: DOI:10.1038/s41577-020-00452-4
has db xref: DOI:10.1073/pnas.1818488116
has db xref: DOI:10.1146/annurev-immunol-032713-120216
has db xref: https://www.mdpi.com/journal/cells/special_issues/delta_T

Axiom
annotated source: gamma-delta T cell
annotated property: hasDbXref
annotated target: ZFA:0009336
mapping justification: UnspecifiedMatching

Axiom
annotated source: gamma-delta T cell
annotated property: hasRelatedSynonym
annotated target: gd T cell
has synonym type: OMO_0003000

gamma-delta T cell on CELLxGENE CellGuide
type: Axiom
annotated source: gamma-delta T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000798

immature gamma-delta T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta T cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0042492
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0045058
subclass of: gamma-delta T cell
subclass of: CL_0002420
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0042492
subclass of: Restriction
  on property: RO_0002202
  some values from: DN3 thymocyte
IAO_0000115: A gamma-delta T cell that has an immature phenotype.
has db xref: ZFA:0009337
has exact synonym: immature gamma-delta T lymphocyte
has exact synonym: immature gamma-delta T-cell
has exact synonym: immature gamma-delta T-lymphocyte
comment: Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways.

Axiom
annotated source: immature gamma-delta T cell
annotated property: subClassOf
annotated target: gamma-delta T cell
is inferred: true

Axiom
annotated source: immature gamma-delta T cell
annotated property: IAO_0000115
annotated target: A gamma-delta T cell that has an immature phenotype.
has db xref: GOC:add
has db xref: ISBN:0781735149

Axiom
annotated source: immature gamma-delta T cell
annotated property: hasDbXref
annotated target: ZFA:0009337
mapping justification: UnspecifiedMatching

mature gamma-delta T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta T cell
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0045058
subclass of: gamma-delta T cell
subclass of: CL_0002419
subclass of: Restriction
  on property: RO_0002202
  some values from: immature gamma-delta T cell
IAO_0000115: A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location.
description: Mature gamma-delta (γδ) T-cells represent a distinct subgroup within the diverse T-cell lineage. They are rare in secondary lymphoid organs but enriched in many peripheral tissues, such as the intestines, lungs and skin, where they play key immunological roles in the protection against infections and tumors, tissue healing, and immune regulation. They are ‘unconventional’ T cells defined by the expression of T-cell receptors (TCRs) that are heterodimers composed of γ and δ chains. Unlike their alpha-beta (αβ) T-cell counterparts, which recognize antigens via Major Histocompatibility Complex (MHC) molecules, γδ T-cells are activated in an MHC-independent manner perceive their targets in a more direct manner, reacting to stress-induced self molecules or unprocessed antigens, providing a more rapid immune response. Mature γδ T-cells derive from double-negative CD4− CD8− (DN) thymocytes, which can give rise to either αβ T or γδ T cell lineages. γδ T cells then develop from this precursor following a single selection step mediated by the γδ TCR; unlike cells in the αβ T cell lineage, they do not progress through to a double positive stage. Instead, most γδ T cells remain double-negative and develop into mature γδ T cells before they egress from the thymus. Upon maturation, γδ T-cells characteristics of both innate and adaptive immunity and can have both pro- and anti-inflammatory functions. Mature γδ T-cells fall into distinct IFNγ- and IL-17A-producing cell populations that can be distinguished by CD27 and CCR6 expression, respectively. The mature γδ T-cell population also includes γδ intraepithelial T-cells and dendritic epidermal T cells (DETCs), which are only present in the epidermis of rodents. These phenotypically different mature γδ T-cells are functionally versatile. In addition to their role in immunosurveillance against microbes and tumor cells, aiding in early defense against invaders. They produce a cytokine and chemokine response and exert cytolysis of infe…
has db xref: ZFA:0009338
has exact synonym: mature gamma-delta T lymphocyte
has exact synonym: mature gamma-delta T-cell
has exact synonym: mature gamma-delta T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: mature gamma-delta T cell
annotated property: subClassOf
annotated target: gamma-delta T cell
is inferred: true

Axiom
annotated source: mature gamma-delta T cell
annotated property: IAO_0000115
annotated target: A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: mature gamma-delta T cell
annotated property: description
annotated target: Mature gamma-delta (γδ) T-cells represent a distinct subgroup within the diverse T-cell lineage. They are rare in secondary lymphoid organs but enriched in many peripheral tissues, such as the intestines, lungs and skin, where they play key immunological roles in the protection against infections and tumors, tissue healing, and immune regulation. They are ‘unconventional’ T cells defined by the expression of T-cell receptors (TCRs) that are heterodimers composed of γ and δ chains. Unlike their alpha-beta (αβ) T-cell counterparts, which recognize antigens via Major Histocompatibility Complex (MHC) molecules, γδ T-cells are activated in an MHC-independent manner perceive their targets in a more direct manner, reacting to stress-induced self molecules or unprocessed antigens, providing a more rapid immune response. Mature γδ T-cells derive from double-negative CD4− CD8− (DN) thymocytes, which can give rise to either αβ T or γδ T cell lineages. γδ T cells then develop from this precursor following a single selection step mediated by the γδ TCR; unlike cells in the αβ T cell lineage, they do not progress through to a double positive stage. Instead, most γδ T cells remain double-negative and develop into mature γδ T cells before they egress from the thymus. Upon maturation, γδ T-cells characteristics of both innate and adaptive immunity and can have both pro- and anti-inflammatory functions. Mature γδ T-cells fall into distinct IFNγ- and IL-17A-producing cell populations that can be distinguished by CD27 and CCR6 expression, respectively. The mature γδ T-cell population also includes γδ intraepithelial T-cells and dendritic epidermal T cells (DETCs), which are only present in the epidermis of rodents. These phenotypically different mature γδ T-cells are functionally versatile. In addition to their role in immunosurveillance against microbes and tumor cells, aiding in early defense against invaders. They produce a cytokine and chemokine response and exert cytolysis of infe…
has db xref: DOI:10.1016/j.smim.2022.101662
has db xref: DOI:10.3389/fimmu.2020.00042
has db xref: DOI:10.3389/fimmu.2023.1106652

Axiom
annotated source: mature gamma-delta T cell
annotated property: hasDbXref
annotated target: ZFA:0009338
mapping justification: UnspecifiedMatching

mature gamma-delta T cell on CELLxGENE CellGuide
type: Axiom
annotated source: mature gamma-delta T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000800

gamma-delta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: mature gamma-delta T cell
  intersection of: Restriction
    on property: RO_0001025
    some values from: UBERON_0001277
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002385
subclass of: mature gamma-delta T cell
subclass of: CL_0020035
IAO_0000115: A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses.
description: Gamma-delta intraepithelial T cells, also known as γδ intraepithelial lymphocytes (IELs), are a unique subset of T cells residing in the epithelial layer of mucosal tissues such as the intestine and skin; more are found in intestinal intraepithelial tissue than in other tissues. They are characterized by their distinct T-cell receptor (TCR) that is composed of one gamma (γ) and one delta (δ) chain, unlike the conventional alpha-beta T cells. Most γδ IELs also express the CD8-alpha-alpha homodimer (Cd8-alpha alpha positive, gamma-delta intraepithelial T cells), although some are lacking both co-receptors CD4 and CD8 (CD4-negative CD8-negative gamma-delta intraepithelial T cells). γδ IELs are though to be ‘natural’ IELs as they acquire their activated phenotype in an ‘alternative’ self-antigen-based maturation process in the thymus. Although the function of γδ IELs is still not fully established, current evidence indicates that they serve as a crucial first line of defense against invading pathogens, thus making them an important class of immune cells at the epithelial barrier interfaces. γδ IELs respond to a variety of antigens, including those not recognized by conventional T cells. They are also thought to be involved in recruiting in immune surveillance by promoting homeostasis of host microbiota and in limiting excessive inflammation. In addition to their primary role in immunity, γδ IELs also have roles in epithelial cell homeostasis and repair. They assist in maintaining the epithelial barrier by controlling the equilibrium of epithelial cell growth and death. They also contribute to the healing of lesions and the replacement of damaged epithelial cells. The regulative control exerted by γδ IELs over epithelial cell turnover indirectly influences immunity, underlining the complexity and versatility of these cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it …
has broad synonym: IEL
has broad synonym: intraepithelial lymphocyte
has db xref: ZFA:0009339
has exact synonym: gamma-delta intraepithelial T lymphocyte
has exact synonym: gamma-delta intraepithelial T-cell
has exact synonym: gamma-delta intraepithelial T-lymphocyte

Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: subClassOf
annotated target: mature gamma-delta T cell
is inferred: true

Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: IAO_0000115
annotated target: A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: description
annotated target: Gamma-delta intraepithelial T cells, also known as γδ intraepithelial lymphocytes (IELs), are a unique subset of T cells residing in the epithelial layer of mucosal tissues such as the intestine and skin; more are found in intestinal intraepithelial tissue than in other tissues. They are characterized by their distinct T-cell receptor (TCR) that is composed of one gamma (γ) and one delta (δ) chain, unlike the conventional alpha-beta T cells. Most γδ IELs also express the CD8-alpha-alpha homodimer (Cd8-alpha alpha positive, gamma-delta intraepithelial T cells), although some are lacking both co-receptors CD4 and CD8 (CD4-negative CD8-negative gamma-delta intraepithelial T cells). γδ IELs are though to be ‘natural’ IELs as they acquire their activated phenotype in an ‘alternative’ self-antigen-based maturation process in the thymus. Although the function of γδ IELs is still not fully established, current evidence indicates that they serve as a crucial first line of defense against invading pathogens, thus making them an important class of immune cells at the epithelial barrier interfaces. γδ IELs respond to a variety of antigens, including those not recognized by conventional T cells. They are also thought to be involved in recruiting in immune surveillance by promoting homeostasis of host microbiota and in limiting excessive inflammation. In addition to their primary role in immunity, γδ IELs also have roles in epithelial cell homeostasis and repair. They assist in maintaining the epithelial barrier by controlling the equilibrium of epithelial cell growth and death. They also contribute to the healing of lesions and the replacement of damaged epithelial cells. The regulative control exerted by γδ IELs over epithelial cell turnover indirectly influences immunity, underlining the complexity and versatility of these cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it …
has db xref: DOI:10.1038/s41385-020-0294-6
has db xref: DOI:10.3389/fimmu.2022.1059042
has db xref: DOI:10.3390/cells9030686

Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: hasDbXref
annotated target: ZFA:0009339
mapping justification: UnspecifiedMatching

gamma-delta intraepithelial T cell on CELLxGENE CellGuide
type: Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000801

CD8-alpha alpha positive, gamma-delta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta intraepithelial T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001084
subclass of: gamma-delta intraepithelial T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001084
IAO_0000115: A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive.
description: The CD8-alpha alpha positive, gamma-delta intraepithelial T cell are a subset of intraepithelial lymphocytes (IELs), a highly heterogeneous population of immune cell that resides within the epithelial layer of mucosal barriers. CD8-alpha alpha positive, gamma-delta intraepithelial T cell are predominantly found in the gastrointestinal tract. They are characterized by the expression of both CD8-alpha-alpha homodimer and the gamma-delta (γδ) variant of the T cell receptor (TCR). CD8-alpha alpha positive, gamma-delta are thought to represent the most typical γδ IEL subset in the intestine. The IELs in the intestines are constantly and directly exposed to antigens in the gut lumen and form the first line of immune defense against invading pathogens. Unlike conventional T cells, IELs in the intestine are antigen-experienced and do not require priming. CD8-alpha alpha positive, gamma-delta intraepithelial T cells fall into a subgroup of ‘natural’ IELs, which acquire their activated phenotype in an ‘alternative’ self-antigen-based maturation process in the thymus. CD8-alpha alpha positive, gamma-delta intraepithelial T cell have several key functions. They help maintain the integrity of the epithelium and repair the epithelial barriers in response to physical and inflammatory injury by secreting various factors, including TGFβ1, TGFβ3 and keratinocyte growth factor (KGF). These cells also provide immediate, front-line defense against pathogens. They retain the ability to respond directly to stress-associated and infected cells independent of antigen-presenting cells and major histocompatibility complex molecules. They do this through recognition of antigens present on the surfaces of stressed or infected cells. Once activated, these cells initiate a rapid immune response by releasing cytotoxic granules and engaging death receptors, processes that eliminate harmful cells. Furthermore, CD8-alpha alpha positive, gamma-delta intraepithelial T cells have been implicated in regu…
has broad synonym: IEL
has broad synonym: intraepithelial lymphocyte
has exact synonym: CD8-positive, gamma-delta intraepithelial T lymphocyte
has exact synonym: CD8-positive, gamma-delta intraepithelial T-cell
has exact synonym: CD8-positive, gamma-delta intraepithelial T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD8-alpha alpha positive, gamma-delta intraepithelial T cell
annotated property: subClassOf
annotated target: gamma-delta intraepithelial T cell
is inferred: true

Axiom
annotated source: CD8-alpha alpha positive, gamma-delta intraepithelial T cell
annotated property: IAO_0000115
annotated target: A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

Axiom
annotated source: CD8-alpha alpha positive, gamma-delta intraepithelial T cell
annotated property: description
annotated target: The CD8-alpha alpha positive, gamma-delta intraepithelial T cell are a subset of intraepithelial lymphocytes (IELs), a highly heterogeneous population of immune cell that resides within the epithelial layer of mucosal barriers. CD8-alpha alpha positive, gamma-delta intraepithelial T cell are predominantly found in the gastrointestinal tract. They are characterized by the expression of both CD8-alpha-alpha homodimer and the gamma-delta (γδ) variant of the T cell receptor (TCR). CD8-alpha alpha positive, gamma-delta are thought to represent the most typical γδ IEL subset in the intestine. The IELs in the intestines are constantly and directly exposed to antigens in the gut lumen and form the first line of immune defense against invading pathogens. Unlike conventional T cells, IELs in the intestine are antigen-experienced and do not require priming. CD8-alpha alpha positive, gamma-delta intraepithelial T cells fall into a subgroup of ‘natural’ IELs, which acquire their activated phenotype in an ‘alternative’ self-antigen-based maturation process in the thymus. CD8-alpha alpha positive, gamma-delta intraepithelial T cell have several key functions. They help maintain the integrity of the epithelium and repair the epithelial barriers in response to physical and inflammatory injury by secreting various factors, including TGFβ1, TGFβ3 and keratinocyte growth factor (KGF). These cells also provide immediate, front-line defense against pathogens. They retain the ability to respond directly to stress-associated and infected cells independent of antigen-presenting cells and major histocompatibility complex molecules. They do this through recognition of antigens present on the surfaces of stressed or infected cells. Once activated, these cells initiate a rapid immune response by releasing cytotoxic granules and engaging death receptors, processes that eliminate harmful cells. Furthermore, CD8-alpha alpha positive, gamma-delta intraepithelial T cells have been implicated in regu…
has db xref: DOI:10.1038/nri.2017.101
has db xref: DOI:10.1038/nri3007
has db xref: DOI:10.3389/fimmu.2022.1059042
has db xref: DOI:10.3390/cells9030686

CD8-alpha alpha positive, gamma-delta intraepithelial T cell on CELLxGENE CellGuide
type: Axiom
annotated source: CD8-alpha alpha positive, gamma-delta intraepithelial T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000802

CD4-negative CD8-negative gamma-delta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta intraepithelial T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
subclass of: gamma-delta intraepithelial T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
IAO_0000115: A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative.
has broad synonym: IEL
has broad synonym: intraepithelial lymphocyte
has exact synonym: CD4-positive, gamma-delta intraepithelial T lymphocyte
has exact synonym: CD4-positive, gamma-delta intraepithelial T-cell
has exact synonym: CD4-positive, gamma-delta intraepithelial T-lymphocyte

Axiom
annotated source: CD4-negative CD8-negative gamma-delta intraepithelial T cell
annotated property: subClassOf
annotated target: gamma-delta intraepithelial T cell
is inferred: true

Axiom
annotated source: CD4-negative CD8-negative gamma-delta intraepithelial T cell
annotated property: IAO_0000115
annotated target: A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0781735149

immature single positive thymocyte
type: Class
equivalent class: Class
  intersection of: thymocyte
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001307
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001380
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0043384
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000025402
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001932
subclass of: thymocyte
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001307
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0043384
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000025402
subclass of: Restriction
  on property: RO_0002202
  some values from: DN4 thymocyte
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001932
IAO_0000115: A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive.
has exact synonym: ISP
has exact synonym: T.ISP.th
has exact synonym: immature single positive T cell
has exact synonym: immature single positive T lymphocyte
has exact synonym: immature single positive T-lymphocyte
comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and rearranging the T cell receptor alpha chain and expressing the CD8 coreceptor. This stage comes between the DN4 and DP stages.

Axiom
annotated source: immature single positive thymocyte
annotated property: subClassOf
annotated target: thymocyte
is inferred: true

Axiom
annotated source: immature single positive thymocyte
annotated property: IAO_0000115
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: http://www.immgen.org/index_content.html

DN2 thymocyte
type: Class
equivalent class: Class
  intersection of: thymocyte
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001307
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001380
subclass of: CL_0002489
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001307
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002202
  some values from: DN1 thymic pro-T cell
IAO_0000115: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive.
has exact synonym: DN2 alpha-beta immature T lymphocyte
has exact synonym: DN2 alpha-beta immature T-cell
has exact synonym: DN2 alpha-beta immature T-lymphocyte
has exact synonym: DN2 cell
has exact synonym: DN2 immature T cell
has exact synonym: TN2 cell
has exact synonym: TN2 thymocyte
has exact synonym: double negative 2
has exact synonym: preT.DN2.Th
comment: Note that this type of thymocyte is at the earliest stage of T cell receptor rearrangement of the beta, gamma, and delta T cell receptor chains. Also, there is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.

Axiom
annotated source: DN2 thymocyte
annotated property: IAO_0000115
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

DN3 thymocyte
type: Class
equivalent class: Class
  intersection of: thymocyte
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001307
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0043384
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001380
subclass of: CL_0002489
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001307
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0043384
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002202
  some values from: DN2 thymocyte
IAO_0000115: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain.
has broad synonym: early cortical thymocyte
has exact synonym: DN3 alpha-beta immature T lymphocyte
has exact synonym: DN3 alpha-beta immature T-cell
has exact synonym: DN3 alpha-beta immature T-lymphocyte
has exact synonym: DN3 cell
has exact synonym: DN3 immature T cell
has exact synonym: TN3 cell
has exact synonym: TN3 thymocyte
has exact synonym: double negative 3
has exact synonym: preT.DN3.Th
in subset: cellxgene subset
comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.

Axiom
annotated source: DN3 thymocyte
annotated property: IAO_0000115
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

DN4 thymocyte
type: Class
equivalent class: Class
  intersection of: thymocyte
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001307
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001380
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0043384
subclass of: CL_0002489
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001307
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0043384
subclass of: Restriction
  on property: RO_0002202
  some values from: DN3 thymocyte
IAO_0000115: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive.
has broad synonym: early cortical thymocyte
has exact synonym: DN4 alpha-beta immature T lymphocyte
has exact synonym: DN4 alpha-beta immature T-lymphocyte
has exact synonym: DN4 cell
has exact synonym: DN4 immature T cell
has exact synonym: DN4 immature T-cell
has exact synonym: T.DN4.th
has exact synonym: double negative 4
in subset: cellxgene subset
comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and beginning to rearrange the T cell receptor alpha chain. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.

Axiom
annotated source: DN4 thymocyte
annotated property: IAO_0000115
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

double-positive, alpha-beta thymocyte
type: Class
equivalent class: Class
  intersection of: immature alpha-beta T cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001004
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000025402
subclass of: immature alpha-beta T cell
subclass of: thymocyte
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001004
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000025402
subclass of: Restriction
  on property: RO_0002202
  some values from: immature single positive thymocyte
IAO_0000115: A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors.
description: Double-positive (DP), alpha-beta thymocytes are a developmental stage in the production of mature alpha-beta T cells. These DP cells are found in the thymus. They are named 'double-positive' due to their expression of both CD4 and CD8 co-receptors on their surface, a characteristic that distinguishes them from other types of thymocytes. ‘Alpha-beta' refers to the type of T cell receptor (TCR) they express, differentiating them from gamma-delta T cells. In the preceding double negative (DN) phase, cells undergo an important developmental checkpoint called β-selection in which the β-chain of the TCR is rearranged and only cells expressing functional β-chains, combined with a surrogate α chain forming the pre-TCR, move forward in development. In the DP phase, cells downregulate expression of the surrogate α chain which is replaced by the α chain, which also undergoes gene rearrangements. This developmental stage is characterized by thymic selection processes that ultimately shape the T cell repertoire. Cells with nonfunctional TCRs undergo death by neglect, while cells expressing TCRs that bind strongly to self-peptides presented in the context of major histocompatibility complex (MHC) molecules are removed by negative selection, and cells that express TCRs that weakly interact with self-MHC are kept via positive selection. This ensures that the resulting mature T cells are able to recognize self-MHC without responding too strongly, which could result in autoimmune reactions. The CD4 and CD8 coreceptors play an important role in the selection processes, and the class of self-MHC that was recognized by the cell will dictate whether CD4 or CD8 expression remains on the cell while the other is downregulated. CD4 corresponds to the recognition of MHC class II while CD8 corresponds to MHC class I. The cell will then proceed into the single-positive (SP) phase and ultimately produce mature alpha-beta T cells. (This extended description was generated by ChatGPT and reviewed b…
has broad synonym: late cortical thymocyte
has exact synonym: DP cell
has exact synonym: DP thymocyte
has exact synonym: double-positive, alpha-beta immature T lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Thymocytes of this stage are undergoing positive and negative selection.

Axiom
annotated source: double-positive, alpha-beta thymocyte
annotated property: subClassOf
annotated target: immature alpha-beta T cell
is inferred: true

Axiom
annotated source: double-positive, alpha-beta thymocyte
annotated property: IAO_0000115
annotated target: A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

Axiom
annotated source: double-positive, alpha-beta thymocyte
annotated property: description
annotated target: Double-positive (DP), alpha-beta thymocytes are a developmental stage in the production of mature alpha-beta T cells. These DP cells are found in the thymus. They are named 'double-positive' due to their expression of both CD4 and CD8 co-receptors on their surface, a characteristic that distinguishes them from other types of thymocytes. ‘Alpha-beta' refers to the type of T cell receptor (TCR) they express, differentiating them from gamma-delta T cells. In the preceding double negative (DN) phase, cells undergo an important developmental checkpoint called β-selection in which the β-chain of the TCR is rearranged and only cells expressing functional β-chains, combined with a surrogate α chain forming the pre-TCR, move forward in development. In the DP phase, cells downregulate expression of the surrogate α chain which is replaced by the α chain, which also undergoes gene rearrangements. This developmental stage is characterized by thymic selection processes that ultimately shape the T cell repertoire. Cells with nonfunctional TCRs undergo death by neglect, while cells expressing TCRs that bind strongly to self-peptides presented in the context of major histocompatibility complex (MHC) molecules are removed by negative selection, and cells that express TCRs that weakly interact with self-MHC are kept via positive selection. This ensures that the resulting mature T cells are able to recognize self-MHC without responding too strongly, which could result in autoimmune reactions. The CD4 and CD8 coreceptors play an important role in the selection processes, and the class of self-MHC that was recognized by the cell will dictate whether CD4 or CD8 expression remains on the cell while the other is downregulated. CD4 corresponds to the recognition of MHC class II while CD8 corresponds to MHC class I. The cell will then proceed into the single-positive (SP) phase and ultimately produce mature alpha-beta T cells. (This extended description was generated by ChatGPT and reviewed b…
has db xref: DOI:10.1016/B978-0-12-374279-7.04011-X
has db xref: DOI:10.1016/B978-0-7020-6896-6.00008-9
has db xref: DOI:10.1016/B978-012088451-3.50015-6
has db xref: DOI:10.1016/bs.ai.2015.09.002
has db xref: DOI:10.1038/nri3667

double-positive, alpha-beta thymocyte on CELLxGENE CellGuide
type: Axiom
annotated source: double-positive, alpha-beta thymocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000809

Axiom
annotated source: double-positive, alpha-beta thymocyte
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM322.LZLG.752

CD4-positive, alpha-beta thymocyte
type: Class
equivalent class: Class
  intersection of: immature alpha-beta T cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001004
subclass of: immature alpha-beta T cell
subclass of: thymocyte
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001004
subclass of: Restriction
  on property: RO_0002202
  some values from: double-positive, alpha-beta thymocyte
IAO_0000115: An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative.
description: CD4-positive, alpha-beta thymocytes are a subset of newly developed T cells found within the thymus. This cell type is characterized by the expression of the surface proteins CD4 and T-cell receptor alpha-beta (TCR αβ). T-cell receptors are integral to the function of the T cell, allowing it to recognize and bind to specific antigens presented by other cells, while expression of the CD4 TCR coreceptor designates them as precursors to helper T cells. These cells represent a late stage in T cell development. Progenitor cells reach the thymus, the site of T cell maturation, and begin as double negative (DP) cells that express neither CD4 nor CD8. The cells then become double positive (DP), expressing both CD4 and CD8. The cells undergo negative and positive selection processes, in which cells are removed if they bind too strongly to self-major histocompatibility complex (MHC) molecules presenting self-peptide and cells are given survival signals if they bind weakly to self-MHC, respectively. This ensures that the resulting mature T cells are able to recognize self-MHC without responding too strongly, which could result in autoimmune reactions. The CD4 and CD8 coreceptors play an important role in the selection processes, and the class of self-MHC that was recognized by the cell will dictate whether CD4 or CD8 expression remains on the cell while the other is downregulated. CD4 corresponds to the recognition of MHC class II while CD8 corresponds to MHC class I. The cell will then proceed into the single-positive (SP) phase, producing mature, naive CD4-positive or CD8-positive, alpha-beta thymocytes. Cells are generally committed to the CD4 or CD8 lineage at this stage. These cells will complete their development by tuning their TCR threshold and proliferation, then migrate to the periphery as mature, naive T cells. CD4-positive, alpha-beta thymocytes, upon exiting the thymus, develop into CD4-positive T helper cells. These cells play a crucial role in the immune respons…
has exact synonym: CD4-positive, alpha-beta immature T lymphocyte
has exact synonym: CD4-positive, alpha-beta immature T-cell
has exact synonym: CD4-positive, alpha-beta immature T-lymphocyte
has exact synonym: SP CD4 cell
in subset: cellxgene subset

Axiom
annotated source: CD4-positive, alpha-beta thymocyte
annotated property: subClassOf
annotated target: immature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, alpha-beta thymocyte
annotated property: IAO_0000115
annotated target: An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

Axiom
annotated source: CD4-positive, alpha-beta thymocyte
annotated property: description
annotated target: CD4-positive, alpha-beta thymocytes are a subset of newly developed T cells found within the thymus. This cell type is characterized by the expression of the surface proteins CD4 and T-cell receptor alpha-beta (TCR αβ). T-cell receptors are integral to the function of the T cell, allowing it to recognize and bind to specific antigens presented by other cells, while expression of the CD4 TCR coreceptor designates them as precursors to helper T cells. These cells represent a late stage in T cell development. Progenitor cells reach the thymus, the site of T cell maturation, and begin as double negative (DP) cells that express neither CD4 nor CD8. The cells then become double positive (DP), expressing both CD4 and CD8. The cells undergo negative and positive selection processes, in which cells are removed if they bind too strongly to self-major histocompatibility complex (MHC) molecules presenting self-peptide and cells are given survival signals if they bind weakly to self-MHC, respectively. This ensures that the resulting mature T cells are able to recognize self-MHC without responding too strongly, which could result in autoimmune reactions. The CD4 and CD8 coreceptors play an important role in the selection processes, and the class of self-MHC that was recognized by the cell will dictate whether CD4 or CD8 expression remains on the cell while the other is downregulated. CD4 corresponds to the recognition of MHC class II while CD8 corresponds to MHC class I. The cell will then proceed into the single-positive (SP) phase, producing mature, naive CD4-positive or CD8-positive, alpha-beta thymocytes. Cells are generally committed to the CD4 or CD8 lineage at this stage. These cells will complete their development by tuning their TCR threshold and proliferation, then migrate to the periphery as mature, naive T cells. CD4-positive, alpha-beta thymocytes, upon exiting the thymus, develop into CD4-positive T helper cells. These cells play a crucial role in the immune respons…
has db xref: DOI:10.1016/B978-0-12-374279-7.04011-X
has db xref: DOI:10.1016/B978-0-7020-6896-6.00008-9
has db xref: DOI:10.1016/B978-012088451-3.50015-6
has db xref: DOI:10.1038/nri3667
has db xref: DOI:10.1155/2013/282870

CD4-positive, alpha-beta thymocyte on CELLxGENE CellGuide
type: Axiom
annotated source: CD4-positive, alpha-beta thymocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000810

CD8-positive, alpha-beta thymocyte
type: Class
equivalent class: Class
  intersection of: immature alpha-beta T cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000025402
subclass of: immature alpha-beta T cell
subclass of: thymocyte
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000025402
subclass of: Restriction
  on property: RO_0002202
  some values from: double-positive, alpha-beta thymocyte
IAO_0000115: An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative.
description: CD8-positive, alpha-beta thymocytes are a subset of newly developed T cells found within the thymus. This cell type is characterized by the expression of the surface proteins CD8 and T-cell receptor alpha-beta (TCR αβ). T-cell receptors are integral to the function of the T cell, allowing it to recognize and bind to specific antigens presented by other cells, while expression of the CD8 TCR coreceptor designates them as precursors to cytotoxic T cells. These cells represent a late stage in T cell development. Progenitor cells reach the thymus, the site of T cell maturation, and begin as double negative (DP) cells that express neither CD4 nor CD8. The cells then become double positive (DP), expressing both CD4 and CD8. The cells undergo negative and positive selection processes, in which cells are removed if they bind too strongly to self-major histocompatibility complex (MHC) molecules presenting self-peptide and cells are given survival signals if they bind weakly to self-MHC, respectively. This ensures that the resulting mature T cells are able to recognize self-MHC without responding too strongly, which could result in autoimmune reactions. The CD4 and CD8 coreceptors play an important role in the selection processes, and the class of self-MHC that was recognized by the cell will dictate whether CD4 or CD8 expression remains on the cell while the other is downregulated. CD4 corresponds to the recognition of MHC class II while CD8 corresponds to MHC class I. The cell will then proceed into the single-positive (SP) phase, producing mature, naive CD4-positive or CD8-positive, alpha-beta thymocytes. Cells are generally committed to the CD4 or CD8 lineage at this stage. These cells will complete their development by tuning their TCR threshold and proliferation, then migrate to the periphery as mature, naive T cells. CD8-positive, alpha-beta thymocytes, upon exiting the thymus, develop into CD8-positive cytotoxicT cells. These cells play a crucial role in the immune re…
has exact synonym: CD8-positive, alpha-beta immature T lymphocyte
has exact synonym: CD8-positive, alpha-beta immature T-cell
has exact synonym: CD8-positive, alpha-beta immature T-lymphocyte
has exact synonym: SP CD8 cell
has related synonym: CD8-positive, alpha-beta immature T cell
in subset: cellxgene subset

Axiom
annotated source: CD8-positive, alpha-beta thymocyte
annotated property: subClassOf
annotated target: immature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta thymocyte
annotated property: IAO_0000115
annotated target: An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

Axiom
annotated source: CD8-positive, alpha-beta thymocyte
annotated property: description
annotated target: CD8-positive, alpha-beta thymocytes are a subset of newly developed T cells found within the thymus. This cell type is characterized by the expression of the surface proteins CD8 and T-cell receptor alpha-beta (TCR αβ). T-cell receptors are integral to the function of the T cell, allowing it to recognize and bind to specific antigens presented by other cells, while expression of the CD8 TCR coreceptor designates them as precursors to cytotoxic T cells. These cells represent a late stage in T cell development. Progenitor cells reach the thymus, the site of T cell maturation, and begin as double negative (DP) cells that express neither CD4 nor CD8. The cells then become double positive (DP), expressing both CD4 and CD8. The cells undergo negative and positive selection processes, in which cells are removed if they bind too strongly to self-major histocompatibility complex (MHC) molecules presenting self-peptide and cells are given survival signals if they bind weakly to self-MHC, respectively. This ensures that the resulting mature T cells are able to recognize self-MHC without responding too strongly, which could result in autoimmune reactions. The CD4 and CD8 coreceptors play an important role in the selection processes, and the class of self-MHC that was recognized by the cell will dictate whether CD4 or CD8 expression remains on the cell while the other is downregulated. CD4 corresponds to the recognition of MHC class II while CD8 corresponds to MHC class I. The cell will then proceed into the single-positive (SP) phase, producing mature, naive CD4-positive or CD8-positive, alpha-beta thymocytes. Cells are generally committed to the CD4 or CD8 lineage at this stage. These cells will complete their development by tuning their TCR threshold and proliferation, then migrate to the periphery as mature, naive T cells. CD8-positive, alpha-beta thymocytes, upon exiting the thymus, develop into CD8-positive cytotoxicT cells. These cells play a crucial role in the immune re…
has db xref: DOI:10.1016/B978-0-12-374279-7.04011-X
has db xref: DOI:10.1016/B978-0-7020-6896-6.00008-9
has db xref: DOI:10.1016/B978-012088451-3.50015-6
has db xref: DOI:10.1038/nri3667
has db xref: DOI:10.1155/2013/282870

CD8-positive, alpha-beta thymocyte on CELLxGENE CellGuide
type: Axiom
annotated source: CD8-positive, alpha-beta thymocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000811

memory T cell
type: Class
equivalent class: Class
  intersection of: CL_0002419
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001603
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0002286
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0043379
subclass of: CL_0002419
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001603
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0043379
disjoint with: naive T cell
IAO_0000115: A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure.
has db xref: BTO:0003435
has db xref: ZFA:0009342
has exact synonym: memory T lymphocyte
has exact synonym: memory T-cell
has exact synonym: memory T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: memory T cell
annotated property: subClassOf
annotated target: CL_0002419
is inferred: true

Axiom
annotated source: memory T cell
annotated property: IAO_0000115
annotated target: A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

Axiom
annotated source: memory T cell
annotated property: hasDbXref
annotated target: ZFA:0009342
mapping justification: UnspecifiedMatching

mature NK T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001874
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032394
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045087
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0030217
subclass of: mature alpha-beta T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001874
subclass of: Restriction
  on property: RO_0002202
  some values from: immature NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032394
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045087
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030217
IAO_0000115: A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
description: Mature NK T cells, or natural killer T cells, are a unique subset of alpha-beta T cells that serve as mediators in the immune response. They are named for their distinct ability to express markers typical of natural killer (NK) cells (such as NK1.1) as well as a T cell receptor specific for a limited set of ligands. Similar to mature effector T cells, mature NK T cells represent a heterogeneous group of effector cells, which express different transcription factors and cytokines and hence have different effector functions in both innate and adaptive immune responses. They are CD1d-restricted T lymphocytes: they recognize endogenous and exogenous lipid antigens presented by the MHC-like molecule CD1d. They have been classified into two subpopulations based on their TCR usage and specificity for lipid antigen: Type I NK T cells have an invariant TCRα-chain while type II NK T cells have a more diverse TCR repertoire. Mature NKT cells have been shown to have both pro- and anti-inflammatory functions and modulate immune responses, including cancer, autoimmunity, allergy, infection and graft-versus-host disease. The primary function of mature NK T cells is to rapidly respond to infections by releasing large amounts of cytokines to aid cell-to-cell communication in immune responses. They also play a role in recognizing and eliminating certain types of cancer cells. Upon activation via their TCRs, mature NK T cells can promptly release a plethora of cytokines including interferon-γ (IFN-γ) and interleukin-4 (IL-4). These cytokines subsequently stimulate other immune cells, such as B cells, T cells and macrophages, to respond to the infection or abnormal cell growth. In addition to antibody-mediated responses, NK T cells are capable of cytotoxic responses, a crucial function in managing viral infections. Mature NK T cells can bind to infected cells, inducing cell death and thereby preventing the spread of the infection. Furthermore, they have been found to play an instrumenta…
has exact synonym: mature NK T lymphocyte
has exact synonym: mature NK T-cell
has exact synonym: mature NK T-lymphocyte
has exact synonym: mature NKT cell
has exact synonym: mature natural killer T cell
has exact synonym: mature natural killer T lymphocyte
has exact synonym: mature natural killer T-cell
has exact synonym: mature natural killer T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: mature NK T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: mature NK T cell
annotated property: IAO_0000115
annotated target: A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
has db xref: GOC:add
has db xref: ISBN:0781735149

Axiom
annotated source: mature NK T cell
annotated property: description
annotated target: Mature NK T cells, or natural killer T cells, are a unique subset of alpha-beta T cells that serve as mediators in the immune response. They are named for their distinct ability to express markers typical of natural killer (NK) cells (such as NK1.1) as well as a T cell receptor specific for a limited set of ligands. Similar to mature effector T cells, mature NK T cells represent a heterogeneous group of effector cells, which express different transcription factors and cytokines and hence have different effector functions in both innate and adaptive immune responses. They are CD1d-restricted T lymphocytes: they recognize endogenous and exogenous lipid antigens presented by the MHC-like molecule CD1d. They have been classified into two subpopulations based on their TCR usage and specificity for lipid antigen: Type I NK T cells have an invariant TCRα-chain while type II NK T cells have a more diverse TCR repertoire. Mature NKT cells have been shown to have both pro- and anti-inflammatory functions and modulate immune responses, including cancer, autoimmunity, allergy, infection and graft-versus-host disease. The primary function of mature NK T cells is to rapidly respond to infections by releasing large amounts of cytokines to aid cell-to-cell communication in immune responses. They also play a role in recognizing and eliminating certain types of cancer cells. Upon activation via their TCRs, mature NK T cells can promptly release a plethora of cytokines including interferon-γ (IFN-γ) and interleukin-4 (IL-4). These cytokines subsequently stimulate other immune cells, such as B cells, T cells and macrophages, to respond to the infection or abnormal cell growth. In addition to antibody-mediated responses, NK T cells are capable of cytotoxic responses, a crucial function in managing viral infections. Mature NK T cells can bind to infected cells, inducing cell death and thereby preventing the spread of the infection. Furthermore, they have been found to play an instrumenta…
has db xref: DOI:10.1128/cmr.00232-20
has db xref: DOI:10.3389/fimmu.2018.00367
has db xref: DOI:10.3389/fncel.2019.00245
has db xref: https://www.ncbi.nlm.nih.gov/books/NBK532332/
has db xref: https://www.sciencedirect.com/topics/medicine-and-dentistry/natural-killer-t-cell

mature NK T cell on CELLxGENE CellGuide
type: Axiom
annotated source: mature NK T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000814

regulatory T cell
type: Class
equivalent class: Class
  intersection of: CL_0002419
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050777
subclass of: CL_0002419
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050777
IAO_0000115: A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
description: Regulatory T cells, or Tregs, represent a vital component of the immune system, functioning to maintain immune tolerance and homeostasis. Tregs prevent excessive immune responses and autoimmunity by suppressing or downregulating proliferation or activation of other immune cells. Originating in the thymus, Tregs belong to a larger group of T cells that express CD4 protein on their surface. They can be identified by their expression of the forkhead/winged-helix transcription factor Foxp3, which is a crucial intracellular marker that controls their development and function. Tregs are key players in preventing autoimmune diseases, allergies, and graft-versus-host disease, a potential complication of bone marrow transplantation. By suppressing the immune response, Tregs ensure that the immune system doesn't mistakenly attack the body's own healthy tissues, or harmless substances such as pollen, or transplanted tissue. Abnormalities in Treg number or function can result in a profound dysregulation of immune homeostasis, leading to the development of various immune-mediated diseases. However, Tregs also appear to contribute to tumor development. Developmentally, while Tregs may emerge directly from the thymus, Tregs may also arise peripherally from conventional T cells. Thymic or "natural" Tregs likely arise from thymocytes that strongly recognize self-antigen and contribute to self-tolerance. Peripherally induced Tregs likely recognize foreign antigen and are likely important in maintaining tolerance to non-host antigens, such as intestinal microbiota or food allergens. Understanding the precise functions and mechanisms of regulatory T cells is a continually evolving field, with potential implications for combating autoimmunity, enhancing cancer therapy, and preventing transplant rejection. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain…
has broad synonym: suppressor T cell
has broad synonym: suppressor T lymphocyte
has broad synonym: suppressor T-cell
has broad synonym: suppressor T-lymphocyte
has db xref: BTO:0004520
has db xref: FMA:84070
has db xref: MESH:D050378
has exact synonym: Treg
has exact synonym: regulatory T lymphocyte
has exact synonym: regulatory T-cell
has exact synonym: regulatory T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type may express FoxP3 and CD25 and secretes IL-10 and TGF-beta.

Axiom
annotated source: regulatory T cell
annotated property: subClassOf
annotated target: CL_0002419
is inferred: true

Axiom
annotated source: regulatory T cell
annotated property: IAO_0000115
annotated target: A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
has db xref: GOC:add
has db xref: GO_REF:0000031

Axiom
annotated source: regulatory T cell
annotated property: description
annotated target: Regulatory T cells, or Tregs, represent a vital component of the immune system, functioning to maintain immune tolerance and homeostasis. Tregs prevent excessive immune responses and autoimmunity by suppressing or downregulating proliferation or activation of other immune cells. Originating in the thymus, Tregs belong to a larger group of T cells that express CD4 protein on their surface. They can be identified by their expression of the forkhead/winged-helix transcription factor Foxp3, which is a crucial intracellular marker that controls their development and function. Tregs are key players in preventing autoimmune diseases, allergies, and graft-versus-host disease, a potential complication of bone marrow transplantation. By suppressing the immune response, Tregs ensure that the immune system doesn't mistakenly attack the body's own healthy tissues, or harmless substances such as pollen, or transplanted tissue. Abnormalities in Treg number or function can result in a profound dysregulation of immune homeostasis, leading to the development of various immune-mediated diseases. However, Tregs also appear to contribute to tumor development. Developmentally, while Tregs may emerge directly from the thymus, Tregs may also arise peripherally from conventional T cells. Thymic or "natural" Tregs likely arise from thymocytes that strongly recognize self-antigen and contribute to self-tolerance. Peripherally induced Tregs likely recognize foreign antigen and are likely important in maintaining tolerance to non-host antigens, such as intestinal microbiota or food allergens. Understanding the precise functions and mechanisms of regulatory T cells is a continually evolving field, with potential implications for combating autoimmunity, enhancing cancer therapy, and preventing transplant rejection. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain…
has db xref: DOI:10.1038/nri2343
has db xref: DOI:10.1111/j.1600-065X.2011.01018.x
has db xref: DOI:10.1146/annurev-immunol-042718-041717
has db xref: DOI:10.1146/annurev-immunol-100219-020937
has db xref: DOI:10.3389/fimmu.2020.616949

regulatory T cell on CELLxGENE CellGuide
type: Axiom
annotated source: regulatory T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000815

immature B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0045190
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
subclass of: CL_0001201
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0045190
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002202
  some values from: small pre-B-II cell
IAO_0000115: An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation.
description: Immature B cells, also known as Hardy fraction E, represent an intermediate stage in B cell development. By this stage, the B cell precursors have undergone both heavy and light chain rearrangement, resulting in a diverse pool of B cell receptors (BCR). At this stage, the immature B cells undergo a stringent selection process to maintain B cell central tolerance. If an immature B cell is found to express self-reactive BCR, it can undergo receptor editing, in which rearrangement of its light chain genes is reinitiated, in an attempt to create a new, non-self-reactive BCR. If this editing process is unsuccessful and the BCR remains self-reactive, the cell can then be forced to undergo apoptosis, a process termed clonal deletion, thus preventing the production of auto-reactive, potentially harmful B cells. If the BCR recognizes self-antigen with low affinity, it may become anergic or unresponsive. Immature B cells that successfully pass these selection processes are then released from the bone marrow as transitional B cells and will complete their maturation process in secondary lymphoid organs. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009343
has exact synonym: immature B lymphocyte
has exact synonym: immature B-cell
has exact synonym: immature B-lymphocyte
has exact synonym: newly formed B cell
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive.

Axiom
annotated source: immature B cell
annotated property: IAO_0000115
annotated target: An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: PMID:20081059
has db xref: PMID:20839338

Axiom
annotated source: immature B cell
annotated property: description
annotated target: Immature B cells, also known as Hardy fraction E, represent an intermediate stage in B cell development. By this stage, the B cell precursors have undergone both heavy and light chain rearrangement, resulting in a diverse pool of B cell receptors (BCR). At this stage, the immature B cells undergo a stringent selection process to maintain B cell central tolerance. If an immature B cell is found to express self-reactive BCR, it can undergo receptor editing, in which rearrangement of its light chain genes is reinitiated, in an attempt to create a new, non-self-reactive BCR. If this editing process is unsuccessful and the BCR remains self-reactive, the cell can then be forced to undergo apoptosis, a process termed clonal deletion, thus preventing the production of auto-reactive, potentially harmful B cells. If the BCR recognizes self-antigen with low affinity, it may become anergic or unresponsive. Immature B cells that successfully pass these selection processes are then released from the bone marrow as transitional B cells and will complete their maturation process in secondary lymphoid organs. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1038/80816
has db xref: DOI:10.1038/s41467-021-27232-5

Axiom
annotated source: immature B cell
annotated property: hasDbXref
annotated target: ZFA:0009343
mapping justification: UnspecifiedMatching

Axiom
annotated source: immature B cell
annotated property: hasExactSynonym
annotated target: newly formed B cell
has db xref: ISBN:781735149

immature B cell on CELLxGENE CellGuide
type: Axiom
annotated source: immature B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000816

precursor B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001898
subclass of: CL_0001201
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001898
disjoint with: pro-B cell
IAO_0000115: A precursor B cell is a B cell with the phenotype CD10-positive.
description: Precursor B cells, often abbreviated as pre-B cells, represent an intermediary stage in the development of B cells, the white blood cells that play a crucial role in the body’s adaptive immunity system. They arise from early lymphoid progenitors in the bone marrow, representing a critical point in B cell development between a pro-B cell and an immature B cell. They differ from mature B cells as they still populate the bone marrow and have yet to fully develop the distinctive B cell receptor complex. The primary function of precursor B cells is to undergo proliferation and rearrange their immunoglobulin light chain gene regions which ultimately forms part of the B cell receptor (BCR), an event crucial to B lymphocyte development. This process is closely monitored by the body's quality control mechanisms, ensuring all newly produced B cells have functional (and not self-reactive) receptors. This receptor editing and checking system helps to prevent autoimmune diseases, triggered when immune cells mistakenly attack the body's own cells. Critical mutations required for the maturation of the BCR happen in stages while the cell is a pre-B cell. Pre-B cells are initially characterized as stage called "large pre-B cells," during which proliferation occurs. Additionally, heavy chain recombination is completed and the cell undergoes a checkpoint in which only cells with a functional heavy chain continue to develop. Afterwards, they transition into a "small pre-B cell" phase, where heavy chain rearrangement ends, and light-chain rearrangement begins. Once the B cell receptor is fully formed following heavy and light chain rearrangement, the cell is considered an immature B cell and leaves the bone marrow. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered…
has db xref: BTO:0001133
has db xref: CALOHA:TS-0819
has db xref: ZFA:0009344
has related synonym: pre-B cell
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: precursor B cell
annotated property: subClassOf
annotated target: CL_0001201
is inferred: true

Axiom
annotated source: precursor B cell
annotated property: IAO_0000115
annotated target: A precursor B cell is a B cell with the phenotype CD10-positive.
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031

Axiom
annotated source: precursor B cell
annotated property: description
annotated target: Precursor B cells, often abbreviated as pre-B cells, represent an intermediary stage in the development of B cells, the white blood cells that play a crucial role in the body’s adaptive immunity system. They arise from early lymphoid progenitors in the bone marrow, representing a critical point in B cell development between a pro-B cell and an immature B cell. They differ from mature B cells as they still populate the bone marrow and have yet to fully develop the distinctive B cell receptor complex. The primary function of precursor B cells is to undergo proliferation and rearrange their immunoglobulin light chain gene regions which ultimately forms part of the B cell receptor (BCR), an event crucial to B lymphocyte development. This process is closely monitored by the body's quality control mechanisms, ensuring all newly produced B cells have functional (and not self-reactive) receptors. This receptor editing and checking system helps to prevent autoimmune diseases, triggered when immune cells mistakenly attack the body's own cells. Critical mutations required for the maturation of the BCR happen in stages while the cell is a pre-B cell. Pre-B cells are initially characterized as stage called "large pre-B cells," during which proliferation occurs. Additionally, heavy chain recombination is completed and the cell undergoes a checkpoint in which only cells with a functional heavy chain continue to develop. Afterwards, they transition into a "small pre-B cell" phase, where heavy chain rearrangement ends, and light-chain rearrangement begins. Once the B cell receptor is fully formed following heavy and light chain rearrangement, the cell is considered an immature B cell and leaves the bone marrow. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered…
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1016/C2009-0-62217-0
has db xref: DOI:10.1016/j.febslet.2010.04.057
has db xref: DOI:10.1172/JCI78083

Axiom
annotated source: precursor B cell
annotated property: hasDbXref
annotated target: ZFA:0009344
mapping justification: UnspecifiedMatching

precursor B cell on CELLxGENE CellGuide
type: Axiom
annotated source: precursor B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000817

transitional stage B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0002335
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001932
subclass of: CL_0001201
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0002335
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002202
  some values from: immature B cell
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001932
IAO_0000115: An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen.
description: Transitional stage B cells represent an intermediary stage in B cell development between immature B cells, which are produced within the bone marrow, and mature B cells, which circulate in the blood and peripheral lymphoid tissues. Transitional B cells migrate from the bone marrow to secondary lymphoid organs, usually the spleen. Transitional B cells may still undergo negative and positive selection processes to remove self-reactive B cells and to enhance survival and clonal expansion of antigen-specific cells, respectively. Transitional B cells can mature into either follicular B cells in the splenic follicles following tonic or strong B cell receptor (BCR) signaling and BAFF signaling, or marginal zone B cells between the red and white pulp of the spleen following weak BCR signaling and Notch2 signaling. Some transitional B cells themselves also possess regulatory B cell functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009345
has exact synonym: transitional B cell
has exact synonym: transitional stage B lymphocyte
has exact synonym: transitional stage B-cell
has exact synonym: transitional stage B-lymphocyte
has narrow synonym: T1 B cell
has narrow synonym: T2 B cell
has narrow synonym: T3 B cell
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'.

Axiom
annotated source: transitional stage B cell
annotated property: subClassOf
annotated target: CL_0001201
is inferred: true

Axiom
annotated source: transitional stage B cell
annotated property: IAO_0000115
annotated target: An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen.
has db xref: GOC:add
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: PMID:12810111
has db xref: PMID:22343568

Axiom
annotated source: transitional stage B cell
annotated property: description
annotated target: Transitional stage B cells represent an intermediary stage in B cell development between immature B cells, which are produced within the bone marrow, and mature B cells, which circulate in the blood and peripheral lymphoid tissues. Transitional B cells migrate from the bone marrow to secondary lymphoid organs, usually the spleen. Transitional B cells may still undergo negative and positive selection processes to remove self-reactive B cells and to enhance survival and clonal expansion of antigen-specific cells, respectively. Transitional B cells can mature into either follicular B cells in the splenic follicles following tonic or strong B cell receptor (BCR) signaling and BAFF signaling, or marginal zone B cells between the red and white pulp of the spleen following weak BCR signaling and Notch2 signaling. Some transitional B cells themselves also possess regulatory B cell functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1016/j.jaci.2013.01.046
has db xref: DOI:10.1186/s12967-020-02289-w

Axiom
annotated source: transitional stage B cell
annotated property: hasDbXref
annotated target: ZFA:0009345
mapping justification: UnspecifiedMatching

Axiom
annotated source: transitional stage B cell
annotated property: hasExactSynonym
annotated target: transitional B cell
has db xref: PMID:22343568

transitional stage B cell on CELLxGENE CellGuide
type: Axiom
annotated source: transitional stage B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000818

B-1 B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001014
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001879
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045087
  intersection of: Restriction
    on property: RO_0015015
    some values from: GO_0071753
subclass of: mature B cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001014
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001879
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045087
subclass of: Restriction
  on property: RO_0015015
  some values from: GO_0071753
IAO_0000115: A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive.
description: B-1 B cells represent a unique subset of B lymphocytes distinguished by their functional and phenotypic characteristics. These cells have been well studied in mice, though their human counterparts remain more difficult to characterize. These cells are predominantly found in the peritoneal and pleural cavities and play a crucial role in the body's immune response, being a part of the adaptive immune system. They are significant producers of natural antibodies even in the absence of an identifiable pathogen, making them a pivotal link between the innate and adaptive immune responses. They can be further subdivided into B-1a and B-1b cells. One of the defining features of B-1 B cells is the innate-like pattern of their immune response. Unlike conventional B cells (B-2 cells), which require interaction with T helper cells to initiate antibody production, B-1a B cells respond rapidly to microbial challenges, with an immediate production of low-affinity, polyreactive antibodies. These antibodies readily bind to various pathogens and provide an immediate first line of defence against invading microbes. In addition to their protective role, these antibodies also play a crucial part in maintaining homeostasis by facilitating the clearance of cellular debris and apoptotic cells. However, these antibodies can also be autoreactive and contribute to autoimmunity. Meanwhile, B-1b cells appear to produce antibodies specific to T-independent antigens. Moreover, B-1 B cells possess the unique ability to self-renew, akin to stem cells. This distinctive property contrasts with conventional B-2 cells, which are replenished by the bone marrow. Whereas B-2 cells primarily contribute to secondary antibody responses, B-1 B cells are known for their role in primary and early secondary immune responses. By exhibiting characteristics of both innate and adaptive immunity, B-1 B cells bridge the gap between these two divisions of the immune system, providing comprehensive protection against pat…
has exact synonym: B-1 B lymphocyte
has exact synonym: B-1 B-cell
has exact synonym: B-1 B-lymphocyte
has exact synonym: B-1 cell
has exact synonym: B1 B cell
has exact synonym: B1 B lymphocyte
has exact synonym: B1 B-cell
has exact synonym: B1 B-lymphocyte
has exact synonym: B1 cell
in subset: cellxgene subset
comment: There are small numbers of B-1 cells found in the lymph nodes and spleen, while larger numbers can be found in the peritoneal and pleural cavities. B-1 B cells are reportedly CD11b-positive, CD20-positive, CD21-positive, CD27-positive, CD44-positive, CD45RB-positive, CD48-positive, CD70-negative, CD150-positive, CD244-negative, CD352-positive, sIgM-positive, and sIgD-low.

Axiom
annotated source: B-1 B cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: B-1 B cell
annotated property: IAO_0000115
annotated target: A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GO_REF:0000031
has db xref: PMID:11861604
has db xref: PMID:20933013
has db xref: PMID:21220451
has db xref: http://en.wikipedia.org/wiki/B-1_cell

Axiom
annotated source: B-1 B cell
annotated property: description
annotated target: B-1 B cells represent a unique subset of B lymphocytes distinguished by their functional and phenotypic characteristics. These cells have been well studied in mice, though their human counterparts remain more difficult to characterize. These cells are predominantly found in the peritoneal and pleural cavities and play a crucial role in the body's immune response, being a part of the adaptive immune system. They are significant producers of natural antibodies even in the absence of an identifiable pathogen, making them a pivotal link between the innate and adaptive immune responses. They can be further subdivided into B-1a and B-1b cells. One of the defining features of B-1 B cells is the innate-like pattern of their immune response. Unlike conventional B cells (B-2 cells), which require interaction with T helper cells to initiate antibody production, B-1a B cells respond rapidly to microbial challenges, with an immediate production of low-affinity, polyreactive antibodies. These antibodies readily bind to various pathogens and provide an immediate first line of defence against invading microbes. In addition to their protective role, these antibodies also play a crucial part in maintaining homeostasis by facilitating the clearance of cellular debris and apoptotic cells. However, these antibodies can also be autoreactive and contribute to autoimmunity. Meanwhile, B-1b cells appear to produce antibodies specific to T-independent antigens. Moreover, B-1 B cells possess the unique ability to self-renew, akin to stem cells. This distinctive property contrasts with conventional B-2 cells, which are replenished by the bone marrow. Whereas B-2 cells primarily contribute to secondary antibody responses, B-1 B cells are known for their role in primary and early secondary immune responses. By exhibiting characteristics of both innate and adaptive immunity, B-1 B cells bridge the gap between these two divisions of the immune system, providing comprehensive protection against pat…
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1038/nri2901

B-1 B cell on CELLxGENE CellGuide
type: Axiom
annotated source: B-1 B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000819

B-1a B cell
type: Class
equivalent class: Class
  intersection of: B-1 B cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001839
subclass of: B-1 B cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001839
IAO_0000115: A B-1 B cell that has the phenotype CD5-positive.
description: B-1a B cells are a subset of B cells, which are major components of the adaptive immune system, primarily responsible for humoral immunity. B-1 cells can be subdivided into B-1a and B-1b cells. Unlike their conventional B-2 B cell counterparts, B-1a B cells are self-renewing and mainly found in the peritoneal and pleural cavities, although they can also be detected in the spleen and the bone marrow. The distinguishing factor for B-1a B cells is the expression of CD5 on their cell surface, in addition to the common B cell markers, such as CD19 and CD20. In terms of function, B-1a B cells are crucial for the production of low-affinity, polyreactive natural antibodies, which are predominantly of the IgM class. These natural antibodies are produced even in the absence of pathogenic stimulation and play a substantial role in maintaining immune homeostasis. They can recognize highly conserved structures primarily found on the surface of common pathogens, and self-antigens released from damaged or dying cells. It appears that these autoreactive antibodies can contribute to autoimmunity. B-1a B cells also have a significant role in the early immune response as they can respond rapidly to pathogenic assault without requiring additional signals for activation and proliferation. This rapid response feature is mediated by the secretion of large amounts of immunoglobulins in response to Toll-like receptor (TLR) ligands. The B-1a B cells also exhibit potent phagocytic capabilities, perform antigen presentation to T cells, and exert regulatory functions through their production of IL-10, a cytokine suppressing inflammatory and autoimmune reactions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: B-1a B lymphocyte
has exact synonym: B-1a B-cell
has exact synonym: B-1a B-lymphocyte
has exact synonym: B1a B cell
has exact synonym: B1a B lymphocyte
has exact synonym: B1a B-cell
has exact synonym: B1a B-lymphocyte
has exact synonym: B1a cell
has exact synonym: CD5(+) B1 cell
has exact synonym: CD5+ B1 cell
has exact synonym: CD5-positive B1 cell
in subset: cellxgene subset

Axiom
annotated source: B-1a B cell
annotated property: subClassOf
annotated target: B-1 B cell
is inferred: true

Axiom
annotated source: B-1a B cell
annotated property: IAO_0000115
annotated target: A B-1 B cell that has the phenotype CD5-positive.
has db xref: GOC:add
has db xref: PMID:11861604

Axiom
annotated source: B-1a B cell
annotated property: description
annotated target: B-1a B cells are a subset of B cells, which are major components of the adaptive immune system, primarily responsible for humoral immunity. B-1 cells can be subdivided into B-1a and B-1b cells. Unlike their conventional B-2 B cell counterparts, B-1a B cells are self-renewing and mainly found in the peritoneal and pleural cavities, although they can also be detected in the spleen and the bone marrow. The distinguishing factor for B-1a B cells is the expression of CD5 on their cell surface, in addition to the common B cell markers, such as CD19 and CD20. In terms of function, B-1a B cells are crucial for the production of low-affinity, polyreactive natural antibodies, which are predominantly of the IgM class. These natural antibodies are produced even in the absence of pathogenic stimulation and play a substantial role in maintaining immune homeostasis. They can recognize highly conserved structures primarily found on the surface of common pathogens, and self-antigens released from damaged or dying cells. It appears that these autoreactive antibodies can contribute to autoimmunity. B-1a B cells also have a significant role in the early immune response as they can respond rapidly to pathogenic assault without requiring additional signals for activation and proliferation. This rapid response feature is mediated by the secretion of large amounts of immunoglobulins in response to Toll-like receptor (TLR) ligands. The B-1a B cells also exhibit potent phagocytic capabilities, perform antigen presentation to T cells, and exert regulatory functions through their production of IL-10, a cytokine suppressing inflammatory and autoimmune reactions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1038/nri2901

B-1a B cell on CELLxGENE CellGuide
type: Axiom
annotated source: B-1a B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000820

B-1b B cell
type: Class
equivalent class: Class
  intersection of: B-1 B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
subclass of: B-1 B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
IAO_0000115: A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell.
description: B-1b B cells are a subtype of B cells, which are part of the humoral immune system. B cells can be divided into B-1 and B-2 cells, and B-1 cells can be further subdivided into B-1a and B-1b cells. B-1b B cells are especially abundant in the pleural and peritoneal cavities in humans and mice, and they differ from B-1a B cells in that they lack the expression of the surface molecule CD5. Functionally, B-1b B cells are vital players in the immune response, particularly in providing defense against pathogens. They appear to specialize in recognizing T-independent, pathogen-associated antigens. B-1b B cells can respond to these antigens by rapidly proliferating and differentiating into cells capable of producing natural antibodies, primarily of the IgM class. These antibodies are of low affinity but broad specificity, allowing for the rapid targeting of a wide range of pathogens before the adaptive immune response has fully developed. These cells, unlike B-1a B cells, appear to undergo clonal expansion in response to antigen exposure. B-1b B cells are also thought to contribute to immunological memory. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: B-1b B lymphocyte
has exact synonym: B-1b B-cell
has exact synonym: B-1b B-lymphocyte
has exact synonym: B1b B cell
has exact synonym: B1b B lymphocyte
has exact synonym: B1b B-cell
has exact synonym: B1b B-lymphocyte
has exact synonym: B1b cell
in subset: cellxgene subset

Axiom
annotated source: B-1b B cell
annotated property: subClassOf
annotated target: B-1 B cell
is inferred: true

Axiom
annotated source: B-1b B cell
annotated property: IAO_0000115
annotated target: A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell.
has db xref: GOC:add
has db xref: PMID:11861604

Axiom
annotated source: B-1b B cell
annotated property: description
annotated target: B-1b B cells are a subtype of B cells, which are part of the humoral immune system. B cells can be divided into B-1 and B-2 cells, and B-1 cells can be further subdivided into B-1a and B-1b cells. B-1b B cells are especially abundant in the pleural and peritoneal cavities in humans and mice, and they differ from B-1a B cells in that they lack the expression of the surface molecule CD5. Functionally, B-1b B cells are vital players in the immune response, particularly in providing defense against pathogens. They appear to specialize in recognizing T-independent, pathogen-associated antigens. B-1b B cells can respond to these antigens by rapidly proliferating and differentiating into cells capable of producing natural antibodies, primarily of the IgM class. These antibodies are of low affinity but broad specificity, allowing for the rapid targeting of a wide range of pathogens before the adaptive immune response has fully developed. These cells, unlike B-1a B cells, appear to undergo clonal expansion in response to antigen exposure. B-1b B cells are also thought to contribute to immunological memory. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1038/nri2901

B-1b B cell on CELLxGENE CellGuide
type: Axiom
annotated source: B-1b B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000821

B-2 B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001879
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
subclass of: mature B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001879
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
IAO_0000115: A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative.
description: B-2 B cells, also known as conventional B cells, play a critical role in the humoral immune response. They are distinguished from B-1 cells, which can respond more rapidly and broadly to antigens. B-2 B cells are typically generated in the bone marrow, where they become mature immunocompetent cells before transporting to secondary lymphoid organs like the spleen, lymph nodes, and Peyer's patches. Functionally, B-2 B cells are quintessential components of the adaptive immune system. They are responsible for producing high-affinity, isotype-switched antibodies in response to antigens. In contrast to B-1 B cells that produce natural, low-affinity antibodies, B-2 B cells undergo a meticulous process of affinity maturation and clonal selection upon activation. These cells are antigen-specific and require interaction with T helper cells for proper activation. When presented with the antigen, B-2 B cells internalize, process, and present it to T cells via major histocompatibility complex II (MHC II), leading to B cell proliferation and differentiation into plasma cells or memory B cells. Plasma cells generated from B-2 B cells secrete vast amounts of antibodies to neutralize the invading pathogen, offering immediate protection. On the other hand, memory B cells provide long-term immunity by maintaining recognition of the antigen and prompting a rapid and potent response upon reinfection. The versatile roles of B-2 B cells in the immune response make them key players in immunization and vaccine development. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: B-2 B lymphocyte
has exact synonym: B-2 B-cell
has exact synonym: B-2 B-lymphocyte
has exact synonym: B2 B cell
has exact synonym: B2 B lymphocyte
has exact synonym: B2 B-cell
has exact synonym: B2 B-lymphocyte
has exact synonym: B2 cell
has related synonym: B-0 B cell
in subset: cellxgene subset
comment: B-2 B cells are reportedly CD48-positive, CD244-negative, and CD352-positive.

Axiom
annotated source: B-2 B cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: B-2 B cell
annotated property: IAO_0000115
annotated target: A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0781735149
has db xref: PMID:11861604
has db xref: PMID:20933013

Axiom
annotated source: B-2 B cell
annotated property: description
annotated target: B-2 B cells, also known as conventional B cells, play a critical role in the humoral immune response. They are distinguished from B-1 cells, which can respond more rapidly and broadly to antigens. B-2 B cells are typically generated in the bone marrow, where they become mature immunocompetent cells before transporting to secondary lymphoid organs like the spleen, lymph nodes, and Peyer's patches. Functionally, B-2 B cells are quintessential components of the adaptive immune system. They are responsible for producing high-affinity, isotype-switched antibodies in response to antigens. In contrast to B-1 B cells that produce natural, low-affinity antibodies, B-2 B cells undergo a meticulous process of affinity maturation and clonal selection upon activation. These cells are antigen-specific and require interaction with T helper cells for proper activation. When presented with the antigen, B-2 B cells internalize, process, and present it to T cells via major histocompatibility complex II (MHC II), leading to B cell proliferation and differentiation into plasma cells or memory B cells. Plasma cells generated from B-2 B cells secrete vast amounts of antibodies to neutralize the invading pathogen, offering immediate protection. On the other hand, memory B cells provide long-term immunity by maintaining recognition of the antigen and prompting a rapid and potent response upon reinfection. The versatile roles of B-2 B cells in the immune response make them key players in immunization and vaccine development. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/978-981-15-3532-1_1
has db xref: DOI:10.1016/B978-0-12-397933-9.00007-2

B-2 B cell on CELLxGENE CellGuide
type: Axiom
annotated source: B-2 B cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000822

immature natural killer cell
type: Class
equivalent class: Class
  intersection of: natural killer cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001501
subclass of: natural killer cell
subclass of: CL_0001082
subclass of: Restriction
  on property: RO_0002202
  some values from: pre-natural killer cell
disjoint with: mature natural killer cell
disjoint with: pre-natural killer cell
IAO_0000115: A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR).
has db xref: ZFA:0009346
has exact synonym: immature NK cell
has related synonym: p-NK
in subset: cellxgene subset
comment: In mouse the NKR are Ly49 molecules and in human these cells express KIR molecules.

Axiom
annotated source: immature natural killer cell
annotated property: IAO_0000115
annotated target: A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR).
has db xref: GOC:add
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: PMID:12457618

Axiom
annotated source: immature natural killer cell
annotated property: hasDbXref
annotated target: ZFA:0009346
mapping justification: UnspecifiedMatching

Axiom
annotated source: immature natural killer cell
annotated property: hasRelatedSynonym
annotated target: p-NK
has db xref: PMID:12457618

mature natural killer cell
type: Class
equivalent class: Class
  intersection of: natural killer cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001701
subclass of: natural killer cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001701
subclass of: Restriction
  on property: RO_0002202
  some values from: immature natural killer cell
IAO_0000115: A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules.
has broad synonym: LAK cell
has broad synonym: lymphokine activated killer cell
has db xref: ZFA:0009347
has exact synonym: mature NK cell
in subset: human reference atlas

Axiom
annotated source: mature natural killer cell
annotated property: IAO_0000115
annotated target: A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules.
has db xref: GOC:add
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: PMID:14685782

Axiom
annotated source: mature natural killer cell
annotated property: hasBroadSynonym
annotated target: LAK cell
has db xref: PMID:14685782

Axiom
annotated source: mature natural killer cell
annotated property: hasBroadSynonym
annotated target: lymphokine activated killer cell
has db xref: PMID:14685782

Axiom
annotated source: mature natural killer cell
annotated property: hasDbXref
annotated target: ZFA:0009347
mapping justification: UnspecifiedMatching

pro-NK cell
type: Class
equivalent class: Class
  intersection of: lymphoid lineage restricted progenitor cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001874
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001381
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001898
subclass of: lymphoid lineage restricted progenitor cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001874
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001015
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001381
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001898
subclass of: Restriction
  on property: RO_0002202
  some values from: common lymphoid progenitor
IAO_0000115: A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative.
has db xref: ZFA:0009348
has exact synonym: NKP
has exact synonym: natural killer cell progenitor
has exact synonym: pro-natural killer cell
has related synonym: null cell
has related synonym: preNK cell
comment: Most markers only described for human pro NK cells.

Axiom
annotated source: pro-NK cell
annotated property: subClassOf
annotated target: lymphoid lineage restricted progenitor cell
is inferred: true

Axiom
annotated source: pro-NK cell
annotated property: IAO_0000115
annotated target: A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GO_REF:0000031
has db xref: PMID:11532393
has db xref: PMID:12457618
has db xref: PMID:15032583
has db xref: PMID:15766674

Axiom
annotated source: pro-NK cell
annotated property: hasDbXref
annotated target: ZFA:0009348
mapping justification: UnspecifiedMatching

Axiom
annotated source: pro-NK cell
annotated property: hasExactSynonym
annotated target: NKP
has db xref: PMID:12457618
has db xref: PMID:15032583
has db xref: PMID:15766674

Axiom
annotated source: pro-NK cell
annotated property: hasRelatedSynonym
annotated target: null cell
has db xref: PMID:11532393

Axiom
annotated source: pro-NK cell
annotated property: hasRelatedSynonym
annotated target: preNK cell
has db xref: PMID:11532393

pro-B cell
type: Class
equivalent class: Class
  intersection of: lymphoid lineage restricted progenitor cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001903
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000006611
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0033152
subclass of: lymphoid lineage restricted progenitor cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001903
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000006611
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0033152
subclass of: Restriction
  on property: RO_0002202
  some values from: common lymphoid progenitor
IAO_0000115: A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs.
has broad synonym: pre-pro B cell
has db xref: BTO:0003104
has db xref: ZFA:0009349
has exact synonym: pro-B lymphocyte
has exact synonym: pro-B-cell
has exact synonym: pro-B-lymphocyte
has exact synonym: progenitor B cell
has exact synonym: progenitor B lymphocyte
has exact synonym: progenitor B-cell
has exact synonym: progenitor B-lymphocyte
has related synonym: pre-B cell (Philadelphia nomenclature)
in subset: cellxgene subset
in subset: human reference atlas
comment: Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative.

Axiom
annotated source: pro-B cell
annotated property: subClassOf
annotated target: lymphoid lineage restricted progenitor cell
is inferred: true

Axiom
annotated source: pro-B cell
annotated property: IAO_0000115
annotated target: A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: ISBN:0781735149
has db xref: PMID:12633665
has db xref: PMID:16551251
has db xref: PMID:18432934

Axiom
annotated source: pro-B cell
annotated property: hasBroadSynonym
annotated target: pre-pro B cell
has db xref: PMID:17582343

Axiom
annotated source: pro-B cell
annotated property: hasDbXref
annotated target: ZFA:0009349
mapping justification: UnspecifiedMatching

Axiom
annotated source: pro-B cell
annotated property: hasRelatedSynonym
annotated target: pre-B cell (Philadelphia nomenclature)
has db xref: PMID:11244048

pro-T cell
type: Class
equivalent class: Class
  intersection of: lymphoid lineage restricted progenitor cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030217
subclass of: lymphoid lineage restricted progenitor cell
subclass of: Restriction
  on property: RO_0002202
  some values from: common lymphoid progenitor
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030217
IAO_0000115: A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.
description: The pro-T cell is a T cell progenitor that will develop into cells of the T lymphocyte lineage. These cells derive from the bone marrow, originally differentiating from hematopoietic stem cells, and are found in the thymus, where T cell development takes place. Pro-T cells represent the stage in T cell development prior to T cell-specific gene rearrangement. Their primary function is to proliferate and differentiate into mature T cells, which play a critical role in adaptive immunity, helping the body respond efficiently to foreign pathogens. In the bone marrow, hematopoietic stem cells can differentiate into common lymphoid progenitor cells. These cells are able to enter circulation and enter the thymus as thymus-seeding progenitor cells. These cells then differentiate into early thymic progenitors which proceed with T cell specification, developing from double negative (DN) to double positive (DP) to single positive (SP) T cells. Over the course of these developmental phases, the cells will commit to the T cell lineage and rearrange T cell receptor genes. In this pathway, pro-T cells can give rise to both alpha-beta and gamma-delta T cells and natural killer T (NKT) cells. Pro-T cells are a key constituent of the immune system, presenting a critical stage in the T cell developmental process. T cells are important players in adaptive immunity and help to initiate and orchestrate the immune response and eliminate pathogens and tumor cells. Pro-T cells are also an area of interest in the context of regenerative medicine to reconstitute T cells and adoptive T cell therapies as a potential source of T cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: ZFA:0009350
has exact synonym: pro-T lymphocyte
has exact synonym: progenitor T cell
has narrow synonym: DN1 cell
has narrow synonym: DN1 thymocyte
has narrow synonym: TN1 cell
in subset: cellxgene subset

Axiom
annotated source: pro-T cell
annotated property: subClassOf
annotated target: lymphoid lineage restricted progenitor cell
is inferred: true

Axiom
annotated source: pro-T cell
annotated property: IAO_0000115
annotated target: A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.
has db xref: GOC:add
has db xref: ISBN:0781735149

Axiom
annotated source: pro-T cell
annotated property: description
annotated target: The pro-T cell is a T cell progenitor that will develop into cells of the T lymphocyte lineage. These cells derive from the bone marrow, originally differentiating from hematopoietic stem cells, and are found in the thymus, where T cell development takes place. Pro-T cells represent the stage in T cell development prior to T cell-specific gene rearrangement. Their primary function is to proliferate and differentiate into mature T cells, which play a critical role in adaptive immunity, helping the body respond efficiently to foreign pathogens. In the bone marrow, hematopoietic stem cells can differentiate into common lymphoid progenitor cells. These cells are able to enter circulation and enter the thymus as thymus-seeding progenitor cells. These cells then differentiate into early thymic progenitors which proceed with T cell specification, developing from double negative (DN) to double positive (DP) to single positive (SP) T cells. Over the course of these developmental phases, the cells will commit to the T cell lineage and rearrange T cell receptor genes. In this pathway, pro-T cells can give rise to both alpha-beta and gamma-delta T cells and natural killer T (NKT) cells. Pro-T cells are a key constituent of the immune system, presenting a critical stage in the T cell developmental process. T cells are important players in adaptive immunity and help to initiate and orchestrate the immune response and eliminate pathogens and tumor cells. Pro-T cells are also an area of interest in the context of regenerative medicine to reconstitute T cells and adoptive T cell therapies as a potential source of T cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/JLB.1MR1217-496R
has db xref: DOI:10.1016/j.it.2020.12.004
has db xref: DOI:10.1093/intimm/dxy051

Axiom
annotated source: pro-T cell
annotated property: hasDbXref
annotated target: ZFA:0009350
mapping justification: UnspecifiedMatching

pro-T cell on CELLxGENE CellGuide
type: Axiom
annotated source: pro-T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000827

thromboblast
type: Class
equivalent class: Class
  intersection of: myeloid lineage restricted progenitor cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002574
subclass of: single nucleate cell
subclass of: myeloid cell
subclass of: myeloid lineage restricted progenitor cell
subclass of: Restriction
  on property: RO_0002202
  some values from: megakaryocyte-erythroid progenitor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002574
IAO_0000115: A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates.
has db xref: ZFA:0009351
comment: Note that this is a non-mammalian cell type.

Axiom
annotated source: thromboblast
annotated property: subClassOf
annotated target: myeloid lineage restricted progenitor cell
is inferred: true

Axiom
annotated source: thromboblast
annotated property: IAO_0000115
annotated target: A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:7758949

Axiom
annotated source: thromboblast
annotated property: hasDbXref
annotated target: ZFA:0009351
mapping justification: UnspecifiedMatching

basophilic myeloblast
type: Class
equivalent class: Class
  intersection of: myeloblast
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030221
subclass of: myeloblast
subclass of: Restriction
  on property: RO_0002202
  some values from: basophil progenitor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030221
IAO_0000115: A myeloblast committed to the basophil lineage.

Axiom
annotated source: basophilic myeloblast
annotated property: subClassOf
annotated target: myeloblast
is inferred: true

Axiom
annotated source: basophilic myeloblast
annotated property: IAO_0000115
annotated target: A myeloblast committed to the basophil lineage.
has db xref: GOC:add
has db xref: ISBN:0721601464

basophilic promyelocyte
type: Class
equivalent class: Class
  intersection of: promyelocyte
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030221
subclass of: promyelocyte
subclass of: Restriction
  on property: RO_0002202
  some values from: basophilic myeloblast
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030221
IAO_0000115: A promyelocyte committed to the basophil lineage.
has db xref: FMA:84208

Axiom
annotated source: basophilic promyelocyte
annotated property: subClassOf
annotated target: promyelocyte
is inferred: true

Axiom
annotated source: basophilic promyelocyte
annotated property: IAO_0000115
annotated target: A promyelocyte committed to the basophil lineage.
has db xref: GOC:add
has db xref: ISBN:0721601464

mast cell progenitor
type: Class
equivalent class: Class
  intersection of: myeloid lineage restricted progenitor cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007857
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000007858
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000005307
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001963
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002979
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002980
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000005178
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000016401
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0060374
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000009143
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000007431
subclass of: myeloid cell
subclass of: myeloid lineage restricted progenitor cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007857
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000007858
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000005307
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001963
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002979
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002980
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000005178
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000016401
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002028
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0060374
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000009143
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000007431
IAO_0000115: A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative.
has exact synonym: MCP
has related synonym: CFU-MC
has related synonym: CFU-Mast
has related synonym: colony forming unit mast cell
comment: MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa.

Axiom
annotated source: mast cell progenitor
annotated property: subClassOf
annotated target: myeloid lineage restricted progenitor cell
is inferred: true

Axiom
annotated source: mast cell progenitor
annotated property: IAO_0000115
annotated target: A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: PMCID:PMC1183570
has db xref: PMCID:PMC1312421
has db xref: PMID:8629001
has db xref: PMID:9354811
has db xref: http://www.copewithcytokines.de

eosinophilic myeloblast
type: Class
equivalent class: Class
  intersection of: myeloblast
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030222
subclass of: myeloblast
subclass of: Restriction
  on property: RO_0002202
  some values from: eosinophil progenitor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030222
IAO_0000115: A myeloblast committed to the eosinophil lineage.

Axiom
annotated source: eosinophilic myeloblast
annotated property: subClassOf
annotated target: myeloblast
is inferred: true

Axiom
annotated source: eosinophilic myeloblast
annotated property: IAO_0000115
annotated target: A myeloblast committed to the eosinophil lineage.
has db xref: GOC:add
has db xref: ISBN:0721601464

eosinophilic promyelocyte
type: Class
equivalent class: Class
  intersection of: promyelocyte
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030222
subclass of: promyelocyte
subclass of: Restriction
  on property: RO_0002202
  some values from: eosinophilic myeloblast
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030222
IAO_0000115: A promyelocyte committed to the eosinophil lineage.
has db xref: FMA:84199

Axiom
annotated source: eosinophilic promyelocyte
annotated property: subClassOf
annotated target: promyelocyte
is inferred: true

Axiom
annotated source: eosinophilic promyelocyte
annotated property: IAO_0000115
annotated target: A promyelocyte committed to the eosinophil lineage.
has db xref: GOC:add
has db xref: ISBN:0721601464

neutrophil progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002191
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030223
subclass of: myeloid cell
subclass of: CL_0002191
subclass of: Restriction
  on property: RO_0002202
  some values from: granulocyte monocyte progenitor cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030223
IAO_0000115: A progenitor cell of the neutrophil lineage.
has db xref: ZFA:0009352
has related synonym: neutrophil stem cell
in subset: cellxgene subset

Axiom
annotated source: neutrophil progenitor cell
annotated property: subClassOf
annotated target: CL_0002191
is inferred: true

Axiom
annotated source: neutrophil progenitor cell
annotated property: IAO_0000115
annotated target: A progenitor cell of the neutrophil lineage.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: ISBN:0721601464

Axiom
annotated source: neutrophil progenitor cell
annotated property: hasDbXref
annotated target: ZFA:0009352
mapping justification: UnspecifiedMatching

myeloblast
type: Class
equivalent class: Class
  intersection of: CL_0002191
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017503
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0000791
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0042582
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0040072
subclass of: myeloid cell
subclass of: CL_0002191
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017503
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0000791
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0042582
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0040072
subclass of: Restriction
  on property: RO_0002202
  some values from: granulocyte monocyte progenitor cell
IAO_0000115: The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow.
has db xref: BTO:0000187
has db xref: FMA:83524
has db xref: ZFA:0009353

Axiom
annotated source: myeloblast
annotated property: subClassOf
annotated target: CL_0002191
is inferred: true

Axiom
annotated source: myeloblast
annotated property: IAO_0000115
annotated target: The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow.
has db xref: GOC:add
has db xref: ISBN:0721601464
has db xref: http://en.wikipedia.org/wiki/Myeloblast
has db xref: http://www.cap.org

Axiom
annotated source: myeloblast
annotated property: hasDbXref
annotated target: ZFA:0009353
mapping justification: UnspecifiedMatching

promyelocyte
type: Class
equivalent class: Class
  intersection of: myeloid lineage restricted progenitor cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: CL_0017503
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005730
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0042582
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001483
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001932
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0040072
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001456
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001892
subclass of: myeloid cell
subclass of: CL_0002191
subclass of: Restriction
  on property: BFO_0000051
  some values from: CL_0017503
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0005730
subclass of: Restriction
  on property: BFO_0000051
  some values from: GO_0042582
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001483
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001932
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0040072
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001456
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001892
subclass of: Restriction
  on property: RO_0002202
  some values from: myeloblast
IAO_0000115: A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative.
has db xref: CALOHA:TS-0825
has db xref: FMA:83530
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: promyelocyte
annotated property: IAO_0000115
annotated target: A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: ISBN:0721601464
has db xref: http://www.cap.org

hematopoietic multipotent progenitor cell
type: Class
equivalent class: Class
  intersection of: hematopoietic cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001869
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001402
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: CL_0008001
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001869
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001402
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002202
  some values from: hematopoietic stem cell
disjoint with: CL_0002032
IAO_0000115: A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
has db xref: BTO:0000725
has db xref: CALOHA:TS-0448
has db xref: ZFA:0009354
has exact synonym: MPP
has exact synonym: hemopoietic progenitor cell
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Markers differ between mouse and human.

Axiom
annotated source: hematopoietic multipotent progenitor cell
annotated property: IAO_0000115
annotated target: A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:19022770

Axiom
annotated source: hematopoietic multipotent progenitor cell
annotated property: hasDbXref
annotated target: ZFA:0009354
mapping justification: UnspecifiedMatching

lymphoid lineage restricted progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002031
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030098
subclass of: CL_0002031
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030098
disjoint with: myeloid lineage restricted progenitor cell
IAO_0000115: A progenitor cell restricted to the lymphoid lineage.
has broad synonym: lymphoid progenitor cell
has db xref: BTO:0004731
has db xref: CALOHA:TS-2025
has db xref: FMA:70338
has db xref: ZFA:0009355
in subset: cellxgene subset
comment: Note that this is a class of cell types, not an identified single cell type.

Axiom
annotated source: lymphoid lineage restricted progenitor cell
annotated property: subClassOf
annotated target: CL_0002031
is inferred: true

Axiom
annotated source: lymphoid lineage restricted progenitor cell
annotated property: IAO_0000115
annotated target: A progenitor cell restricted to the lymphoid lineage.
has db xref: GOC:add
has db xref: GOC:tfm

Axiom
annotated source: lymphoid lineage restricted progenitor cell
annotated property: hasDbXref
annotated target: ZFA:0009355
mapping justification: UnspecifiedMatching

myeloid lineage restricted progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002031
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030099
subclass of: CL_0002031
subclass of: CL_0011026
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030099
IAO_0000115: A progenitor cell restricted to the myeloid lineage.
has broad synonym: myeloid progenitor cell
has db xref: BTO:0004730
has db xref: CALOHA:TS-2099
has db xref: FMA:70339
has db xref: ZFA:0009356
in subset: cellxgene subset
in subset: human reference atlas
comment: Note that this is a class of cell types, not an identified single cell type.

Axiom
annotated source: myeloid lineage restricted progenitor cell
annotated property: subClassOf
annotated target: CL_0002031
is inferred: true

Axiom
annotated source: myeloid lineage restricted progenitor cell
annotated property: IAO_0000115
annotated target: A progenitor cell restricted to the myeloid lineage.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:19022770

Axiom
annotated source: myeloid lineage restricted progenitor cell
annotated property: hasDbXref
annotated target: ZFA:0009356
mapping justification: UnspecifiedMatching

immature conventional dendritic cell
type: Class
equivalent class: Class
  intersection of: conventional dendritic cell
  intersection of: Restriction
    on property: RO_0015016
    some values from: GO_0042613
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001412
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001438
subclass of: myeloid leukocyte
subclass of: conventional dendritic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: common dendritic progenitor
subclass of: Restriction
  on property: RO_0015016
  some values from: GO_0042613
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001412
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001438
IAO_0000115: An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low.
has narrow synonym: immature myeloid dendritic cell
in subset: human reference atlas

Axiom
annotated source: immature conventional dendritic cell
annotated property: subClassOf
annotated target: conventional dendritic cell
is inferred: true

Axiom
annotated source: immature conventional dendritic cell
annotated property: IAO_0000115
annotated target: An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:9521319

mature conventional dendritic cell
type: Class
equivalent class: Class
  intersection of: conventional dendritic cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001310
  intersection of: Restriction
    on property: RO_0015015
    some values from: GO_0042613
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001412
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001438
subclass of: myeloid leukocyte
subclass of: conventional dendritic cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001310
subclass of: Restriction
  on property: RO_0002202
  some values from: immature conventional dendritic cell
subclass of: Restriction
  on property: RO_0015015
  some values from: GO_0042613
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001412
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001438
IAO_0000115: A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node.
has broad synonym: mature dendritic cell
has db xref: FMA:83038
has narrow synonym: mature myeloid dendritic cell
in subset: cellxgene subset

Axiom
annotated source: mature conventional dendritic cell
annotated property: subClassOf
annotated target: conventional dendritic cell
is inferred: true

Axiom
annotated source: mature conventional dendritic cell
annotated property: IAO_0000115
annotated target: A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:9521319

Axiom
annotated source: mature conventional dendritic cell
annotated property: hasBroadSynonym
annotated target: mature dendritic cell
has db xref: GOC:add

mononuclear leukocyte
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001407
subclass of: single nucleate cell
subclass of: leukocyte
IAO_0000115: A leukocyte with a single non-segmented nucleus in the mature form.
has db xref: BTO:0000878
has db xref: CALOHA:TS-0768
has db xref: FMA:86713
has db xref: ZFA:0009357
has exact synonym: mononuclear cell
has narrow synonym: peripheral blood mononuclear cell
in subset: blood and immune upper slim
in subset: cellxgene subset

Axiom
annotated source: mononuclear leukocyte
annotated property: subClassOf
annotated target: leukocyte
is inferred: true

Axiom
annotated source: mononuclear leukocyte
annotated property: IAO_0000115
annotated target: A leukocyte with a single non-segmented nucleus in the mature form.
has db xref: GOC:add

Axiom
annotated source: mononuclear leukocyte
annotated property: hasDbXref
annotated target: ZFA:0009357
mapping justification: UnspecifiedMatching

follicular B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001879
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002037
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001014
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001338
subclass of: B-2 B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002037
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001014
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001338
IAO_0000115: A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative.
has exact synonym: Fo B cell
has exact synonym: Fo B-cell
has exact synonym: follicular B lymphocyte
has exact synonym: follicular B-cell
has exact synonym: follicular B-lymphocyte
in subset: cellxgene subset
comment: Follicular B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive.

Axiom
annotated source: follicular B cell
annotated property: IAO_0000115
annotated target: A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: ISBN:0781735149
has db xref: PMCID:PMC2193793
has db xref: PMID:20933013
has db xref: http://en.wikipedia.org/wiki/Follicular_B_Cells

germinal center B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0010754
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
subclass of: mature B cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0010754
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002202
  some values from: follicular B cell
IAO_0000115: A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation.
has exact synonym: GC B cell
has exact synonym: GC B lymphocyte
has exact synonym: GC B-cell
has exact synonym: GC B-lymphocyte
has exact synonym: germinal center B lymphocyte
has exact synonym: germinal center B-cell
has exact synonym: germinal center B-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Germinal center B cells are also reportedly CD10-positive, CD19-positive, CD20-positive, CD38-positive, CD44-low, CD45-positive, CD48-positive, CD95-positive, CD352-positive, and HLA-DR-positive. Transcription factors: BCL6-positive, Ets1-positive, IRF8-positive, MTA3-positive, OBF1-positive, PAX5-positive, SpiB-positive, and STAT3-positive.

Axiom
annotated source: germinal center B cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: germinal center B cell
annotated property: IAO_0000115
annotated target: A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:tfm
has db xref: ISBN:0781735149
has db xref: PMID:19447676
has db xref: PMID:20933013

marginal zone B cell of spleen
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001251
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001880
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002037
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001338
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0042742
  intersection of: Restriction
    on property: RO_0015015
    some values from: GO_0071753
subclass of: mature B cell
subclass of: CL_2000074
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001251
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001880
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002037
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001338
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042742
subclass of: Restriction
  on property: RO_0015015
  some values from: GO_0071753
IAO_0000115: A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high.
has broad synonym: MZ B cell
has broad synonym: MZ B lymphocyte
has broad synonym: MZ B-cell
has broad synonym: MZ B-lymphocyte
has broad synonym: marginal zone B cell
has broad synonym: marginal zone B lymphocyte
has broad synonym: marginal zone B-cell
has broad synonym: marginal zone B-lymphocyte
has exact synonym: B cell of marginal zone of spleen
has exact synonym: marginal zone of spleen B cell
in subset: human reference atlas
comment: MZ B cells are reportedly CD1-positive (mice), CD20-positive, CD48-positive, CD84-positive, CD150-positive, CD229-positive, and CD352-positive.

Axiom
annotated source: marginal zone B cell of spleen
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: marginal zone B cell of spleen
annotated property: IAO_0000115
annotated target: A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: ISBN:0781735149
has db xref: PMID:10933592
has db xref: PMID:20933013
has db xref: http://en.wikipedia.org/wiki/Marginal-zone_B_cell

ciliated olfactory receptor neuron
type: Class
equivalent class: Class
  intersection of: olfactory receptor cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: GO_0005929
subclass of: ciliated cell
subclass of: olfactory receptor cell
IAO_0000115: An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob.
has db xref: ZFA:0009358
has exact synonym: ciliated olfactory sensory neuron
has exact synonym: ciliated sensory neuron

Axiom
annotated source: ciliated olfactory receptor neuron
annotated property: IAO_0000115
annotated target: An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob.
has db xref: PMID:16841163

Axiom
annotated source: ciliated olfactory receptor neuron
annotated property: hasDbXref
annotated target: ZFA:0009358
mapping justification: UnspecifiedMatching

serotonergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0060096
subclass of: serotonin secreting cell
subclass of: neuron
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0060096
IAO_0000115: A neuron that releases serotonin as a neurotransmitter.
has db xref: FBbt:00005133
has db xref: MESH:D059326
has db xref: WBbt:0006837
has db xref: ZFA:0009361
has exact synonym: 5-HT neuron
has exact synonym: 5-hydroxytryptamine neuron
has related synonym: serotinergic neuron
in subset: cellxgene subset

Axiom
annotated source: serotonergic neuron
annotated property: IAO_0000115
annotated target: A neuron that releases serotonin as a neurotransmitter.
has db xref: SANBI:mhl

Axiom
annotated source: serotonergic neuron
annotated property: hasDbXref
annotated target: FBbt:00005133
mapping justification: ManualMappingCuration

Axiom
annotated source: serotonergic neuron
annotated property: hasDbXref
annotated target: ZFA:0009361
mapping justification: UnspecifiedMatching

neuromast mantle cell
type: Class
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0008904
disjoint with: sensory hair cell
IAO_0000115: Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded.
has db xref: ZFA:0009362

Axiom
annotated source: neuromast mantle cell
annotated property: IAO_0000115
annotated target: Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded.
has db xref: ISBN:0125296509

Axiom
annotated source: neuromast mantle cell
annotated property: hasDbXref
annotated target: ZFA:0009362
mapping justification: UnspecifiedMatching

neuromast supporting cell
type: Class
subclass of: eukaryotic cell
subclass of: supporting cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0008904
disjoint with: sensory hair cell
IAO_0000115: Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells.
has db xref: ZFA:0009363
has exact synonym: neuromast support cell

Axiom
annotated source: neuromast supporting cell
annotated property: IAO_0000115
annotated target: Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells.
has db xref: ISBN:0125296509

Axiom
annotated source: neuromast supporting cell
annotated property: hasDbXref
annotated target: ZFA:0009363
mapping justification: UnspecifiedMatching

sensory hair cell
type: Class
subclass of: mechanoreceptor cell
IAO_0000115: Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
has broad synonym: hair cell
has db xref: BTO:0004744
has db xref: ZFA:0009366

Axiom
annotated source: sensory hair cell
annotated property: IAO_0000115
annotated target: Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
has db xref: SANBI:mhl

Axiom
annotated source: sensory hair cell
annotated property: hasDbXref
annotated target: ZFA:0009366
mapping justification: UnspecifiedMatching

neuromast hair cell
type: Class
equivalent class: Class
  intersection of: sensory hair cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0008904
subclass of: gravity sensitive cell
subclass of: sensory hair cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0008904
IAO_0000115: Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface.
has db xref: ZFA:0009367

Axiom
annotated source: neuromast hair cell
annotated property: IAO_0000115
annotated target: Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface.
has db xref: SANBI:mhl

Axiom
annotated source: neuromast hair cell
annotated property: hasDbXref
annotated target: ZFA:0009367
mapping justification: UnspecifiedMatching

slow muscle myoblast
type: Class
equivalent class: Class
  intersection of: myoblast
  intersection of: Restriction
    on property: RO_0002203
    some values from: slow muscle cell
subclass of: skeletal muscle myoblast
subclass of: Restriction
  on property: RO_0002203
  some values from: slow muscle cell
IAO_0000115: A skeletal muscle myoblast that differentiates into slow muscle fibers.
has db xref: ZFA:0009368

Axiom
annotated source: slow muscle myoblast
annotated property: IAO_0000115
annotated target: A skeletal muscle myoblast that differentiates into slow muscle fibers.
has db xref: SANBI:mhl

Axiom
annotated source: slow muscle myoblast
annotated property: hasDbXref
annotated target: ZFA:0009368
mapping justification: UnspecifiedMatching

classical monocyte
type: Class
equivalent class: Class
  intersection of: monocyte
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002548
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0006909
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0006954
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001199
subclass of: monocyte
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002548
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0006954
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001199
IAO_0000115: A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes.
description: Classical monocytes are a subtype of monocytes in humans are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. In mice, classical monocytes are characterized by high expression levels of the Gr1 cell surface marker. The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
description: Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: inflammatory monocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Markers: CCR2+CXCCR1<low> (human, mouse, rat).

Axiom
annotated source: classical monocyte
annotated property: subClassOf
annotated target: monocyte
is inferred: true

Axiom
annotated source: classical monocyte
annotated property: IAO_0000115
annotated target: A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes.
has db xref: GOC:add
has db xref: GO_REF:0000031
has db xref: PMID:16322748
has db xref: PMID:18303997
has db xref: PMID:20628149
has db xref: PMID:20870168

Axiom
annotated source: classical monocyte
annotated property: description
annotated target: Classical monocytes are a subtype of monocytes in humans are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. In mice, classical monocytes are characterized by high expression levels of the Gr1 cell surface marker. The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/nri.2017.28
has db xref: DOI:10.1111/sji.12883
has db xref: DOI:10.1182/blood-2009-07-235028
has db xref: DOI:10.3389/fimmu.2015.00423/full
has db xref: DOI:10.3389/fimmu.2019.02035

Axiom
annotated source: classical monocyte
annotated property: description
annotated target: Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1038/nri.2017.28
has db xref: DOI:10.1111/sji.12883
has db xref: DOI:10.1182/blood-2009-07-235028
has db xref: DOI:10.3389/fimmu.2015.00423/full
has db xref: DOI:10.3389/fimmu.2019.02035

classical monocyte on CELLxGENE CellGuide
type: Axiom
annotated source: classical monocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000860

elicited macrophage
type: Class
equivalent class: Class
  intersection of: macrophage
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0006954
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001813
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002064
subclass of: macrophage
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0006954
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001813
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002064
subclass of: Restriction
  on property: RO_0002202
  some values from: classical monocyte
IAO_0000115: A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive.
description: The elicited macrophage, also commonly referred to as an activated macrophage, is a specialized type of cell that forms a critical part of the immune response. These cells originate from monocytes, a type of white blood cell that circulates in the bloodstream. In response to infection, inflammation, or tissue injury, monocytes leave the bloodstream, enters the inflamed tissue, and differentiates into a macrophage. The term "elicited" indicates that these cells have been activated or stimulated, usually through exposure to mediators such as lipopolysaccharide (LPS) or interferon-gamma (IFN-gamma), and have acquired enhanced microbicidal and tumoricidal capabilities. One of the hallmark features of elicited macrophages is their remarkable plasticity, which enables them to assume distinct activation states depending on the signals they receive. Macrophage activation states span a spectrum of phenotypes and functions, but are often classified into a few groups for simplicity. Classically activated macrophages, also known as M1 macrophages, are typically induced by pro-inflammatory cytokines such as interferon-gamma (IFN-γ) and microbial products like lipopolysaccharide (LPS). These M1 macrophages exhibit potent microbicidal and pro-inflammatory functions, aiding in the clearance of pathogens and the initiation of immune responses. Alternatively activated macrophages, or M2 macrophages, are typically associated with tissue repair, wound healing, and immunoregulation. They are induced by anti-inflammatory cytokines such as interleukin-4 (IL-4) and interleukin-13 (IL-13), as well as factors released during tissue remodeling. Elicited macrophages can transition between phenotypes in response to changing environmental cues, thereby exerting context-dependent effects on immune and tissue homeostasis. Elicited macrophages perform a range of functions in order to respond to the type of insult that has occurred. They can phagocytose cellular debris, foreign substances, microbes,…
has db xref: FMA:84643
has db xref: FMA:84645
has exact synonym: free macrophage
has exact synonym: wandering histiocyte
in subset: cellxgene subset
comment: Markers: CD11b+, CD68+; Mouse: F4/80+; role or process: immune, inflammation (inflammatory response).

Axiom
annotated source: elicited macrophage
annotated property: subClassOf
annotated target: macrophage
is inferred: true

Axiom
annotated source: elicited macrophage
annotated property: IAO_0000115
annotated target: A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive.
has db xref: GOC:add
has db xref: GOC:ana
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:15771589

Axiom
annotated source: elicited macrophage
annotated property: description
annotated target: The elicited macrophage, also commonly referred to as an activated macrophage, is a specialized type of cell that forms a critical part of the immune response. These cells originate from monocytes, a type of white blood cell that circulates in the bloodstream. In response to infection, inflammation, or tissue injury, monocytes leave the bloodstream, enters the inflamed tissue, and differentiates into a macrophage. The term "elicited" indicates that these cells have been activated or stimulated, usually through exposure to mediators such as lipopolysaccharide (LPS) or interferon-gamma (IFN-gamma), and have acquired enhanced microbicidal and tumoricidal capabilities. One of the hallmark features of elicited macrophages is their remarkable plasticity, which enables them to assume distinct activation states depending on the signals they receive. Macrophage activation states span a spectrum of phenotypes and functions, but are often classified into a few groups for simplicity. Classically activated macrophages, also known as M1 macrophages, are typically induced by pro-inflammatory cytokines such as interferon-gamma (IFN-γ) and microbial products like lipopolysaccharide (LPS). These M1 macrophages exhibit potent microbicidal and pro-inflammatory functions, aiding in the clearance of pathogens and the initiation of immune responses. Alternatively activated macrophages, or M2 macrophages, are typically associated with tissue repair, wound healing, and immunoregulation. They are induced by anti-inflammatory cytokines such as interleukin-4 (IL-4) and interleukin-13 (IL-13), as well as factors released during tissue remodeling. Elicited macrophages can transition between phenotypes in response to changing environmental cues, thereby exerting context-dependent effects on immune and tissue homeostasis. Elicited macrophages perform a range of functions in order to respond to the type of insult that has occurred. They can phagocytose cellular debris, foreign substances, microbes,…
has db xref: DOI:10.1016/j.chembiol.2020.12.005
has db xref: DOI:10.1038/nri2448
has db xref: DOI:10.1038/s41586-023-06002-x
has db xref: DOI:10.3389/fimmu.2020.00269
has db xref: DOI:10.3389/fimmu.2021.708186

elicited macrophage on CELLxGENE CellGuide
type: Axiom
annotated source: elicited macrophage
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000861

suppressor macrophage
type: Class
equivalent class: Class
  intersection of: elicited macrophage
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050777
subclass of: elicited macrophage
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050777
IAO_0000115: A macrophage that suppresses immune responses.
comment: Markers: May express: IL10, TGFbeta.

Axiom
annotated source: suppressor macrophage
annotated property: subClassOf
annotated target: elicited macrophage
is inferred: true

Axiom
annotated source: suppressor macrophage
annotated property: IAO_0000115
annotated target: A macrophage that suppresses immune responses.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: PMID:20402419

M1 macrophage
type: Class
equivalent class: Class
  intersection of: elicited macrophage
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032611
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032635
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032640
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0042554
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0042742
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045428
subclass of: elicited macrophage
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0020017
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032611
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032635
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032640
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042554
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042742
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045428
IAO_0000115: An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity.
description: Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who a…
has exact synonym: classically activated macrophage
has exact synonym: inflammatory macrophage
in subset: cellxgene subset
comment: Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reactive oxygen species, nitric oxide; role or process: immune, inflammation (inflammatory response).

Axiom
annotated source: M1 macrophage
annotated property: subClassOf
annotated target: elicited macrophage
is inferred: true

Axiom
annotated source: M1 macrophage
annotated property: IAO_0000115
annotated target: An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity.
has db xref: GOC:ana
has db xref: GO_REF:0000031
has db xref: PMID:19132917

Axiom
annotated source: M1 macrophage
annotated property: description
annotated target: Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who a…
has db xref: DOI:10.1038/s41392-023-01452-1
has db xref: DOI:10.1186/s12935-021-02089-2
has db xref: DOI:10.3389/fimmu.2015.00263
has db xref: DOI:10.3389/fimmu.2020.583084

Axiom
annotated source: M1 macrophage
annotated property: hasExactSynonym
annotated target: classically activated macrophage
has db xref: PMID:30861466

M1 macrophage on CELLxGENE CellGuide
type: Axiom
annotated source: M1 macrophage
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000863

tissue-resident macrophage
type: Class
equivalent class: Class
  intersection of: macrophage
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0000479
subclass of: macrophage
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0000479
IAO_0000115: A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
description: Tissue-resident macrophages refer to a heterogeneous group of specialized macrophages that permanently reside within specific tissues, performing integral functions essential to tissue homeostasis. Most tissue-resident macrophages arise from embryonic populations and self-renew. Some macrophages may also originate from circulating monocytes released from the bone marrow and differentiate into macrophages upon entering tissue. Tissue-resident macrophages are given different names depending upon the tissue in which they reside, such as Kupffer cells in the liver, alveolar macrophages in the lungs, and microglia in the brain. Tissue-resident macrophages are responsible for the phagocytosis of pathogenic substances and dead cells, serving as part of the foremost line of defense against invading microorganisms. They utilize pattern recognition receptors to identify foreign substances and function as antigen-presenting cells to induce adaptive immunity. Additionally, they produce a variety of cytokines and chemokines, signaling molecules that recruit additional immune cells to sites of infection or inflammation and regulate immune responses. In addition to their immunological roles, tissue-resident macrophages also have tissue-unique functions. In the liver, Kupffer cells play a role in iron homeostasis, while in the brain, microglia are responsible for synaptic pruning during development. In the lungs, alveolar macrophages are involved in the removal of airborne particles and debris. This underscores their significance in not only providing pathological immunity but also in maintaining the optimal function of the tissues in which they reside. " (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: FMA:84642
has db xref: FMA:84644
has exact synonym: fixed macrophage
has exact synonym: resting histiocyte
in subset: cellxgene subset

Axiom
annotated source: tissue-resident macrophage
annotated property: subClassOf
annotated target: macrophage
is inferred: true

Axiom
annotated source: tissue-resident macrophage
annotated property: IAO_0000115
annotated target: A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
has db xref: GOC:ana
has db xref: GO_REF:0000031
has db xref: PMID:19770654

Axiom
annotated source: tissue-resident macrophage
annotated property: description
annotated target: Tissue-resident macrophages refer to a heterogeneous group of specialized macrophages that permanently reside within specific tissues, performing integral functions essential to tissue homeostasis. Most tissue-resident macrophages arise from embryonic populations and self-renew. Some macrophages may also originate from circulating monocytes released from the bone marrow and differentiate into macrophages upon entering tissue. Tissue-resident macrophages are given different names depending upon the tissue in which they reside, such as Kupffer cells in the liver, alveolar macrophages in the lungs, and microglia in the brain. Tissue-resident macrophages are responsible for the phagocytosis of pathogenic substances and dead cells, serving as part of the foremost line of defense against invading microorganisms. They utilize pattern recognition receptors to identify foreign substances and function as antigen-presenting cells to induce adaptive immunity. Additionally, they produce a variety of cytokines and chemokines, signaling molecules that recruit additional immune cells to sites of infection or inflammation and regulate immune responses. In addition to their immunological roles, tissue-resident macrophages also have tissue-unique functions. In the liver, Kupffer cells play a role in iron homeostasis, while in the brain, microglia are responsible for synaptic pruning during development. In the lungs, alveolar macrophages are involved in the removal of airborne particles and debris. This underscores their significance in not only providing pathological immunity but also in maintaining the optimal function of the tissues in which they reside. " (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.immuni.2016.02.015
has db xref: DOI:10.1038/s41392-023-01452-1
has db xref: DOI:10.1093/intimm/dxy054
has db xref: DOI:10.1146/annurev-immunol-032414-112220

tissue-resident macrophage on CELLxGENE CellGuide
type: Axiom
annotated source: tissue-resident macrophage
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000864

thymic macrophage
type: Class
equivalent class: Class
  intersection of: tissue-resident macrophage
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0043277
subclass of: tissue-resident macrophage
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002370
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0043277
IAO_0000115: A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes.
in subset: cellxgene subset
in subset: human reference atlas
comment: Role or process: immune, clearance of apoptotic thymocytes, antigen-presentation.

Axiom
annotated source: thymic macrophage
annotated property: subClassOf
annotated target: tissue-resident macrophage
is inferred: true

Axiom
annotated source: thymic macrophage
annotated property: IAO_0000115
annotated target: A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes.
has db xref: GOC:ana
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:9048205

non-classical monocyte
type: Class
equivalent class: Class
  intersection of: monocyte
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0000587
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0031294
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0030224
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001206
subclass of: monocyte
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0000587
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002393
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0031294
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030224
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001206
IAO_0000115: A type of monocyte characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, and decrease size relative to classical monocytes, but increased co-stimulatory activity. May also play a role in tissue repair.
description: Non-classical monocytes, also known as patrolling monocytes, are a subtype of monocytes in the circulation, accounting for approximately 5-10% of total human monocytes. These monocytes are characterized by the differential expression of two surface markers, CD14 and CD16, with non-classical monocytes expressing CD14 and high levels of CD16 (CD14+ CD16++). Classical monocytes are released from the bone marrow into the circulation and can transition to intermediate followed by non-classical monocytes. Non-classical monocytes patrol the endothelium and, upon sensing inflammation or injury, migrate across it. Non-classical monocytes are also involved in the removal of damaged cells via phagocytosis. This process enables the cells to engulf and destroy pathogens, debris, and apoptotic cells. During homeostasis, these monocytes appear to have an important function in maintaining vascular integrity. Non-classical monocytes are also able to induce CD4+ T cell proliferation and sense viruses. They can produce and secrete a wide range of inflammatory cytokines and chemokines to reinforce and shape the immune response. Non-classical monocytes also appear to play a role in different inflammatory diseases states including atherosclerosis, multiple sclerosis, and rheumatoid arthritis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: patrolling monocyte
has exact synonym: resident monocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Markers: CCR2-CX3CCR1+ (human, mouse, rat); human: CD16+, CCR5+, CD32/FcgRII-high, MHCII+, CD86+; mouse: CD62L-Ly6C-.

Axiom
annotated source: non-classical monocyte
annotated property: subClassOf
annotated target: monocyte
is inferred: true

Axiom
annotated source: non-classical monocyte
annotated property: IAO_0000115
annotated target: A type of monocyte characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, and decrease size relative to classical monocytes, but increased co-stimulatory activity. May also play a role in tissue repair.
has db xref: GOC:add
has db xref: GO_REF:0000031
has db xref: PMID:16322748
has db xref: PMID:18303997
has db xref: PMID:20628149
has db xref: PMID:20870168

Axiom
annotated source: non-classical monocyte
annotated property: description
annotated target: Non-classical monocytes, also known as patrolling monocytes, are a subtype of monocytes in the circulation, accounting for approximately 5-10% of total human monocytes. These monocytes are characterized by the differential expression of two surface markers, CD14 and CD16, with non-classical monocytes expressing CD14 and high levels of CD16 (CD14+ CD16++). Classical monocytes are released from the bone marrow into the circulation and can transition to intermediate followed by non-classical monocytes. Non-classical monocytes patrol the endothelium and, upon sensing inflammation or injury, migrate across it. Non-classical monocytes are also involved in the removal of damaged cells via phagocytosis. This process enables the cells to engulf and destroy pathogens, debris, and apoptotic cells. During homeostasis, these monocytes appear to have an important function in maintaining vascular integrity. Non-classical monocytes are also able to induce CD4+ T cell proliferation and sense viruses. They can produce and secrete a wide range of inflammatory cytokines and chemokines to reinforce and shape the immune response. Non-classical monocytes also appear to play a role in different inflammatory diseases states including atherosclerosis, multiple sclerosis, and rheumatoid arthritis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.immuni.2018.10.005
has db xref: DOI:10.1111/sji.12883
has db xref: DOI:10.1146/annurev-immunol-042617-053119

non-classical monocyte on CELLxGENE CellGuide
type: Axiom
annotated source: non-classical monocyte
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000875

central nervous system macrophage
type: Class
equivalent class: Class
  intersection of: tissue-resident macrophage
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001017
subclass of: tissue-resident macrophage
subclass of: CL_0002319
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001017
IAO_0000115: A tissue-resident macrophage found in the central nervous system.
description: Central Nervous System (CNS) macrophages represent an integral part of the brain's innate immune system. These immune cells play crucial roles in maintenance and regulation, homeostasis, and disease response, thereby helping in the overall cognitive functioning of an organism. There are different macrophage populations in the CNS, often classified into microglial cells, which reside in the parenchyma, and non-parenchymal macrophages at the interface between the brain and the periphery, including the perivascular spaces, the choroid plexus, and the meninges. CNS macrophages are derived from erythromyeloid progenitors in the yolk sac. CNS macrophages have distinct morphologies: Meningeal and perivascular macrophages have a more elongated shape than microglia, which are characterized by a small cell body with fine processes; in contrast, choroid plexus macrophages typically have a stellate shape. Microglia are the most abundant abundant mononuclear phagocytes and have been shown to play a number of physiological roles, including proinflammatory and anti-inflammatory functions, synaptic pruning and remodeling, and apoptotic cell removal through phagocytosis. Non-parenchymal CAMs primarily support the barrier function against external antigens. Meningeal macrophages have been shown to respond to peripheral microbial challenges and to protect the brain against fatal viral infection. CNS macrophages are also involved in the initiation and progression of many neurological diseases, such as Alzheimer's disease and Parkinson's disease as well as multiple sclerosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: CNS macrophage
in subset: cellxgene subset

Axiom
annotated source: central nervous system macrophage
annotated property: subClassOf
annotated target: tissue-resident macrophage
is inferred: true

Axiom
annotated source: central nervous system macrophage
annotated property: IAO_0000115
annotated target: A tissue-resident macrophage found in the central nervous system.
has db xref: GO_REF:0000031
has db xref: PMID:16322748

Axiom
annotated source: central nervous system macrophage
annotated property: description
annotated target: Central Nervous System (CNS) macrophages represent an integral part of the brain's innate immune system. These immune cells play crucial roles in maintenance and regulation, homeostasis, and disease response, thereby helping in the overall cognitive functioning of an organism. There are different macrophage populations in the CNS, often classified into microglial cells, which reside in the parenchyma, and non-parenchymal macrophages at the interface between the brain and the periphery, including the perivascular spaces, the choroid plexus, and the meninges. CNS macrophages are derived from erythromyeloid progenitors in the yolk sac. CNS macrophages have distinct morphologies: Meningeal and perivascular macrophages have a more elongated shape than microglia, which are characterized by a small cell body with fine processes; in contrast, choroid plexus macrophages typically have a stellate shape. Microglia are the most abundant abundant mononuclear phagocytes and have been shown to play a number of physiological roles, including proinflammatory and anti-inflammatory functions, synaptic pruning and remodeling, and apoptotic cell removal through phagocytosis. Non-parenchymal CAMs primarily support the barrier function against external antigens. Meningeal macrophages have been shown to respond to peripheral microbial challenges and to protect the brain against fatal viral infection. CNS macrophages are also involved in the initiation and progression of many neurological diseases, such as Alzheimer's disease and Parkinson's disease as well as multiple sclerosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/s00281-013-0382-8
has db xref: DOI:10.1016/j.immuni.2022.10.005
has db xref: DOI:10.1016/j.tins.2021.07.002
has db xref: DOI:10.1038/s41583-019-0201-x

central nervous system macrophage on CELLxGENE CellGuide
type: Axiom
annotated source: central nervous system macrophage
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000878

thymic medullary macrophage
type: Class
equivalent class: Class
  intersection of: thymic macrophage
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002124
subclass of: thymic macrophage
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002124
IAO_0000115: A thymic macrophage found in the thymic medulla.
in subset: human reference atlas

Axiom
annotated source: thymic medullary macrophage
annotated property: subClassOf
annotated target: thymic macrophage
is inferred: true

Axiom
annotated source: thymic medullary macrophage
annotated property: IAO_0000115
annotated target: A thymic macrophage found in the thymic medulla.
has db xref: GOC:ana
has db xref: GO_REF:0000031
has db xref: PMID:9048205

Axiom
annotated source: thymic medullary macrophage
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM322.LZLG.752

myeloid suppressor cell
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001501
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001006
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050777
subclass of: myeloid leukocyte
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001501
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001006
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0050777
IAO_0000115: An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive.
in subset: blood and immune upper slim
in subset: cellxgene subset
comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis.

Axiom
annotated source: myeloid suppressor cell
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: myeloid suppressor cell
annotated property: IAO_0000115
annotated target: An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive.
has db xref: GOC:add
has db xref: GOC:ana
has db xref: GO_REF:0000031
has db xref: PMID:16168663
has db xref: PMID:17016554
has db xref: PMID:17016559

foam cell
type: Class
subclass of: cell
IAO_0000115: A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
has db xref: BTO:0003872
has db xref: FMA:83586
has db xref: MESH:D005487

Axiom
annotated source: foam cell
annotated property: IAO_0000115
annotated target: A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
has db xref: GOC:add

smooth muscle cell derived foam cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: foam cell
subclass of: Restriction
  on property: RO_0002202
  some values from: smooth muscle cell
IAO_0000115: A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.

Axiom
annotated source: smooth muscle cell derived foam cell
annotated property: IAO_0000115
annotated target: A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
has db xref: GOC:add
has db xref: PMID:30664015

thymocyte
type: Class
equivalent class: Class
  intersection of: T cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0045058
subclass of: CL_0002420
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002370
IAO_0000115: An immature T cell located in the thymus.
has broad synonym: immature T cell
has broad synonym: immature T lymphocyte
has broad synonym: immature T-cell
has broad synonym: immature T-lymphocyte
has db xref: BTO:0001372
has db xref: CALOHA:TS-1042
has db xref: FMA:72202
has db xref: MESH:D060168
has db xref: XAO:0003159
has exact synonym: thymic lymphocyte
in subset: cellxgene subset

Axiom
annotated source: thymocyte
annotated property: subClassOf
annotated target: CL_0002420
is inferred: true

Axiom
annotated source: thymocyte
annotated property: IAO_0000115
annotated target: An immature T cell located in the thymus.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:12415312

DN1 thymic pro-T cell
type: Class
equivalent class: Class
  intersection of: pro-T cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001380
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001307
subclass of: pro-T cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002370
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001307
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002425
IAO_0000115: A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative.
has exact synonym: DN1 thymic pro-T lymphocyte
has exact synonym: DN1 thymic pro-T-cell
has exact synonym: DN1 thymic pro-T-lymphocyte
has exact synonym: DN1 thymic progenitor T cell
has exact synonym: DN1 thymocyte
has exact synonym: double negative 1
has exact synonym: preT.DN1.Th

Axiom
annotated source: DN1 thymic pro-T cell
annotated property: subClassOf
annotated target: pro-T cell
is inferred: true

Axiom
annotated source: DN1 thymic pro-T cell
annotated property: IAO_0000115
annotated target: A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031

naive thymus-derived CD4-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001380
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001203
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001869
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001318
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001307
subclass of: CD4-positive, alpha-beta T cell
subclass of: naive T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002436
IAO_0000115: An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low.
has broad synonym: naive CD4+ T cell
has exact synonym: T.4Nve.Sp
has exact synonym: Th0
has exact synonym: naive thymus-derived CD4-positive, alpha-beta T lymphocyte
has exact synonym: naive thymus-derived CD4-positive, alpha-beta T-cell
has exact synonym: naive thymus-derived CD4-positive, alpha-beta T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: These cells have not been exposed to antigen following thymic T-cell selection; found in blood and secondary lymphoid organs. This cell type is compatible with the HIPC Lyoplate markers for 'naive CD4+ T cell', but includes additional markers known to be expressed on naive CD4+ T cells.

Axiom
annotated source: naive thymus-derived CD4-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: naive thymus-derived CD4-positive, alpha-beta T cell
annotated property: IAO_0000115
annotated target: An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:19100699
has db xref: PMID:22343568
has db xref: http://www.immgen.org/index_content.html

Axiom
annotated source: naive thymus-derived CD4-positive, alpha-beta T cell
annotated property: hasBroadSynonym
annotated target: naive CD4+ T cell
has db xref: PMID:22343568

Axiom
annotated source: naive thymus-derived CD4-positive, alpha-beta T cell
annotated property: hasExactSynonym
annotated target: Th0
has db xref: GOC:tfm

activated CD4-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001318
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001869
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001380
subclass of: CD4-positive, alpha-beta T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001318
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001869
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002202
  some values from: naive thymus-derived CD4-positive, alpha-beta T cell
IAO_0000115: A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive.
has exact synonym: activated CD4-positive, alpha-beta T lymphocyte
has exact synonym: activated CD4-positive, alpha-beta T-cell
has exact synonym: activated CD4-positive, alpha-beta T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: activated CD4-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: activated CD4-positive, alpha-beta T cell
annotated property: IAO_0000115
annotated target: A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GO_REF:0000031

CD4-positive, alpha-beta memory T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001603
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0002286
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0043379
subclass of: CD4-positive, alpha-beta T cell
subclass of: memory T cell
IAO_0000115: A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell.
contributor: https://orcid.org/0000-0001-9990-8331
has exact synonym: CD4-positive, alpha-beta memory T lymphocyte
has exact synonym: CD4-positive, alpha-beta memory T-cell
has exact synonym: CD4-positive, alpha-beta memory T-lymphocyte
has related synonym: T4.Mem.Sp
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD4-positive, alpha-beta memory T cell
annotated property: IAO_0000115
annotated target: A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell.
has db xref: GOC:add
has db xref: ISBN:0781735149
has db xref: http://www.immgen.org/index_content.html

naive T cell
type: Class
equivalent class: Class
  intersection of: CL_0002419
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001203
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001869
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0045058
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001318
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001307
subclass of: CL_0002419
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001015
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001203
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001869
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001318
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001307
IAO_0000115: Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low.
has exact synonym: naive T lymphocyte
has exact synonym: naive T-cell
has exact synonym: naive T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: naive T cell
annotated property: subClassOf
annotated target: CL_0002419
is inferred: true

Axiom
annotated source: naive T cell
annotated property: IAO_0000115
annotated target: Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:19100699

T-helper 17 cell
type: Class
equivalent class: Class
  intersection of: CD4-positive helper T cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003455
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001207
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001202
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032620
subclass of: CD4-positive helper T cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003455
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001207
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001202
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032620
IAO_0000115: CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CXCR3-negative, CCR6-positive, and capable of producing IL-17.
has db xref: MESH:D058504
has exact synonym: IL-17-producing CD4+ T helper
has exact synonym: T helper cells type 17
has exact synonym: T(H)-17 cell
has exact synonym: Th17 CD4+ T cell
has exact synonym: Th17 T cell
has exact synonym: Th17 T lymphocyte
has exact synonym: Th17 T-cell
has exact synonym: Th17 T-lymphocyte
has exact synonym: Th17 cell
has exact synonym: helper T cell type 17
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'Th17 CD4+ T cell', but its logical definition includes additional known characteristics of T-helper 17 T cells.

Axiom
annotated source: T-helper 17 cell
annotated property: subClassOf
annotated target: CD4-positive helper T cell
is inferred: true

Axiom
annotated source: T-helper 17 cell
annotated property: IAO_0000115
annotated target: CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CXCR3-negative, CCR6-positive, and capable of producing IL-17.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GO_REF:0000031
has db xref: PMID:20303875
has db xref: PMID:20969597
has db xref: PMID:22343568

Axiom
annotated source: T-helper 17 cell
annotated property: hasExactSynonym
annotated target: Th17 CD4+ T cell
has db xref: PMID:22343568

naive thymus-derived CD8-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001380
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001203
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001869
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001318
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001307
subclass of: CD8-positive, alpha-beta T cell
subclass of: naive T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002437
IAO_0000115: A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low.
has broad synonym: naive CD8+ T cell
has exact synonym: naive thymus-dervied CD8-positive, alpha-beta T lymphocyte
has exact synonym: naive thymus-dervied CD8-positive, alpha-beta T-cell
has exact synonym: naive thymus-dervied CD8-positive, alpha-beta T-lymphocyte
has narrow synonym: T.8Nve.Sp
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell traffics in secondary lymphoid organs and blood. This cell type is compatible with the HIPC Lyoplate markers for 'naive CD8+ T cell', but includes additional markers known to be expressed on naive CD8+ T cells.

Axiom
annotated source: naive thymus-derived CD8-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: naive thymus-derived CD8-positive, alpha-beta T cell
annotated property: IAO_0000115
annotated target: A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149
has db xref: PMID:22343568
has db xref: http://www.immgen.org/index_content.html

Axiom
annotated source: naive thymus-derived CD8-positive, alpha-beta T cell
annotated property: hasBroadSynonym
annotated target: naive CD8+ T cell
has db xref: PMID:22343568

Tr1 cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032613
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0050777
subclass of: CD4-positive helper T cell
subclass of: regulatory T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032613
IAO_0000115: CD4-positive alpha-beta T cell with regulatory function that produces IL-10.
has exact synonym: T-regulatory T cell type 1
has exact synonym: Tr1 T cell
has exact synonym: Tr1 T lymphocyte
has exact synonym: Tr1 T-cell
has exact synonym: Tr1 T-lymphocyte
comment: These cells are reportedly induced by IL-10 and are capable of producing IFN-gamma, IL-5, IL-10, and TGF-beta.)

Axiom
annotated source: Tr1 cell
annotated property: IAO_0000115
annotated target: CD4-positive alpha-beta T cell with regulatory function that produces IL-10.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GO_REF:0000031
has db xref: PMID:16903904

activated CD8-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001203
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001318
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001869
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001380
subclass of: CD8-positive, alpha-beta T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001203
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001318
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001869
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002202
  some values from: naive thymus-derived CD8-positive, alpha-beta T cell
IAO_0000115: A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative.
has exact synonym: activated CD8-positive, alpha-beta T lymphocyte
has exact synonym: activated CD8-positive, alpha-beta T-cell
has exact synonym: activated CD8-positive, alpha-beta T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: activated CD8-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: activated CD8-positive, alpha-beta T cell
annotated property: IAO_0000115
annotated target: A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031

CD8-positive, alpha-beta cytokine secreting effector T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001318
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001869
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001380
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001816
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0030217
subclass of: CD8-positive, alpha-beta T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001318
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001869
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001380
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD8-positive, alpha-beta T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001816
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030217
IAO_0000115: A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines.
has exact synonym: CD8-positive, alpha-beta cytokine secreting effector T lymphocyte
has exact synonym: CD8-positive, alpha-beta cytokine secreting effector T-cell
has exact synonym: CD8-positive, alpha-beta cytokine secreting effector T-lymphocyte

Axiom
annotated source: CD8-positive, alpha-beta cytokine secreting effector T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta cytokine secreting effector T cell
annotated property: IAO_0000115
annotated target: A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:20146720

CD8-positive, alpha-beta memory T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001603
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0002286
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0043379
subclass of: CD8-positive, alpha-beta T cell
subclass of: memory T cell
IAO_0000115: A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell.
contributor: https://orcid.org/0000-0001-9990-8331
has exact synonym: CD8-positive, alpha-beta memory T lymphocyte
has exact synonym: CD8-positive, alpha-beta memory T-cell
has exact synonym: CD8-positive, alpha-beta memory T-lymphocyte
has related synonym: T.8Mem.Sp
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD8-positive, alpha-beta memory T cell
annotated property: IAO_0000115
annotated target: A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell.
has db xref: GOC:add
has db xref: PMID:20146720

cytotoxic T cell
type: Class
equivalent class: Class
  intersection of: effector T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001913
subclass of: effector T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001913
IAO_0000115: A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive.
has db xref: BTO:0000289
has db xref: CALOHA:TS-0190
has db xref: FMA:70573
has exact synonym: cytotoxic T lymphocyte
has exact synonym: cytotoxic T-cell
has exact synonym: cytotoxic T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: cytotoxic T cell
annotated property: subClassOf
annotated target: effector T cell
is inferred: true

Axiom
annotated source: cytotoxic T cell
annotated property: IAO_0000115
annotated target: A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:18395547

effector T cell
type: Class
equivalent class: Class
  intersection of: CL_0002419
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0045026
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0030217
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0045058
subclass of: CL_0002419
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0045026
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030217
IAO_0000115: A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response.
has exact synonym: effector T lymphocyte
has exact synonym: effector T-cell
has exact synonym: effector T-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: effector T cell
annotated property: subClassOf
annotated target: CL_0002419
is inferred: true

Axiom
annotated source: effector T cell
annotated property: IAO_0000115
annotated target: A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response.
has db xref: GOC:PAM-ADD
has db xref: GOC:tfm
has db xref: ISBN:0877799148
has db xref: PMID:18395547

helper T cell
type: Class
equivalent class: Class
  intersection of: effector T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001816
subclass of: effector T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001816
IAO_0000115: A effector T cell that provides help in the form of secreted cytokines to other immune cells.
has db xref: BTO:0002417
has db xref: MESH:D006377
has exact synonym: T-helper cell
has exact synonym: helper T lymphocyte
has exact synonym: helper T-cell
has exact synonym: helper T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: helper T cell
annotated property: subClassOf
annotated target: effector T cell
is inferred: true

Axiom
annotated source: helper T cell
annotated property: IAO_0000115
annotated target: A effector T cell that provides help in the form of secreted cytokines to other immune cells.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:18395547

immature NK T cell
type: Class
equivalent class: Class
  intersection of: immature alpha-beta T cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003469
subclass of: immature alpha-beta T cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003469
subclass of: Restriction
  on property: RO_0002202
  some values from: double-positive, alpha-beta thymocyte
IAO_0000115: An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers.
has exact synonym: immature NK T lymphocyte
has exact synonym: immature NK T-cell
has exact synonym: immature NK T-lymphocyte
has exact synonym: immature NKT cell
in subset: cellxgene subset

Axiom
annotated source: immature NK T cell
annotated property: subClassOf
annotated target: immature alpha-beta T cell
is inferred: true

Axiom
annotated source: immature NK T cell
annotated property: IAO_0000115
annotated target: An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17589542
has db xref: PMID:19169262

CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: alpha-beta intraepithelial T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001084
subclass of: alpha-beta intraepithelial T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001084
subclass of: Restriction
  on property: RO_0002202
  some values from: CD8-positive, alpha-beta thymocyte
IAO_0000115: An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative.
description: The CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell, often abbreviated as CD8αα IEL, is a specialized immune cell found within the epithelial layer of mucosal surfaces, such as the intestines. CD8αα IEL have been studied extensively in mice, but equivalent cells are thought to be present in humans, albeit at lower numbers. These cells represent a subset of intraepithelial T lymphocytes characterized by the expression of both CD8-alpha-alpha homodimer and the alpha-beta variant of the T cell receptor (TCR). Other features shared with intraepithelial T lymphocytes include the expression of T-bet, a master transcription factor that controls expression of proinflammatory cytokines, natural killer cell receptors, and an activated phenotype (high expression of CD69). Functionally, CD8αα IELs are thought to play a role in maintaining epithelial integrity, local immune surveillance, and protection against microbial pathogens. Upon detecting alterations associated with infection or inflammation, these cells orchestrate immune responses to restore tissue homeostasis, primarily through the secretion of cytokines and chemokines, and directly eliminating infected cells. CD8αα IELs have been shown require β2 microglobulin-dependent MHC class I expression for their generation and/or homeostasis. They share some characteristics with natural killer cells and might have similar suppressive and regulatory roles which they perform through the production of IL-10 and TGFβ. For example, they have been shown the prevent induced colitis, indicating that by modulating immune responses, CD8αα IELs prevent excessive and damaging immune activation that can lead to chronic inflammatory conditions or autoimmunity. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be consider…
has exact synonym: CD8-alpha-alpha-positive, alpha-beta intraepithelial T lymphocyte
has exact synonym: CD8-alpha-alpha-positive, alpha-beta intraepithelial T-cell
has exact synonym: CD8-alpha-alpha-positive, alpha-beta intraepithelial T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell
annotated property: subClassOf
annotated target: alpha-beta intraepithelial T cell
is inferred: true

Axiom
annotated source: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell
annotated property: IAO_0000115
annotated target: An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GO_REF:0000031
has db xref: PMID:11685222

Axiom
annotated source: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell
annotated property: description
annotated target: The CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell, often abbreviated as CD8αα IEL, is a specialized immune cell found within the epithelial layer of mucosal surfaces, such as the intestines. CD8αα IEL have been studied extensively in mice, but equivalent cells are thought to be present in humans, albeit at lower numbers. These cells represent a subset of intraepithelial T lymphocytes characterized by the expression of both CD8-alpha-alpha homodimer and the alpha-beta variant of the T cell receptor (TCR). Other features shared with intraepithelial T lymphocytes include the expression of T-bet, a master transcription factor that controls expression of proinflammatory cytokines, natural killer cell receptors, and an activated phenotype (high expression of CD69). Functionally, CD8αα IELs are thought to play a role in maintaining epithelial integrity, local immune surveillance, and protection against microbial pathogens. Upon detecting alterations associated with infection or inflammation, these cells orchestrate immune responses to restore tissue homeostasis, primarily through the secretion of cytokines and chemokines, and directly eliminating infected cells. CD8αα IELs have been shown require β2 microglobulin-dependent MHC class I expression for their generation and/or homeostasis. They share some characteristics with natural killer cells and might have similar suppressive and regulatory roles which they perform through the production of IL-10 and TGFβ. For example, they have been shown the prevent induced colitis, indicating that by modulating immune responses, CD8αα IELs prevent excessive and damaging immune activation that can lead to chronic inflammatory conditions or autoimmunity. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be consider…
has db xref: DOI:10.1016/j.coi.2019.04.010
has db xref: DOI:10.1093/cei/uxad049
has db xref: DOI:10.1111/j.1600-065X.2006.00488.x
has db xref: DOI:10.3389/fimmu.2022.1059042

CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell on CELLxGENE CellGuide
type: Axiom
annotated source: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000915

dendritic epidermal T cell
type: Class
equivalent class: Class
  intersection of: mature gamma-delta T cell
  intersection of: Restriction
    on property: RO_0001025
    some values from: UBERON_0001003
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0060054
subclass of: mature gamma-delta T cell
subclass of: Restriction
  on property: RO_0001025
  some values from: UBERON_0001003
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002401
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0060054
IAO_0000115: A mature gamma-delta T cell located in the epidermis that regulates wound healing.
has exact synonym: DETC
has exact synonym: dendritic epidermal T lymphocyte
has exact synonym: dendritic epidermal T-cell
has exact synonym: dendritic epidermal T-lymphocyte
comment: In mice, DETC have an invariant T cell receptor.

Axiom
annotated source: dendritic epidermal T cell
annotated property: subClassOf
annotated target: mature gamma-delta T cell
is inferred: true

Axiom
annotated source: dendritic epidermal T cell
annotated property: IAO_0000115
annotated target: A mature gamma-delta T cell located in the epidermis that regulates wound healing.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:11976459

Tc2 cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta cytokine secreting effector T cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000001941
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001202
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001207
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
subclass of: CD8-positive, alpha-beta cytokine secreting effector T cell
subclass of: CL_0001052
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000001941
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
IAO_0000115: A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4.
has db xref: BTO:0004794
has db xref: FMA:84794
has exact synonym: CD8-positive Th2 cell
has exact synonym: T-cytotoxic T cell type 2
has exact synonym: Tc2 T cell
has exact synonym: Tc2 T lymphocyte
has exact synonym: Tc2 T-cell
has exact synonym: Tc2 T-lymphocyte
has exact synonym: Th2 CD8-positive T cell
has exact synonym: Th2 non-TFH CD8-positive T cell
comment: This cell type is compatible with the HIPC Lyoplate markers for 'non-Tc1/Tc17 CD8+ T cell' (see CL:0001052), but includes the additional necessary and sufficient conditions to allow classification as a Tc2 T cell.

Axiom
annotated source: Tc2 cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta cytokine secreting effector T cell
is inferred: true

Axiom
annotated source: Tc2 cell
annotated property: IAO_0000115
annotated target: A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:9914231

type I NK T cell
type: Class
equivalent class: Class
  intersection of: mature NK T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0043208
subclass of: mature NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0043208
IAO_0000115: An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d.
has exact synonym: classical NK T cell
has exact synonym: type I NK T lymphocyte
has exact synonym: type I NK T-cell
has exact synonym: type I NK T-lymphocyte
has exact synonym: type I NKT cell
has related synonym: invariant NK T cell
in subset: cellxgene subset
in subset: human reference atlas
comment: In mouse the canonical TCR is V-alpha-14, and in humans it is V-alpha 24.

Axiom
annotated source: type I NK T cell
annotated property: subClassOf
annotated target: mature NK T cell
is inferred: true

Axiom
annotated source: type I NK T cell
annotated property: IAO_0000115
annotated target: An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:15039760

type II NK T cell
type: Class
equivalent class: Class
  intersection of: mature NK T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0051132
subclass of: mature NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0051132
IAO_0000115: An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d.
has exact synonym: type II NK T lymphocyte
has exact synonym: type II NK T-cell
has exact synonym: type II NK T-lymphocyte
has exact synonym: type II NKT cell
in subset: cellxgene subset

Axiom
annotated source: type II NK T cell
annotated property: subClassOf
annotated target: mature NK T cell
is inferred: true

Axiom
annotated source: type II NK T cell
annotated property: IAO_0000115
annotated target: An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:15039760

CD4-positive type I NK T cell
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001004
subclass of: type I NK T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001004
IAO_0000115: A type I NK T cell that has the phenotype CD4-positive.
has exact synonym: CD4-positive type I NK T lymphocyte
has exact synonym: CD4-positive type I NK T-cell
has exact synonym: CD4-positive type I NK T-lymphocyte
has exact synonym: CD4-positive type I NKT cell
has narrow synonym: NKT.4+.SP

Axiom
annotated source: CD4-positive type I NK T cell
annotated property: subClassOf
annotated target: type I NK T cell
is inferred: true

Axiom
annotated source: CD4-positive type I NK T cell
annotated property: IAO_0000115
annotated target: A type I NK T cell that has the phenotype CD4-positive.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17303398

CD4-negative, CD8-negative type I NK T cell
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
subclass of: type I NK T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
IAO_0000115: A type I NK T cell that has the phenotype CD4-negative and CD8-negative.
has exact synonym: CD4-negative, CD8-negative type I NK T lymphocyte
has exact synonym: CD4-negative, CD8-negative type I NK T-cell
has exact synonym: CD4-negative, CD8-negative type I NK T-lymphocyte
has exact synonym: CD4-negative, CD8-negative type I NKT cell
has narrow synonym: NKT.4-.Sp

Axiom
annotated source: CD4-negative, CD8-negative type I NK T cell
annotated property: subClassOf
annotated target: type I NK T cell
is inferred: true

Axiom
annotated source: CD4-negative, CD8-negative type I NK T cell
annotated property: IAO_0000115
annotated target: A type I NK T cell that has the phenotype CD4-negative and CD8-negative.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:18997862

activated CD4-positive type I NK T cell
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001004
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032609
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
subclass of: CD4-positive type I NK T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002202
  some values from: CD4-positive type I NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032609
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
IAO_0000115: A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers.
has exact synonym: activated CD4-positive type I NK T lymphocyte
has exact synonym: activated CD4-positive type I NK T-cell
has exact synonym: activated CD4-positive type I NK T-lymphocyte
has exact synonym: activated CD4-positive type I NKT cell

Axiom
annotated source: activated CD4-positive type I NK T cell
annotated property: IAO_0000115
annotated target: A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17303398

CD4-positive type I NK T cell secreting interferon-gamma
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001004
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002827
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032609
subclass of: CD4-positive type I NK T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD4-positive type I NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002827
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032609
IAO_0000115: A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses.
has exact synonym: CD4-positive type I NK T cell secreting IFN-gamma
has exact synonym: CD4-positive type I NK T lymphocyte secreting interferon-gamma
has exact synonym: CD4-positive type I NK T-cell secreting interferon-gamma
has exact synonym: CD4-positive type I NK T-lymphocyte secreting interferon-gamma
has exact synonym: CD4-positive type I NKT cell secreting interferon-gamma

Axiom
annotated source: CD4-positive type I NK T cell secreting interferon-gamma
annotated property: IAO_0000115
annotated target: A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17303398

CD4-positive type I NK T cell secreting interleukin-4
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001004
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002830
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032616
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
subclass of: CD4-positive type I NK T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD4-positive type I NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002830
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032616
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
IAO_0000115: A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses.
has exact synonym: CD4-positive type I NK T cell secreting IL-4
has exact synonym: CD4-positive type I NK T lymphocyte secreting interleukin-4
has exact synonym: CD4-positive type I NK T-cell secreting interleukin-4
has exact synonym: CD4-positive type I NK T-lymphocyte secreting interleukin-4
has exact synonym: CD4-positive type I NKT cell secreting interleukin-4

Axiom
annotated source: CD4-positive type I NK T cell secreting interleukin-4
annotated property: IAO_0000115
annotated target: A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031

activated CD4-negative, CD8-negative type I NK T cell
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002369
subclass of: CD4-negative, CD8-negative type I NK T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002202
  some values from: CD4-negative, CD8-negative type I NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002369
IAO_0000115: A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers.
has exact synonym: activated CD4-negative, CD8-negative type I NK T lymphocyte
has exact synonym: activated CD4-negative, CD8-negative type I NK T-cell
has exact synonym: activated CD4-negative, CD8-negative type I NK T-lymphocyte
has exact synonym: activated CD4-negative, CD8-negative type I NKT cell
in subset: cellxgene subset

Axiom
annotated source: activated CD4-negative, CD8-negative type I NK T cell
annotated property: IAO_0000115
annotated target: A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17303398

CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002827
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032609
subclass of: CD4-negative, CD8-negative type I NK T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD4-negative, CD8-negative type I NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002827
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032609
IAO_0000115: A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses.
has exact synonym: CD4-negative, CD8-negative type I NK T cell secreting IFN-gamma
has exact synonym: CD4-negative, CD8-negative type I NK T lymphocyte secreting interferon-gamma
has exact synonym: CD4-negative, CD8-negative type I NK T-cell secreting interferon-gamma
has exact synonym: CD4-negative, CD8-negative type I NK T-lymphocyte secreting interferon-gamma
has exact synonym: CD4-negative, CD8-negative type I NKT cell secreting interferon-gamma

Axiom
annotated source: CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma
annotated property: IAO_0000115
annotated target: A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17303398

CD4-negative, CD8-negative type I NK T cell secreting interleukin-4
type: Class
equivalent class: Class
  intersection of: type I NK T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002830
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
subclass of: CD4-negative, CD8-negative type I NK T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD4-negative, CD8-negative type I NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002830
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
IAO_0000115: A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses.
has exact synonym: CD4-negative, CD8-negative type I NK T cell secreting IL-4
has exact synonym: CD4-negative, CD8-negative type I NK T lymphocyte secreting interleukin-4
has exact synonym: CD4-negative, CD8-negative type I NK T-cell secreting interleukin-4
has exact synonym: CD4-negative, CD8-negative type I NK T-lymphocyte secreting interleukin-4
has exact synonym: CD4-negative, CD8-negative type I NKT cell secreting interleukin-4

Axiom
annotated source: CD4-negative, CD8-negative type I NK T cell secreting interleukin-4
annotated property: IAO_0000115
annotated target: A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17303398

activated type II NK T cell
type: Class
equivalent class: Class
  intersection of: type II NK T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002369
subclass of: type II NK T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002369
IAO_0000115: A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers.
has exact synonym: activated type II NK T lymphocyte
has exact synonym: activated type II NK T-cell
has exact synonym: activated type II NK T-lymphocyte
has exact synonym: activated type II NKT cell
in subset: cellxgene subset

Axiom
annotated source: activated type II NK T cell
annotated property: subClassOf
annotated target: type II NK T cell
is inferred: true

Axiom
annotated source: activated type II NK T cell
annotated property: IAO_0000115
annotated target: A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17964217

type II NK T cell secreting interferon-gamma
type: Class
equivalent class: Class
  intersection of: type II NK T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032609
subclass of: type II NK T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002202
  some values from: activated type II NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032609
IAO_0000115: A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers.
has exact synonym: type II NK T cell secreting IFN-gamma
has exact synonym: type II NK T lymphocyte secreting interferon-gamma
has exact synonym: type II NK T-cell secreting interferon-gamma
has exact synonym: type II NK T-lymphocyte secreting interferon-gamma
has exact synonym: type II NKT cell secreting interferon-gamma

Axiom
annotated source: type II NK T cell secreting interferon-gamma
annotated property: subClassOf
annotated target: type II NK T cell
is inferred: true

Axiom
annotated source: type II NK T cell secreting interferon-gamma
annotated property: IAO_0000115
annotated target: A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GO_REF:0000031
has db xref: PMID:17964217

type II NK T cell secreting interleukin-4
type: Class
equivalent class: Class
  intersection of: type II NK T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001343
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
subclass of: type II NK T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001343
subclass of: Restriction
  on property: RO_0002202
  some values from: activated type II NK T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
IAO_0000115: A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers.
has exact synonym: type II NK T cell secreting IL-4
has exact synonym: type II NK T lymphocyte secreting interleukin-4
has exact synonym: type II NK T-cell secreting interleukin-4
has exact synonym: type II NK T-lymphocyte secreting interleukin-4
has exact synonym: type II NKT cell secreting interleukin-4

Axiom
annotated source: type II NK T cell secreting interleukin-4
annotated property: subClassOf
annotated target: type II NK T cell
is inferred: true

Axiom
annotated source: type II NK T cell secreting interleukin-4
annotated property: IAO_0000115
annotated target: A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17964217

CD4-positive, alpha-beta cytotoxic T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001913
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0030217
subclass of: CD4-positive, alpha-beta T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: activated CD4-positive, alpha-beta T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001913
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030217
IAO_0000115: A CD4-positive, alpha-beta T cell that has cytotoxic function.
has exact synonym: CD4-positive, alpha-beta cytotoxic T lymphocyte
has exact synonym: CD4-positive, alpha-beta cytotoxic T-cell
has exact synonym: CD4-positive, alpha-beta cytotoxic T-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: CD4-positive, alpha-beta cytotoxic T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, alpha-beta cytotoxic T cell
annotated property: IAO_0000115
annotated target: A CD4-positive, alpha-beta T cell that has cytotoxic function.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:18440213

early lymphoid progenitor
type: Class
equivalent class: Class
  intersection of: hematopoietic multipotent progenitor cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001460
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002001
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002979
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0030098
subclass of: hematopoietic multipotent progenitor cell
subclass of: CL_0011026
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001460
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002001
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002979
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002035
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0030098
IAO_0000115: A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative.
has exact synonym: lymphoid-primed multipotent progenitor
has related synonym: ELP
has related synonym: GMLP
has related synonym: LMPP
in subset: cellxgene subset
in subset: human reference atlas
comment: Markers are associated with mouse cells. ELP transcription factors include E2A-positive, Ikaros-positive, EBF-negative, Pax5-negative, PU.1-negative.

Axiom
annotated source: early lymphoid progenitor
annotated property: subClassOf
annotated target: hematopoietic multipotent progenitor cell
is inferred: true

Axiom
annotated source: early lymphoid progenitor
annotated property: IAO_0000115
annotated target: A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:19022770

Axiom
annotated source: early lymphoid progenitor
annotated property: hasRelatedSynonym
annotated target: ELP
has synonym type: OMO_0003000

Axiom
annotated source: early lymphoid progenitor
annotated property: hasRelatedSynonym
annotated target: GMLP
has db xref: PMID:18371378
has synonym type: OMO_0003000

Axiom
annotated source: early lymphoid progenitor
annotated property: hasRelatedSynonym
annotated target: LMPP
has synonym type: OMO_0003000

pre-natural killer cell
type: Class
equivalent class: Class
  intersection of: natural killer cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001381
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002065
subclass of: natural killer cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001381
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002065
IAO_0000115: Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins.
has exact synonym: pre-NK cell
in subset: cellxgene subset
comment: These cells are also reportedly CD7-low, CD10-negative, CD45RA-positive, alpha-4-beta-7 integrin-high.

Axiom
annotated source: pre-natural killer cell
annotated property: IAO_0000115
annotated target: Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:16551251
has db xref: PMID:17100874

mucosal-associated invariant T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002227
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032394
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0030217
subclass of: mature alpha-beta T cell
subclass of: Restriction
  on property: RO_0002202
  some values from: double-positive, alpha-beta thymocyte
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002227
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032394
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0030217
IAO_0000115: An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule. This cell develops from double-positive, alpha-beta thymocyte.
has exact synonym: mucosal invariant T cell
has exact synonym: mucosal invariant T lymphocyte
has exact synonym: mucosal invariant T-cell
has exact synonym: mucosal invariant T-lymphocyte
has exact synonym: mucosal-associated invariant T lymphocyte
has exact synonym: mucosal-associated invariant T-cell
has exact synonym: mucosal-associated invariant T-lymphocyte
has related synonym: MAIT
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: mucosal-associated invariant T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: mucosal-associated invariant T cell
annotated property: IAO_0000115
annotated target: An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule. This cell develops from double-positive, alpha-beta thymocyte.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:19416870
has db xref: PMID:33352411

Axiom
annotated source: mucosal-associated invariant T cell
annotated property: hasRelatedSynonym
annotated target: MAIT
has db xref: PMID:40781543
has synonym type: OMO_0003000

thymic conventional dendritic cell
type: Class
equivalent class: Class
  intersection of: conventional dendritic cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001013
subclass of: conventional dendritic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002370
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001015
subclass of: Restriction
  on property: RO_0002202
  some values from: DN1 thymic pro-T cell
IAO_0000115: A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative.
comment: In the mouse this cell expresses CD8-alpha-alpha.

Axiom
annotated source: thymic conventional dendritic cell
annotated property: subClassOf
annotated target: conventional dendritic cell
is inferred: true

Axiom
annotated source: thymic conventional dendritic cell
annotated property: IAO_0000115
annotated target: A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GO_REF:0000031
has db xref: PMID:19273629

thymic plasmacytoid dendritic cell
type: Class
equivalent class: Class
  intersection of: plasmacytoid dendritic cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001865
subclass of: plasmacytoid dendritic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0002370
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001015
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001865
subclass of: Restriction
  on property: RO_0002202
  some values from: DN1 thymic pro-T cell
IAO_0000115: A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive.
in subset: human reference atlas

Axiom
annotated source: thymic plasmacytoid dendritic cell
annotated property: subClassOf
annotated target: plasmacytoid dendritic cell
is inferred: true

Axiom
annotated source: thymic plasmacytoid dendritic cell
annotated property: IAO_0000115
annotated target: A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive.
has db xref: GOC:add
has db xref: GOC:pam
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:19941119

Axiom
annotated source: thymic plasmacytoid dendritic cell
annotated property: depiction
licence: http://creativecommons.org/licenses/by/4.0/
has db xref: doi:10.48539/HBM322.LZLG.752

Be1 Cell
type: Class
equivalent class: Class
  intersection of: Be cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032609
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032623
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032640
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045627
subclass of: Be cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032609
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032623
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032640
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045627
IAO_0000115: A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma.
has exact synonym: B effector 1 cell
has related synonym: B effector cell type 1
comment: Be1 cells are also reportedly capable of secreting IL-6, IL-10, and IL-12. They are also reportedly CD11b-negative and B220-positive.

Axiom
annotated source: Be1 Cell
annotated property: subClassOf
annotated target: Be cell
is inferred: true

Axiom
annotated source: Be1 Cell
annotated property: IAO_0000115
annotated target: A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:11101868
has db xref: PMID:20224569

Axiom
annotated source: Be1 Cell
annotated property: hasExactSynonym
annotated target: B effector 1 cell
has db xref: PMID:11101868
has db xref: PMID:20224569

Be2 cell
type: Class
equivalent class: Class
  intersection of: Be cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032613
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032623
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032633
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032635
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0045630
subclass of: Be cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032613
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032623
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032633
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032635
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0045630
IAO_0000115: A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6.
has exact synonym: B effector 2 cell
has related synonym: B effector cell type 2
comment: Be2 cells are also reportedly capable of secreting IL-13 and TNF. They are also reportedly CD11b-negative and B220-positive.

Axiom
annotated source: Be2 cell
annotated property: subClassOf
annotated target: Be cell
is inferred: true

Axiom
annotated source: Be2 cell
annotated property: IAO_0000115
annotated target: A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:11101868
has db xref: PMID:20224569

Axiom
annotated source: Be2 cell
annotated property: hasExactSynonym
annotated target: B effector 2 cell
has db xref: PMID:11101868
has db xref: PMID:20224569

lymphocyte of B lineage
type: Class
subclass of: lymphocyte
subclass of: Restriction
  on property: RO_0002202
  some values from: pro-B cell
IAO_0000115: A lymphocyte of B lineage with the commitment to express an immunoglobulin complex.
in subset: cellxgene subset
in subset: human reference atlas
comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex).

Axiom
annotated source: lymphocyte of B lineage
annotated property: subClassOf
annotated target: lymphocyte
is inferred: true

Axiom
annotated source: lymphocyte of B lineage
annotated property: IAO_0000115
annotated target: A lymphocyte of B lineage with the commitment to express an immunoglobulin complex.
has db xref: GOC:add
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0781735149

antibody secreting cell
type: Class
equivalent class: Class
  intersection of: lymphocyte of B lineage
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0042571
subclass of: lymphocyte of B lineage
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0042571
IAO_0000115: A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin.
description: Antibody secreting cells, such as short-lived plasmablasts and long-lived plasma cells, form a key component of the adaptive immune system. These cells originate from B-lymphocytes upon exposure to antigens. They are primarily characterized by their capacity to produce and secrete large amounts of antibodies (immunoglobulins) that help to neutralize the pathogens, defining the primary role of these cells in the humoral immune response. Antibody secreting cells are found predominantly within the lymph nodes, spleen, and mucosa-associated lymphoid tissues. They are characterized by an extensive rough endoplasmic reticulum, reflecting the high antibody production. The interesting dynamics of these cells, switching from a nonsecreting, antigen-specific B-cell state to a high-rate immunoglobulin-secreting cell state, is a major factor in sustaining an effective adaptive immune system: Derived from a single clone, the secreted immunoglobulins have a unique antigen specificity inherited from the parent B cell. They are able to recognize specific extracellular antigens, aiding in marking harmful invaders such as viruses and bacteria for elimination, either by direct neutralization or by recruiting other immune cells for assistance. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
in subset: cellxgene subset

Axiom
annotated source: antibody secreting cell
annotated property: subClassOf
annotated target: lymphocyte of B lineage
is inferred: true

Axiom
annotated source: antibody secreting cell
annotated property: IAO_0000115
annotated target: A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin.
has db xref: GOC:add
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:0721601464
has db xref: ISBN:0781735149

Axiom
annotated source: antibody secreting cell
annotated property: description
annotated target: Antibody secreting cells, such as short-lived plasmablasts and long-lived plasma cells, form a key component of the adaptive immune system. These cells originate from B-lymphocytes upon exposure to antigens. They are primarily characterized by their capacity to produce and secrete large amounts of antibodies (immunoglobulins) that help to neutralize the pathogens, defining the primary role of these cells in the humoral immune response. Antibody secreting cells are found predominantly within the lymph nodes, spleen, and mucosa-associated lymphoid tissues. They are characterized by an extensive rough endoplasmic reticulum, reflecting the high antibody production. The interesting dynamics of these cells, switching from a nonsecreting, antigen-specific B-cell state to a high-rate immunoglobulin-secreting cell state, is a major factor in sustaining an effective adaptive immune system: Derived from a single clone, the secreted immunoglobulins have a unique antigen specificity inherited from the parent B cell. They are able to recognize specific extracellular antigens, aiding in marking harmful invaders such as viruses and bacteria for elimination, either by direct neutralization or by recruiting other immune cells for assistance. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1002/eji.1830161018
has db xref: DOI:10.1038/nri3795

antibody secreting cell on CELLxGENE CellGuide
type: Axiom
annotated source: antibody secreting cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000946

IgE plasma cell
type: Class
equivalent class: Class
  intersection of: long lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071743
subclass of: long lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071743
IAO_0000115: A long lived plasma cell that secretes IgE.

Axiom
annotated source: IgE plasma cell
annotated property: subClassOf
annotated target: long lived plasma cell
is inferred: true

Axiom
annotated source: IgE plasma cell
annotated property: IAO_0000115
annotated target: A long lived plasma cell that secretes IgE.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

IgE memory B cell
type: Class
equivalent class: Class
  intersection of: class switched memory B cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071742
subclass of: CL_4052108
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071742
IAO_0000115: A class switched memory B cell that expresses IgE on the cell surface.
has exact synonym: IgE memory B lymphocyte
has exact synonym: IgE memory B-cell
has exact synonym: IgE memory B-lymphocyte
has exact synonym: memory IgE B cell
has exact synonym: memory IgE B lymphocyte
has exact synonym: memory IgE B-cell
has exact synonym: memory IgE B-lymphocyte

Axiom
annotated source: IgE memory B cell
annotated property: IAO_0000115
annotated target: A class switched memory B cell that expresses IgE on the cell surface.
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: ISBN:0781765196

IgD plasmablast
type: Class
equivalent class: Class
  intersection of: plasmablast
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071739
subclass of: plasmablast
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071739
IAO_0000115: A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult.

Axiom
annotated source: IgD plasmablast
annotated property: subClassOf
annotated target: plasmablast
is inferred: true

Axiom
annotated source: IgD plasmablast
annotated property: IAO_0000115
annotated target: A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult.
has db xref: GOC:msz
has db xref: GO_REF:0000031

IgE plasmablast
type: Class
equivalent class: Class
  intersection of: plasmablast
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071743
subclass of: plasmablast
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071743
IAO_0000115: A plasmablast that secretes IgE.

Axiom
annotated source: IgE plasmablast
annotated property: subClassOf
annotated target: plasmablast
is inferred: true

Axiom
annotated source: IgE plasmablast
annotated property: IAO_0000115
annotated target: A plasmablast that secretes IgE.
has db xref: GOC:msz
has db xref: GO_REF:0000031

IgE short lived plasma cell
type: Class
equivalent class: Class
  intersection of: short lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071743
subclass of: short lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071743
IAO_0000115: A short lived plasma cell that secretes IgE.

Axiom
annotated source: IgE short lived plasma cell
annotated property: subClassOf
annotated target: short lived plasma cell
is inferred: true

Axiom
annotated source: IgE short lived plasma cell
annotated property: IAO_0000115
annotated target: A short lived plasma cell that secretes IgE.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

preBCR-positive large pre-B-II cell
type: Class
equivalent class: Class
  intersection of: large pre-B-II cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0071708
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0035369
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001858
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001859
subclass of: large pre-B-II cell
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0071708
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0035369
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001858
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001859
IAO_0000115: An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface.

Axiom
annotated source: preBCR-positive large pre-B-II cell
annotated property: subClassOf
annotated target: large pre-B-II cell
is inferred: true

Axiom
annotated source: preBCR-positive large pre-B-II cell
annotated property: IAO_0000115
annotated target: An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface.
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:9785673

preBCR-negative large pre-B-II cell
type: Class
equivalent class: Class
  intersection of: large pre-B-II cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0071708
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0035369
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001858
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001859
subclass of: large pre-B-II cell
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0071708
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0035369
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001858
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001859
IAO_0000115: A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes.

Axiom
annotated source: preBCR-negative large pre-B-II cell
annotated property: subClassOf
annotated target: large pre-B-II cell
is inferred: true

Axiom
annotated source: preBCR-negative large pre-B-II cell
annotated property: IAO_0000115
annotated target: A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes.
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:9785673

small pre-B-II cell
type: Class
equivalent class: Class
  intersection of: pre-B-II cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003457
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003460
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0019815
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0035369
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0071708
subclass of: pre-B-II cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003457
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003460
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0019815
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0035369
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0071708
IAO_0000115: A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes.
has exact synonym: small pre-BII cell
in subset: cellxgene subset
comment: Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive.

Axiom
annotated source: small pre-B-II cell
annotated property: subClassOf
annotated target: pre-B-II cell
is inferred: true

Axiom
annotated source: small pre-B-II cell
annotated property: IAO_0000115
annotated target: A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes.
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:16551251
has db xref: PMID:18432934
has db xref: PMID:9785673

pre-B-II cell
type: Class
equivalent class: Class
  intersection of: precursor B cell
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000006611
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0071707
subclass of: precursor B cell
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000006611
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0071707
disjoint with: pre-B-I cell
IAO_0000115: A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain.
has db xref: BTO:0001133
has db xref: CALOHA:TS-0819
has exact synonym: pre-B-lymphocyte
has exact synonym: pre-BII cell
comment: pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive.

Axiom
annotated source: pre-B-II cell
annotated property: subClassOf
annotated target: precursor B cell
is inferred: true

Axiom
annotated source: pre-B-II cell
annotated property: IAO_0000115
annotated target: A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain.
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:9785673

pre-B-I cell
type: Class
equivalent class: Class
  intersection of: precursor B cell
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003457
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000003460
  intersection of: Restriction
    on property: BFO_0000051
    some values from: PR_000006611
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0071707
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001858
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001859
subclass of: precursor B cell
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003457
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000003460
subclass of: Restriction
  on property: BFO_0000051
  some values from: PR_000006611
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0071707
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001858
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001859
IAO_0000115: A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein.
description: The pre-B-I cell, also known as an early pre-B cell, is an integral step in the B cell development pathway in the bone marrow. These precursor B cells are characterized by expression of CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, as well as TdT, Rag1,and Rag2 intracellularly; they carry a D-JH DNA rearrangement, and lack expression of immunglobulin heavy chain protein. This cell type represents the stage subsequent to pro-B cells but precedes pre-B-II cells. At the pre-B-I cell stage, cells undergo VH to D-JH recombination. At this point, if the rearranged μ heavy chain can be produced and paired with a surrogate light chain, this can be expressed on the cell surface as the pre-B cell receptor (pre-BCR), forming the next stage of development, the pre-B-II cell. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has exact synonym: pre-BI cell
has related synonym: pro-B cell (Philadelphia nomenclature)
in subset: cellxgene subset
comment: Human pre-B-I cells are reportedly CD10-positive, CD19-positive, CD22-positive, CD38-positive, CD45-low, CD79a-positive, CD127-negative, pre-BCR-negative, IgM-negative, IgD-negative, and Tdt-positive. Transcription factors expressed: Pax5-positive.

Axiom
annotated source: pre-B-I cell
annotated property: subClassOf
annotated target: precursor B cell
is inferred: true

Axiom
annotated source: pre-B-I cell
annotated property: IAO_0000115
annotated target: A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein.
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:16551251
has db xref: PMID:18432934
has db xref: PMID:20839338
has db xref: PMID:9785673

Axiom
annotated source: pre-B-I cell
annotated property: description
annotated target: The pre-B-I cell, also known as an early pre-B cell, is an integral step in the B cell development pathway in the bone marrow. These precursor B cells are characterized by expression of CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, as well as TdT, Rag1,and Rag2 intracellularly; they carry a D-JH DNA rearrangement, and lack expression of immunglobulin heavy chain protein. This cell type represents the stage subsequent to pro-B cells but precedes pre-B-II cells. At the pre-B-I cell stage, cells undergo VH to D-JH recombination. At this point, if the rearranged μ heavy chain can be produced and paired with a surrogate light chain, this can be expressed on the cell surface as the pre-B cell receptor (pre-BCR), forming the next stage of development, the pre-B-II cell. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/j.febslet.2010.04.057
has db xref: DOI:10.1016/j.it.2022.01.003
has db xref: DOI:10.1111/j.1600-065X.2000.imr017512.x
has db xref: DOI:10.4049/jimmunol.170.3.1354

Axiom
annotated source: pre-B-I cell
annotated property: hasRelatedSynonym
annotated target: pro-B cell (Philadelphia nomenclature)
has db xref: PMID:11244048

pre-B-I cell on CELLxGENE CellGuide
type: Axiom
annotated source: pre-B-I cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000956

large pre-B-II cell
type: Class
equivalent class: Class
  intersection of: pre-B-II cell
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000003457
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000003460
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0046651
subclass of: pre-B-II cell
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000003457
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000003460
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0046651
IAO_0000115: A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative.
has broad synonym: large pre-B cell
has exact synonym: large pre-BII cell
in subset: cellxgene subset
comment: Large pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-positive, pre-BCR-positive, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive.

Axiom
annotated source: large pre-B-II cell
annotated property: subClassOf
annotated target: pre-B-II cell
is inferred: true

Axiom
annotated source: large pre-B-II cell
annotated property: IAO_0000115
annotated target: A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative.
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: PMID:16551251
has db xref: PMID:18432934
has db xref: PMID:9785673

Axiom
annotated source: large pre-B-II cell
annotated property: hasBroadSynonym
annotated target: large pre-B cell
has db xref: PMID:11244048

T1 B cell
type: Class
equivalent class: Class
  intersection of: transitional stage B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001318
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001338
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001880
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002037
subclass of: transitional stage B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071738
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001318
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001338
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001880
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002037
IAO_0000115: A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative.
has exact synonym: T1 B lymphocyte
has exact synonym: T1 B-cell
has exact synonym: T1 B-lymphocyte
has exact synonym: transitional stage 1 B cell
comment: T1 B cells are also reportedly CD10-negative/positive??, CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive.

Axiom
annotated source: T1 B cell
annotated property: subClassOf
annotated target: transitional stage B cell
is inferred: true

Axiom
annotated source: T1 B cell
annotated property: IAO_0000115
annotated target: A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMCID:PMC2193793
has db xref: PMID:12810111

T2 B cell
type: Class
equivalent class: Class
  intersection of: transitional stage B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001318
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001338
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001880
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002037
subclass of: transitional stage B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001318
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001338
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001880
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002037
subclass of: Restriction
  on property: RO_0002202
  some values from: T1 B cell
IAO_0000115: A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive.
has exact synonym: T2 B lymphocyte
has exact synonym: T2 B-cell
has exact synonym: T2 B-lymphocyte
has exact synonym: transitional stage 2 B cell
comment: T2 B cells are also reportedly CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive.

Axiom
annotated source: T2 B cell
annotated property: subClassOf
annotated target: transitional stage B cell
is inferred: true

Axiom
annotated source: T2 B cell
annotated property: IAO_0000115
annotated target: A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMCID:PMC2193793
has db xref: PMID:12810111

T3 B cell
type: Class
equivalent class: Class
  intersection of: transitional stage B cell
  intersection of: Restriction
    on property: RO_0000056
    some values from: GO_0002515
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001318
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001338
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001880
subclass of: transitional stage B cell
subclass of: Restriction
  on property: RO_0000056
  some values from: GO_0002515
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001318
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001338
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001880
subclass of: Restriction
  on property: RO_0002202
  some values from: T2 B cell
IAO_0000115: A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM).
has exact synonym: An1 B cell
has exact synonym: T3 B lymphocyte
has exact synonym: T3 B-cell
has exact synonym: T3 B-lymphocyte
has exact synonym: transitional stage 3 B cell

Axiom
annotated source: T3 B cell
annotated property: subClassOf
annotated target: transitional stage B cell
is inferred: true

Axiom
annotated source: T3 B cell
annotated property: IAO_0000115
annotated target: A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM).
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:12810111
has db xref: PMID:17174121
has db xref: http://www.immgen.org/index_content.html

Axiom
annotated source: T3 B cell
annotated property: hasExactSynonym
annotated target: An1 B cell
has db xref: PMID:17174121

Bm1 B cell
type: Class
equivalent class: Class
  intersection of: follicular B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001408
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001880
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 9606
subclass of: follicular B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001408
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001880
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon 9606
IAO_0000115: A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells.
has exact synonym: Bm1 B lymphocyte
has exact synonym: Bm1 B-cell
has exact synonym: Bm1 B-lymphocyte
comment: These cells are also reportedly CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative.

Axiom
annotated source: Bm1 B cell
annotated property: subClassOf
annotated target: follicular B cell
is inferred: true

Axiom
annotated source: Bm1 B cell
annotated property: IAO_0000115
annotated target: A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: PMID:11564773
has db xref: PMID:17992590
has db xref: PMID:18432934
has db xref: PMID:19350211
has db xref: PMID:31681331
has db xref: PMID:8006591

Bm2 B cell
type: Class
equivalent class: Class
  intersection of: follicular B cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001880
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 9606
subclass of: follicular B cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001880
subclass of: Restriction
  on property: RO_0002202
  some values from: Bm1 B cell
IAO_0000115: A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells.
has exact synonym: Bm2 B lymphocyte
has exact synonym: Bm2 B-cell
has exact synonym: Bm2 B-lymphocyte
comment: These cells are also CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative.

Axiom
annotated source: Bm2 B cell
annotated property: subClassOf
annotated target: follicular B cell
is inferred: true

Axiom
annotated source: Bm2 B cell
annotated property: IAO_0000115
annotated target: A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: PMID:11564773
has db xref: PMID:17992590
has db xref: PMID:18432934
has db xref: PMID:19350211
has db xref: PMID:31681331
has db xref: PMID:8006591

Bm3-delta B cell
type: Class
equivalent class: Class
  intersection of: germinal center B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
subclass of: germinal center B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002202
  some values from: Bm3 B cell
IAO_0000115: A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive.
has exact synonym: Bm3-delta B lymphocyte
has exact synonym: Bm3-delta B-cell
has exact synonym: Bm3-delta B-lymphocyte

Axiom
annotated source: Bm3-delta B cell
annotated property: subClassOf
annotated target: germinal center B cell
is inferred: true

Axiom
annotated source: Bm3-delta B cell
annotated property: IAO_0000115
annotated target: A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive.
has db xref: GOC:add
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:9280752

Bm2' B cell
type: Class
equivalent class: Class
  intersection of: germinal center B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001880
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 9606
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0002634
subclass of: germinal center B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001880
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002202
  some values from: Bm2 B cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0002634
IAO_0000115: A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative.
has exact synonym: Bm2' B lymphocyte
has exact synonym: Bm2' B-cell
has exact synonym: Bm2-prime B cell
has exact synonym: Bm2-prime B-lymphocyte
has related synonym: germinal center founder cell
comment: Bm2' B cells are also reportedly CD10-positive, CD39-negative, CD44-negative, CD71-positive, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative.

Axiom
annotated source: Bm2' B cell
annotated property: subClassOf
annotated target: germinal center B cell
is inferred: true

Axiom
annotated source: Bm2' B cell
annotated property: IAO_0000115
annotated target: A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:11564773
has db xref: PMID:17992590
has db xref: PMID:18432934
has db xref: PMID:19350211
has db xref: PMID:31681331
has db xref: PMID:8006591

Bm3 B cell
type: Class
equivalent class: Class
  intersection of: germinal center B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000003516
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 9606
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0016446
subclass of: germinal center B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000003516
subclass of: Restriction
  on property: RO_0002202
  some values from: Bm2' B cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0016446
IAO_0000115: A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type.
has exact synonym: Bm3 B lymphocyte
has exact synonym: Bm3 B-cell
has exact synonym: Bm3 B-lymphocyte
has related synonym: centroblast
comment: Bm3 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-negative, CD71-positive, and CD77-positive.

Axiom
annotated source: Bm3 B cell
annotated property: subClassOf
annotated target: germinal center B cell
is inferred: true

Axiom
annotated source: Bm3 B cell
annotated property: IAO_0000115
annotated target: A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: PMID:11564773
has db xref: PMID:18432934
has db xref: PMID:19350211
has db xref: PMID:31681331
has db xref: PMID:8006591

Axiom
annotated source: Bm3 B cell
annotated property: hasRelatedSynonym
annotated target: centroblast
has db xref: PMID:8006591

Bm4 B cell
type: Class
equivalent class: Class
  intersection of: germinal center B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000003516
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 9606
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0016446
subclass of: germinal center B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071738
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000003516
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002202
  some values from: Bm3-delta B cell
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0016446
IAO_0000115: A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor.
has exact synonym: Bm4 B lymphocyte
has exact synonym: Bm4 B-cell
has exact synonym: Bm4 B-lymphocyte
has related synonym: centrocyte
comment: Bm4 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-positive, and CD71-positive.

Axiom
annotated source: Bm4 B cell
annotated property: subClassOf
annotated target: germinal center B cell
is inferred: true

Axiom
annotated source: Bm4 B cell
annotated property: IAO_0000115
annotated target: A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: PMID:11564773
has db xref: PMID:18432934
has db xref: PMID:19350211
has db xref: PMID:31681331
has db xref: PMID:8006591

Axiom
annotated source: Bm4 B cell
annotated property: hasRelatedSynonym
annotated target: centrocyte
has db xref: PMID:17992590

Bm5 B cell
type: Class
equivalent class: Class
  intersection of: memory B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002162
    some values from: NCBITaxon 9606
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0002314
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0016446
subclass of: CL_0001053
subclass of: Restriction
  on property: RO_0002202
  some values from: Bm4 B cell
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0002314
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0016446
IAO_0000115: A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes.
has exact synonym: Bm5 B lymphocyte
has exact synonym: Bm5 B-cell
has exact synonym: Bm5 B-lymphocyte
comment: Bm5 B cells are also reportedly CD10-positive, CD23-negative, CD38-negative, CD39-positive, CD44-positive, CD71-positive, and CD77-negative.

Axiom
annotated source: Bm5 B cell
annotated property: IAO_0000115
annotated target: A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:11564773
has db xref: PMID:18432934
has db xref: PMID:19350211
has db xref: PMID:31681331
has db xref: PMID:8006591

Be cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001289
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0001816
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0043370
subclass of: mature B cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001289
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0001816
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0043370
IAO_0000115: A mature B cell that produces cytokines that can influence CD4 T cell differentiation.
has exact synonym: B effector cell
has exact synonym: effector B cell
has exact synonym: effector B lymphocyte
has exact synonym: effector B-cell
has exact synonym: effector B-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: Be cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: Be cell
annotated property: IAO_0000115
annotated target: A mature B cell that produces cytokines that can influence CD4 T cell differentiation.
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:11101868
has db xref: PMID:20224569

unswitched memory B cell
type: Class
equivalent class: Class
  intersection of: memory B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071735
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071742
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071745
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001935
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001963
subclass of: memory B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071735
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071742
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071745
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071738
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001963
subclass of: Restriction
  on property: RO_0002202
  some values from: plasmablast
IAO_0000115: An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive, IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative.
has broad synonym: IgD+ memory B cell
has exact synonym: non-class-switched memory B cell
has exact synonym: unswitched memory B lymphocyte
has exact synonym: unswitched memory B-cell
has exact synonym: unswitched memory B-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'IgD+ memory B cell'. Per DSD: Unswitched memory B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive.

Axiom
annotated source: unswitched memory B cell
annotated property: subClassOf
annotated target: memory B cell
is inferred: true

Axiom
annotated source: unswitched memory B cell
annotated property: IAO_0000115
annotated target: An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive, IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: ISBN:0781765196
has db xref: PMID:20933013
has db xref: PMID:22343568

Axiom
annotated source: unswitched memory B cell
annotated property: hasBroadSynonym
annotated target: IgD+ memory B cell
has db xref: PMID:22343568

Axiom
annotated source: unswitched memory B cell
annotated property: hasExactSynonym
annotated target: non-class-switched memory B cell
has db xref: HP:0032126

IgM memory B cell
type: Class
equivalent class: Class
  intersection of: memory B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071753
subclass of: CL_0001053
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071753
IAO_0000115: An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative.
has exact synonym: IgM memory B lymphocyte
has exact synonym: IgM memory B-cell
has exact synonym: IgM memory B-lymphocyte
has exact synonym: memory IgM B cell
has exact synonym: memory IgM B lymphocyte
has exact synonym: memory IgM B-cell
has exact synonym: memory IgM B-lymphocyte
comment: IgM memory B cells are also reportedly CD1c-positive, CD95-positive, CD80-positive, CD84-positive, CD86-positive, CD150-negative, CD229-positive, CD289-positive, and CD290-positive. Transcription factors: Notch2-positive, PAX5-positive, SpiB-positive, Ets1-positive, and OBF1-positive.

Axiom
annotated source: IgM memory B cell
annotated property: IAO_0000115
annotated target: An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative.
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: ISBN:0781765196
has db xref: PMID:19447676

class switched memory B cell
type: Class
equivalent class: Class
  intersection of: memory B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071753
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001963
  intersection of: Restriction
    on property: RO_0002353
    some values from: GO_0045190
subclass of: memory B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071753
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001963
subclass of: Restriction
  on property: RO_0002202
  some values from: unswitched memory B cell
subclass of: Restriction
  on property: RO_0002353
  some values from: GO_0045190
IAO_0000115: A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are CD27-positive and have either IgG, IgE, or IgA on the cell surface.
has exact synonym: class switched memory B lymphocyte
has exact synonym: class switched memory B-cell
has exact synonym: class switched memory B-lymphocyte
in subset: cellxgene subset
in subset: human reference atlas
comment: Per DSD: Class switched memory B cells are also reportedly CD48-positive, CD229-positive, and CD352-positive.

Axiom
annotated source: class switched memory B cell
annotated property: subClassOf
annotated target: memory B cell
is inferred: true

Axiom
annotated source: class switched memory B cell
annotated property: IAO_0000115
annotated target: A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are CD27-positive and have either IgG, IgE, or IgA on the cell surface.
has db xref: GOC:add
has db xref: GOC:dsd
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: ISBN:0781765196
has db xref: PMID:20933013
has db xref: PMID:9295047

IgA memory B cell
type: Class
equivalent class: Class
  intersection of: class switched memory B cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071745
subclass of: CL_4052108
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071745
IAO_0000115: A class switched memory B cell that expresses IgA.
has exact synonym: IgA memory B lymphocyte
has exact synonym: IgA memory B-cell
has exact synonym: IgA memory B-lymphocyte
has exact synonym: memory IgA B cell
has exact synonym: memory IgA B lymphocyte
has exact synonym: memory IgA B-cell
has exact synonym: memory IgA B-lymphocyte
comment: IgA memory B cell are also reportedly RORalpha-positive.

Axiom
annotated source: IgA memory B cell
annotated property: IAO_0000115
annotated target: A class switched memory B cell that expresses IgA.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:0781765196

long lived plasma cell
type: Class
equivalent class: Class
  intersection of: plasma cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0019814
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0042613
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001208
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001935
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001002
subclass of: plasma cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002202
  some values from: short lived plasma cell
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001208
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001935
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001002
IAO_0000115: A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow.

Axiom
annotated source: long lived plasma cell
annotated property: subClassOf
annotated target: plasma cell
is inferred: true

Axiom
annotated source: long lived plasma cell
annotated property: IAO_0000115
annotated target: A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow.
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: ISBN:9780781765190
has db xref: PMID:16014527

short lived plasma cell
type: Class
equivalent class: Class
  intersection of: plasma cell
  intersection of: Restriction
    on property: RO_0000053
    some values from: PATO_0001604
subclass of: plasma cell
subclass of: Restriction
  on property: RO_0000053
  some values from: PATO_0001604
IAO_0000115: A fully differentiated plasma cell that lives for months.

Axiom
annotated source: short lived plasma cell
annotated property: subClassOf
annotated target: plasma cell
is inferred: true

Axiom
annotated source: short lived plasma cell
annotated property: IAO_0000115
annotated target: A fully differentiated plasma cell that lives for months.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: PMID:16014527

IgA short lived plasma cell
type: Class
equivalent class: Class
  intersection of: short lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071746
subclass of: short lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071746
IAO_0000115: A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system.

Axiom
annotated source: IgA short lived plasma cell
annotated property: subClassOf
annotated target: short lived plasma cell
is inferred: true

Axiom
annotated source: IgA short lived plasma cell
annotated property: IAO_0000115
annotated target: A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

IgG short lived plasma cell
type: Class
equivalent class: Class
  intersection of: short lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071736
subclass of: short lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071736
IAO_0000115: A short lived plasma cell that secretes IgG.

Axiom
annotated source: IgG short lived plasma cell
annotated property: subClassOf
annotated target: short lived plasma cell
is inferred: true

Axiom
annotated source: IgG short lived plasma cell
annotated property: IAO_0000115
annotated target: A short lived plasma cell that secretes IgG.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

IgM short lived plasma cell
type: Class
equivalent class: Class
  intersection of: short lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071754
subclass of: short lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071754
IAO_0000115: A short lived plasma cell that secretes IgM.

Axiom
annotated source: IgM short lived plasma cell
annotated property: subClassOf
annotated target: short lived plasma cell
is inferred: true

Axiom
annotated source: IgM short lived plasma cell
annotated property: IAO_0000115
annotated target: A short lived plasma cell that secretes IgM.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

IgG memory B cell
type: Class
equivalent class: Class
  intersection of: class switched memory B cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: GO_0071735
subclass of: class switched memory B cell
subclass of: Restriction
  on property: RO_0002104
  some values from: GO_0071735
IAO_0000115: An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface.
has exact synonym: IgG memory B lymphocyte
has exact synonym: IgG memory B-cell
has exact synonym: IgG memory B-lymphocyte
has exact synonym: memory IgG B cell
has exact synonym: memory IgG B lymphocyte
has exact synonym: memory IgG B-cell
has exact synonym: memory IgG B-lymphocyte
in subset: cellxgene subset

Axiom
annotated source: IgG memory B cell
annotated property: subClassOf
annotated target: class switched memory B cell
is inferred: true

Axiom
annotated source: IgG memory B cell
annotated property: IAO_0000115
annotated target: An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface.
has db xref: GOC:rhs
has db xref: GO_REF:0000031
has db xref: ISBN:0781765196

plasmablast
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001935
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0042571
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001963
subclass of: mature B cell
subclass of: antibody secreting cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001935
subclass of: Restriction
  on property: RO_0002202
  some values from: mature B cell
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001963
IAO_0000115: An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative.
has broad synonym: CD20-negative B cell
has db xref: FMA:84371
has exact synonym: CD27-positive, CD38-positive, CD20-negative B cell
in subset: cellxgene subset
in subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative.

Axiom
annotated source: plasmablast
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: plasmablast
annotated property: IAO_0000115
annotated target: An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative.
has db xref: GOC:dsd
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMCID:PMC2673126

double negative memory B cell
type: Class
equivalent class: Class
  intersection of: memory B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001963
subclass of: CL_0001053
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001963
IAO_0000115: A memory B cell with the phenotype IgD-negative and CD27-negative.
has exact synonym: dn memory B cell
has exact synonym: dn memory B lymphocyte
has exact synonym: dn memory B-cell
has exact synonym: dn memory B-lymphocyte
has exact synonym: double negative memory B lymphocyte
has exact synonym: double negative memory B-cell
has exact synonym: double negative memory B-lymphocyte

Axiom
annotated source: double negative memory B cell
annotated property: IAO_0000115
annotated target: A memory B cell with the phenotype IgD-negative and CD27-negative.
has db xref: GOC:msz
has db xref: GOC:tfm
has db xref: GO_REF:0000031

IgG plasmablast
type: Class
equivalent class: Class
  intersection of: plasmablast
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071736
subclass of: plasmablast
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071736
IAO_0000115: A plasmablast that secretes IgG.
in subset: cellxgene subset

Axiom
annotated source: IgG plasmablast
annotated property: subClassOf
annotated target: plasmablast
is inferred: true

Axiom
annotated source: IgG plasmablast
annotated property: IAO_0000115
annotated target: A plasmablast that secretes IgG.
has db xref: GOC:msz
has db xref: GO_REF:0000031

IgM plasmablast
type: Class
equivalent class: Class
  intersection of: plasmablast
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071754
subclass of: plasmablast
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071754
IAO_0000115: A plasmablast that secretes IgM.
in subset: cellxgene subset

Axiom
annotated source: IgM plasmablast
annotated property: subClassOf
annotated target: plasmablast
is inferred: true

Axiom
annotated source: IgM plasmablast
annotated property: IAO_0000115
annotated target: A plasmablast that secretes IgM.
has db xref: GOC:msz
has db xref: GO_REF:0000031

IgA plasmablast
type: Class
equivalent class: Class
  intersection of: plasmablast
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071746
subclass of: plasmablast
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071746
IAO_0000115: A plasmablast that secretes IgA.
in subset: cellxgene subset

Axiom
annotated source: IgA plasmablast
annotated property: subClassOf
annotated target: plasmablast
is inferred: true

Axiom
annotated source: IgA plasmablast
annotated property: IAO_0000115
annotated target: A plasmablast that secretes IgA.
has db xref: GOC:msz
has db xref: GO_REF:0000031

IgG plasma cell
type: Class
equivalent class: Class
  intersection of: long lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071736
subclass of: long lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071736
IAO_0000115: A fully differentiated plasma cell that secretes IgG.
in subset: cellxgene subset

Axiom
annotated source: IgG plasma cell
annotated property: subClassOf
annotated target: long lived plasma cell
is inferred: true

Axiom
annotated source: IgG plasma cell
annotated property: IAO_0000115
annotated target: A fully differentiated plasma cell that secretes IgG.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

IgM plasma cell
type: Class
equivalent class: Class
  intersection of: long lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071754
subclass of: long lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071754
IAO_0000115: A fully differentiated plasma cell that secretes IgM.
in subset: cellxgene subset

Axiom
annotated source: IgM plasma cell
annotated property: subClassOf
annotated target: long lived plasma cell
is inferred: true

Axiom
annotated source: IgM plasma cell
annotated property: IAO_0000115
annotated target: A fully differentiated plasma cell that secretes IgM.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

IgA plasma cell
type: Class
equivalent class: Class
  intersection of: long lived plasma cell
  intersection of: Restriction
    on property: RO_0003000
    some values from: GO_0071746
subclass of: long lived plasma cell
subclass of: Restriction
  on property: RO_0003000
  some values from: GO_0071746
IAO_0000115: A fully differentiated plasma cell that secretes IgA.
in subset: cellxgene subset
in subset: human reference atlas

Axiom
annotated source: IgA plasma cell
annotated property: subClassOf
annotated target: long lived plasma cell
is inferred: true

Axiom
annotated source: IgA plasma cell
annotated property: IAO_0000115
annotated target: A fully differentiated plasma cell that secretes IgA.
has db xref: GOC:msz
has db xref: GO_REF:0000031
has db xref: ISBN:781735149

hematopoietic cell
type: Class
subclass of: cell
IAO_0000115: A cell of a hematopoietic lineage.
has db xref: BTO:0000574
has db xref: CALOHA:TS-2017
has db xref: FMA:70366
has db xref: FMA:83598
has db xref: ZFA:0005830
has exact synonym: haematopoietic cell
has exact synonym: haemopoietic cell
has exact synonym: hemopoietic cell
in subset: cellxgene subset
in subset: general cell types upper slim

Axiom
annotated source: hematopoietic cell
annotated property: IAO_0000115
annotated target: A cell of a hematopoietic lineage.
has db xref: GOC:add
has db xref: GO_REF:0000031

Axiom
annotated source: hematopoietic cell
annotated property: hasDbXref
annotated target: ZFA:0005830
mapping justification: UnspecifiedMatching

CD11c-low plasmacytoid dendritic cell
type: Class
equivalent class: Class
  intersection of: plasmacytoid dendritic cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001014
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002978
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001013
subclass of: plasmacytoid dendritic cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001014
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002978
subclass of: Restriction
  on property: RO_0002162
  some values from: NCBITaxon_10090
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001013
IAO_0000115: CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative.
comment: Originally described in the dendritic cell ontology (DC_CL:0000001)(PMID:19243617). These cells are CD281-positive (TLR1), CD282-positive (TLR2), CD285-positive (TLR5), CD286-positive (TLR6), and CD288-positive (TLR8).

Axiom
annotated source: CD11c-low plasmacytoid dendritic cell
annotated property: subClassOf
annotated target: plasmacytoid dendritic cell
is inferred: true

Axiom
annotated source: CD11c-low plasmacytoid dendritic cell
annotated property: IAO_0000115
annotated target: CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative.
has db xref: GOC:amm
has db xref: GOC:dsd
has db xref: GO_REF:0000031
has db xref: PMID:15771572
has db xref: PMID:17850486
has db xref: PMID:19243617
has db xref: PMID:34603298

conventional dendritic cell
type: Class
equivalent class: Class
  intersection of: dendritic cell
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001013
subclass of: dendritic cell
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001013
IAO_0000115: Conventional dendritic cell is a dendritic cell that is CD11c-high.
description: Conventional dendritic cells (cDCs) are primarily responsible for processing antigens and presenting them to T cells to initiate an immune response. Also known as classical dendritic cells, cDCs originate from hematopoietic stem cells in the bone marrow, maturing in peripheral tissues. They are characterized by their distinct morphology, which features a central body with numerous branching extensions known as dendrites. These cells have a pivotal role in adaptive immunity, bridging the gap between the innate and adaptive immune responses. They achieve this by capturing, processing, and presenting antigens to naive T-cells in the secondary lymphoid organs. This antigen presentation, in conjunction with co-stimulatory signals provided by the cDCs, instructs the T cells whether to mount an immune response against the antigen. cDCs are also very effective in the cross-presentation of antigens in the context of major histocompatibility complex (MHC) I, thereby activating CD8+ T cells an initiating a cytotoxic T cell response. In addition to their role in antigen presentation, cDCs have other important functions in maintaining immune homeostasis. They can perceive signals from the surrounding tissue microenvironment, responding to inflammation, and influencing or even polarizing T cell differentiation into various effector subtypes. Importantly, while cDCs are often associated with immunogenic responses, they also play a crucial role in immune tolerance, particularly towards self-antigens, thereby preventing autoimmune reactions. In conclusion, conventional dendritic cells serve as the sentinels of the immune system, monitoring for threat signals and coordinating the appropriate immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered def…
has broad synonym: interdigitating cell
has broad synonym: veiled cell
has db xref: FMA:84191
has exact synonym: DC1
has exact synonym: cDC
has exact synonym: dendritic reticular cell
has exact synonym: type 1 DC
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas
comment: Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive.

Axiom
annotated source: conventional dendritic cell
annotated property: subClassOf
annotated target: dendritic cell
is inferred: true

Axiom
annotated source: conventional dendritic cell
annotated property: IAO_0000115
annotated target: Conventional dendritic cell is a dendritic cell that is CD11c-high.
has db xref: GOC:amm
has db xref: GO_REF:0000031
has db xref: PMID:17850486

Axiom
annotated source: conventional dendritic cell
annotated property: description
annotated target: Conventional dendritic cells (cDCs) are primarily responsible for processing antigens and presenting them to T cells to initiate an immune response. Also known as classical dendritic cells, cDCs originate from hematopoietic stem cells in the bone marrow, maturing in peripheral tissues. They are characterized by their distinct morphology, which features a central body with numerous branching extensions known as dendrites. These cells have a pivotal role in adaptive immunity, bridging the gap between the innate and adaptive immune responses. They achieve this by capturing, processing, and presenting antigens to naive T-cells in the secondary lymphoid organs. This antigen presentation, in conjunction with co-stimulatory signals provided by the cDCs, instructs the T cells whether to mount an immune response against the antigen. cDCs are also very effective in the cross-presentation of antigens in the context of major histocompatibility complex (MHC) I, thereby activating CD8+ T cells an initiating a cytotoxic T cell response. In addition to their role in antigen presentation, cDCs have other important functions in maintaining immune homeostasis. They can perceive signals from the surrounding tissue microenvironment, responding to inflammation, and influencing or even polarizing T cell differentiation into various effector subtypes. Importantly, while cDCs are often associated with immunogenic responses, they also play a crucial role in immune tolerance, particularly towards self-antigens, thereby preventing autoimmune reactions. In conclusion, conventional dendritic cells serve as the sentinels of the immune system, monitoring for threat signals and coordinating the appropriate immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered def…
has db xref: DOI:10.1016/bs.ircmb.2019.07.004
has db xref: DOI:10.1146/annurev-immunol-061020-053707
has db xref: DOI:10.3389/fimmu.2018.03176

conventional dendritic cell on CELLxGENE CellGuide
type: Axiom
annotated source: conventional dendritic cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0000990

immature CD11c-low plasmacytoid dendritic cell
type: Class
equivalent class: Class
  intersection of: CD11c-low plasmacytoid dendritic cell
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001412
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001438
subclass of: myeloid leukocyte
subclass of: CD11c-low plasmacytoid dendritic cell
subclass of: Restriction
  on property: RO_0002202
  some values from: common dendritic progenitor
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001412
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001438
IAO_0000115: Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low.
comment: Originally described in the dendritic cell ontology (DC_CL:0000006)(PMID:19243617).

Axiom
annotated source: immature CD11c-low plasmacytoid dendritic cell
annotated property: subClassOf
annotated target: CD11c-low plasmacytoid dendritic cell
is inferred: true

Axiom
annotated source: immature CD11c-low plasmacytoid dendritic cell
annotated property: IAO_0000115
annotated target: Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low.
has db xref: GOC:amm
has db xref: GO_REF:0000031
has db xref: PMID:15771572
has db xref: PMID:17850486

mature CD11c-low plasmacytoid dendritic cell
type: Class
equivalent class: Class
  intersection of: CD11c-low plasmacytoid dendritic cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001310
  intersection of: Restriction
    on property: RO_0015015
    some values from: GO_0042613
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001412
  intersection of: Restriction
    on property: RO_0015015
    some values from: PR_000001438
subclass of: myeloid leukocyte
subclass of: CD11c-low plasmacytoid dendritic cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001310
subclass of: Restriction
  on property: RO_0002202
  some values from: immature CD11c-low plasmacytoid dendritic cell
subclass of: Restriction
  on property: RO_0015015
  some values from: GO_0042613
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001412
subclass of: Restriction
  on property: RO_0015015
  some values from: PR_000001438
IAO_0000115: Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive.
comment: Originally described in the dendritic cell ontology (DC_CL:0000007)(PMID:19243617).

Axiom
annotated source: mature CD11c-low plasmacytoid dendritic cell
annotated property: subClassOf
annotated target: CD11c-low plasmacytoid dendritic cell
is inferred: true

Axiom
annotated source: mature CD11c-low plasmacytoid dendritic cell
annotated property: IAO_0000115
annotated target: Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive.
has db xref: GOC:amm
has db xref: GO_REF:0000031
has db xref: PMID:15771572
has db xref: PMID:17850486

CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor
type: Class
equivalent class: Class
  union of: CD34-positive, CD38-positive common lymphoid progenitor
  union of: CD34-positive, CD38-positive common myeloid progenitor
subclass of: CL_0001060
subclass of: CL_0011026
has broad synonym: CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid
comment: Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617).

Kit and Sca1-positive hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001014
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001308
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001869
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001896
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002977
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001833
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002979
subclass of: hematopoietic stem cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001014
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001308
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001869
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001896
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002977
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001833
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002979
disjoint with: CD34-positive, CD38-negative hematopoietic stem cell
IAO_0000115: A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative.
has exact synonym: LSK stem cell
has exact synonym: Sca1-positive hematopoietic stem cell
comment: Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617).

Axiom
annotated source: Kit and Sca1-positive hematopoietic stem cell
annotated property: subClassOf
annotated target: hematopoietic stem cell
is inferred: true

Axiom
annotated source: Kit and Sca1-positive hematopoietic stem cell
annotated property: IAO_0000115
annotated target: A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17952047
has db xref: PMID:19022770

CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor
type: Class
equivalent class: Class
  union of: granulocyte monocyte progenitor cell
  union of: CD7-negative lymphoid progenitor cell
subclass of: CL_0001060
subclass of: CL_0011026
comment: Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617).

CD115-positive monocyte OR common dendritic progenitor
type: Class
equivalent class: Class
  union of: CD115-positive monocyte
  union of: common dendritic progenitor
subclass of: myeloid cell
subclass of: CL_0002031
comment: Originally described in the dendritic cell ontology (DC_CL:1111000)(PMID:19243617).

CD34-positive, CD38-positive common lymphoid progenitor
type: Class
equivalent class: Class
  intersection of: common lymphoid progenitor
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001898
subclass of: common lymphoid progenitor
subclass of: CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001015
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001898
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002043
disjoint with: Kit-positive, Sca1-positive common lymphoid progenitor
IAO_0000115: A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive.
has exact synonym: CD10-positive common lymphocyte precursor
has exact synonym: CD10-positive common lymphocyte progenitor
has exact synonym: CD10-positive common lymphoid precursor
comment: These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617).

Axiom
annotated source: CD34-positive, CD38-positive common lymphoid progenitor
annotated property: subClassOf
annotated target: common lymphoid progenitor
is inferred: true

Axiom
annotated source: CD34-positive, CD38-positive common lymphoid progenitor
annotated property: IAO_0000115
annotated target: A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMCID:PMC2346585
has db xref: PMID:19022770

CD115-positive monocyte
type: Class
equivalent class: Class
  intersection of: monocyte
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001012
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002062
subclass of: monocyte
subclass of: myeloid lineage restricted progenitor cell
subclass of: CD115-positive monocyte OR common dendritic progenitor
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001012
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002062
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002001
IAO_0000115: CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive.
comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000033)(PMID:19243617).

Axiom
annotated source: CD115-positive monocyte
annotated property: subClassOf
annotated target: monocyte
is inferred: true

Axiom
annotated source: CD115-positive monocyte
annotated property: IAO_0000115
annotated target: CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GO_REF:0000031
has db xref: PMID:17952047

Kit-positive, CD34-positive common myeloid progenitor
type: Class
equivalent class: Class
  intersection of: CL_0001059
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001869
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002979
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0015016
    some values from: GO_0033001
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001481
subclass of: CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor
subclass of: CL_0001059
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001869
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002979
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002035
subclass of: Restriction
  on property: RO_0015016
  some values from: GO_0033001
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001481
disjoint with: CD34-positive, CD38-positive common myeloid progenitor
IAO_0000115: A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low.
has broad synonym: CD117-positive common myeloid precursor
comment: Markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000034)(PMID:19243617).

Axiom
annotated source: Kit-positive, CD34-positive common myeloid progenitor
annotated property: subClassOf
annotated target: CL_0001059
is inferred: true

Axiom
annotated source: Kit-positive, CD34-positive common myeloid progenitor
annotated property: IAO_0000115
annotated target: A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:1261582
has db xref: PMID:17952047
has db xref: http://www.immgen.org/index_content.html

CD34-positive, CD38-negative hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001408
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001483
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001892
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001945
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001786
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001809
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001843
subclass of: hematopoietic stem cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001408
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001483
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001892
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001945
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001786
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001809
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001843
IAO_0000115: CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive.
has db xref: CALOHA:TS-0448
has exact synonym: CD133-positive hematopoietic stem cell
in subset: cellxgene subset
comment: Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617).

Axiom
annotated source: CD34-positive, CD38-negative hematopoietic stem cell
annotated property: subClassOf
annotated target: hematopoietic stem cell
is inferred: true

Axiom
annotated source: CD34-positive, CD38-negative hematopoietic stem cell
annotated property: IAO_0000115
annotated target: CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:10430905
has db xref: PMID:11750107
has db xref: PMID:16551251
has db xref: PMID:20024907
has db xref: PMID:9389721

Axiom
annotated source: CD34-positive, CD38-negative hematopoietic stem cell
annotated property: hasExactSynonym
annotated target: CD133-positive hematopoietic stem cell
has db xref: PMID:16140871

Kit-positive, Sca1-positive common lymphoid progenitor
type: Class
equivalent class: Class
  intersection of: common lymphoid progenitor
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001014
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001869
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001963
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002001
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002037
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000002065
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000002979
subclass of: common lymphoid progenitor
subclass of: CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001014
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001869
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001963
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002001
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002037
subclass of: Restriction
  on property: RO_0002202
  some values from: early lymphoid progenitor
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000002065
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000002979
IAO_0000115: A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low.
has exact synonym: CD217-positive common lymphocyte precursor
has exact synonym: CD217-positive common lymphocyte progenitor
has exact synonym: CD217-positive common lymphoid precursor
comment: Markers are associated with mouse cells.

Axiom
annotated source: Kit-positive, Sca1-positive common lymphoid progenitor
annotated property: subClassOf
annotated target: common lymphoid progenitor
is inferred: true

Axiom
annotated source: Kit-positive, Sca1-positive common lymphoid progenitor
annotated property: IAO_0000115
annotated target: A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:17952047
has db xref: http://www.immgen.org/index_content.html

CD34-positive, CD38-positive common myeloid progenitor
type: Class
equivalent class: Class
  intersection of: CL_0001059
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001015
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001836
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001867
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001898
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001408
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000001865
subclass of: CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor
subclass of: CL_0001059
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001015
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001836
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001867
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001898
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001408
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002043
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000001865
IAO_0000115: A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative.
has narrow synonym: CD71-positive common myeloid precursor
comment: Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617).

Axiom
annotated source: CD34-positive, CD38-positive common myeloid progenitor
annotated property: IAO_0000115
annotated target: A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative.
has db xref: GOC:add
has db xref: GOC:amm
has db xref: GO_REF:0000031
has db xref: PMCID:PMC2626675
has db xref: PMID:16551251

CD7-negative lymphoid progenitor cell
type: Class
equivalent class: Class
  intersection of: common lymphoid progenitor
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001015
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001836
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
subclass of: common lymphoid progenitor
subclass of: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001015
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001836
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002202
  some values from: CD34-positive, CD38-positive common lymphoid progenitor
IAO_0000115: CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative.
has exact synonym: CD7-negative lymphoid precursor
comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617).

Axiom
annotated source: CD7-negative lymphoid progenitor cell
annotated property: subClassOf
annotated target: common lymphoid progenitor
is inferred: true

Axiom
annotated source: CD7-negative lymphoid progenitor cell
annotated property: IAO_0000115
annotated target: CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative.
has db xref: GOC:amm
has db xref: GO_REF:0000031
has db xref: PMID:16551251

CD7-positive lymphoid progenitor cell
type: Class
equivalent class: Class
  intersection of: common lymphoid progenitor
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001015
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001003
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001836
subclass of: common lymphoid progenitor
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001015
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001003
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001836
subclass of: Restriction
  on property: RO_0002202
  some values from: CD7-negative lymphoid progenitor cell
IAO_0000115: CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative.
has exact synonym: CD7-positive lymphoid precursor
comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000040)(PMID:19243617).

Axiom
annotated source: CD7-positive lymphoid progenitor cell
annotated property: subClassOf
annotated target: common lymphoid progenitor
is inferred: true

Axiom
annotated source: CD7-positive lymphoid progenitor cell
annotated property: IAO_0000115
annotated target: CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative.
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:16551251
has db xref: PMID:19491395

common dendritic progenitor
type: Class
equivalent class: Class
  intersection of: CL_0002031
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002001
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000002062
  intersection of: Restriction
    on property: RO_0015016
    some values from: PR_000002065
subclass of: CD115-positive monocyte OR common dendritic progenitor
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002001
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000002062
subclass of: Restriction
  on property: RO_0002202
  some values from: CL_0002009
subclass of: Restriction
  on property: RO_0015016
  some values from: PR_000002065
IAO_0000115: Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers.
has exact synonym: CDP
has exact synonym: common dendritic precursor
has exact synonym: pro-DCs
in subset: cellxgene subset
comment: Surface markers are for mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000041) CDP are reportedly CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD11c-positive, CD14-negative, CD19-negative, CD20-negative, CD56-negative, B220-negative, Ly6g-negative, MHCII-positive, and Ter119-negative. (PMID:19243617).

Axiom
annotated source: common dendritic progenitor
annotated property: IAO_0000115
annotated target: Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers.
has db xref: GOC:amm
has db xref: GOC:tfm
has db xref: GO_REF:0000031
has db xref: PMID:16551251
has db xref: PMID:17922016
has db xref: PMID:19286519

Axiom
annotated source: common dendritic progenitor
annotated property: hasExactSynonym
annotated target: CDP
has db xref: PMID:21219184

Axiom
annotated source: common dendritic progenitor
annotated property: hasExactSynonym
annotated target: pro-DCs
has db xref: PMID:21219184

CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor
type: Class
equivalent class: Class
  union of: Kit-positive, CD34-positive common myeloid progenitor
  union of: Kit-positive, Sca1-positive common lymphoid progenitor
subclass of: CL_0001060
subclass of: CL_0011026
comment: Originally described in the dendritic cell ontology (DC_CL:1111100)(PMID:19243617).

cerebellar granule cell
type: Class
equivalent class: Class
  intersection of: granule cell
  intersection of: Restriction
    on property: RO_0002100
    some values from: UBERON_0002037
subclass of: granule cell
subclass of: CL_2000028
subclass of: UBERON_0004121
subclass of: Restriction
  on property: RO_0002207
  some values from: CL_0002362
IAO_0000115: An excitatory granule cell with a soma located in the granular layer of cerebellar cortex. A mature cerebellar granule cell has short dendrites with a characteristic claw-like appearance and a long axon that ascends to the molecular layer where it bifurcates (except in non-teleost fish, where it does not bifurcate) and extends mediolaterally to form parallel fibers.
description: The cerebellar granule cell is a predominant type of neuron located in the granular layer of the cerebellum. These cells are among the smallest neurons in the brain, yet they constitute the bulk of the neural cells in the cerebellum, making cerebellar granule cells the most populous type of neuron in mammals. The granule cells of the cerebellum play an essential role in the functioning of the cerebellar cortex by participating in a complex neuronal network that results in coordination and fine-tuning of motor activities. Initiating and controlling movement is the primary functional role of cerebellar granule cells. They achieve this through highly sophisticated neuronal networking. Each granule cell gives rise to an axon that ascends into the molecular layer of the cerebellar cortex, where it bifurcates into T-shape to form parallel fibers that run perpendicular to the Purkinje cell dendrites. This structure allows a single granule cell to make synaptic contact with hundreds of Purkinje cells and thereby influence their output. Cerebellar granule cells contribute to the generation of movement by transforming unstructured input from mossy fibers into organized output to the Purkinje cells. Understanding the role of cerebellar granule cells in neural plasticity is an emerging area of study. Recent research suggests that cerebellar granule cells may be involved in learning and memory processes, particularly those related to motor learning. They display unique synaptic plasticity, equipping them with the ability to adjust their response over time, which aids in the learning and storage of motor patterns. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: BTO:0004278
has db xref: ZFA:0001691
has exact synonym: granule cell of the cerebellum
in subset: cellxgene subset
comment: It has been noted in at least some mammalian species that granule cells are the most numerous cell type in the cerebellum and in the brain, with at least 99% of all cerebellar neurons being granule cells.

Axiom
annotated source: cerebellar granule cell
annotated property: IAO_0000115
annotated target: An excitatory granule cell with a soma located in the granular layer of cerebellar cortex. A mature cerebellar granule cell has short dendrites with a characteristic claw-like appearance and a long axon that ascends to the molecular layer where it bifurcates (except in non-teleost fish, where it does not bifurcate) and extends mediolaterally to form parallel fibers.
has db xref: GOC:mah
has db xref: doi:10.12688/f1000research.15021.1
has db xref: doi:10.3389/fncir.2020.611841

Axiom
annotated source: cerebellar granule cell
annotated property: description
annotated target: The cerebellar granule cell is a predominant type of neuron located in the granular layer of the cerebellum. These cells are among the smallest neurons in the brain, yet they constitute the bulk of the neural cells in the cerebellum, making cerebellar granule cells the most populous type of neuron in mammals. The granule cells of the cerebellum play an essential role in the functioning of the cerebellar cortex by participating in a complex neuronal network that results in coordination and fine-tuning of motor activities. Initiating and controlling movement is the primary functional role of cerebellar granule cells. They achieve this through highly sophisticated neuronal networking. Each granule cell gives rise to an axon that ascends into the molecular layer of the cerebellar cortex, where it bifurcates into T-shape to form parallel fibers that run perpendicular to the Purkinje cell dendrites. This structure allows a single granule cell to make synaptic contact with hundreds of Purkinje cells and thereby influence their output. Cerebellar granule cells contribute to the generation of movement by transforming unstructured input from mossy fibers into organized output to the Purkinje cells. Understanding the role of cerebellar granule cells in neural plasticity is an emerging area of study. Recent research suggests that cerebellar granule cells may be involved in learning and memory processes, particularly those related to motor learning. They display unique synaptic plasticity, equipping them with the ability to adjust their response over time, which aids in the learning and storage of motor patterns. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1016/B978-0-444-63356-9.00002-9
has db xref: DOI:10.1038/nn.4531
has db xref: DOI:10.1038/nrn3312
has db xref: DOI:10.1152/jn.1998.80.5.2521
has db xref: DOI:10.3389/fncir.2020.611841

Axiom
annotated source: cerebellar granule cell
annotated property: hasDbXref
annotated target: ZFA:0001691
mapping justification: UnspecifiedMatching

Axiom
annotated source: cerebellar granule cell
annotated property: hasExactSynonym
annotated target: granule cell of the cerebellum
has db xref: doi:10.3389/fncir.2020.611841

Axiom
annotated source: cerebellar granule cell
annotated property: comment
annotated target: It has been noted in at least some mammalian species that granule cells are the most numerous cell type in the cerebellum and in the brain, with at least 99% of all cerebellar neurons being granule cells.
has db xref: doi:10.3389/fncir.2020.611841

cerebellar granule cell on CELLxGENE CellGuide
type: Axiom
annotated source: cerebellar granule cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0001031

Axiom
annotated source: cerebellar granule cell
annotated property: depiction
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
has db xref: doi:10.1016/j.cnp.2022.11.002

Axiom
annotated source: cerebellar granule cell
annotated property: depiction
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
has db xref: doi:10.3389/fnins.2020.00293

cortical granule cell
type: Class
equivalent class: Class
  intersection of: granule cell
  intersection of: Restriction
    on property: RO_0002100
    some values from: UBERON_0000956
subclass of: granule cell
subclass of: CL_0010012
IAO_0000115: Granule cell that is part of the cerebral cortex.

Axiom
annotated source: cortical granule cell
annotated property: IAO_0000115
annotated target: Granule cell that is part of the cerebral cortex.
has db xref: GOC:mah

hippocampal granule cell
type: Class
equivalent class: Class
  intersection of: granule cell
  intersection of: Restriction
    on property: RO_0002100
    some values from: UBERON_0002421
subclass of: cortical granule cell
subclass of: CL_0002608
IAO_0000115: Granule cell with a soma found in the hippocampus.
in subset: cellxgene subset

Axiom
annotated source: hippocampal granule cell
annotated property: IAO_0000115
annotated target: Granule cell with a soma found in the hippocampus.
has db xref: GOC:mah

bone cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: BFO_0000050
    some values from: UBERON_0001474
subclass of: eukaryotic cell
subclass of: Restriction
  on property: BFO_0000050
  some values from: UBERON_0001474
IAO_0000115: A connective tissue cell found in bone.
contributor: https://orcid.org/0000-0001-9990-8331
description: Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
creation date: 2011-11-16T04:28:16Z
in subset: general cell types upper slim
in subset: human reference atlas

Axiom
annotated source: bone cell
annotated property: IAO_0000115
annotated target: A connective tissue cell found in bone.
has db xref: GOC:add
has db xref: GO_REF:0000034

Axiom
annotated source: bone cell
annotated property: description
annotated target: Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has db xref: DOI:10.1007/s00795-015-0099-y
has db xref: DOI:10.1007/s11914-012-0105-4
has db xref: DOI:10.1016/j.jot.2021.04.005
has db xref: DOI:10.1038/s41413-020-0099-y

bone cell on CELLxGENE CellGuide
type: Axiom
annotated source: bone cell
annotated property: seeAlso
annotated target: https://cellxgene.cziscience.com/cellguide/CL_0001035

CD8-positive, CXCR3-positive, alpha-beta regulatory T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta regulatory T cell
  intersection of: Restriction
    on property: RO_0002104
    some values from: PR_000001207
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032613
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032689
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0042130
subclass of: CD8-positive, alpha-beta regulatory T cell
subclass of: Restriction
  on property: RO_0002104
  some values from: PR_000001207
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032613
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032689
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0042130
IAO_0000115: A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production.
has exact synonym: CD8+CXCR3+ T cell
has exact synonym: CD8+CXCR3+ T lymphocyte
has exact synonym: CD8+CXCR3+ T(reg)
has exact synonym: CD8+CXCR3+ T-cell
has exact synonym: CD8+CXCR3+ Treg
has exact synonym: CD8-positive, CXCR3-positive, T(reg)
has exact synonym: CD8-positive, CXCR3-positive, Treg
has exact synonym: CD8-positive, CXCR3-positive, alpha-beta regulatory T lymphocyte
has exact synonym: CD8-positive, CXCR3-positive, alpha-beta regulatory T-cell
has exact synonym: CD8-positive, CXCR3-positive, alpha-beta regulatory T-lymphocyte
comment: These cells may be the human equivalent of murine CD8-positive, CD122-positive alpha-beta regulatory T cell. They are also found in the CD45RA-negative and CD62L-positive fraction.

Axiom
annotated source: CD8-positive, CXCR3-positive, alpha-beta regulatory T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta regulatory T cell
is inferred: true

Axiom
annotated source: CD8-positive, CXCR3-positive, alpha-beta regulatory T cell
annotated property: IAO_0000115
annotated target: A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production.
has db xref: GOC:dsd
has db xref: PMID:19609979

T-helper 22 cell
type: Class
equivalent class: Class
  intersection of: CD4-positive helper T cell
  intersection of: Restriction
    on property: RO_0002215
    some values from: GO_0032626
subclass of: CD4-positive helper T cell
subclass of: Restriction
  on property: RO_0002215
  some values from: GO_0032626
IAO_0000115: CD4-positive, alpha-beta T cell that produces IL-22.
has exact synonym: T(H)-22 cell
has exact synonym: Th22 T cell
has exact synonym: Th22 T lymphocyte
has exact synonym: Th22 T-cell
has exact synonym: Th22 T-lymphocyte
has exact synonym: Th22 cell
has exact synonym: helper T cell type 22
in subset: cellxgene subset
comment: TH22 cells are also reportedly CCR4-positive, CCR6-positive, CCR10-positive, CXCR3-negative. TH22 cells are reportedly capable of secreting IL-13.

Axiom
annotated source: T-helper 22 cell
annotated property: subClassOf
annotated target: CD4-positive helper T cell
is inferred: true

Axiom
annotated source: T-helper 22 cell
annotated property: IAO_0000115
annotated target: CD4-positive, alpha-beta T cell that produces IL-22.
has db xref: GOC:dsd
has db xref: PMID:19578368
has db xref: PMID:19578369