goslim pir.owl
type: Ontology
version IRI: goslim pir.owl
version info: 2024-09-26

definition
type: AnnotationProperty

term tracker item
type: AnnotationProperty
database_cross_reference: IAO:0000233
has_obo_namespace: external
id: term_tracker_item
is class level: true
is metadata tag: true
shorthand: term_tracker_item

has ontology root term
type: AnnotationProperty
database_cross_reference: IAO:0000700
has_obo_namespace: external
id: has_ontology_root_term
is class level: true
is metadata tag: true
shorthand: has_ontology_root_term

term replaced by
type: AnnotationProperty

chebi ph7 3
type: AnnotationProperty
comment: Rhea list of ChEBI terms representing the major species at pH 7.3.
sub property of: subset_property

gocheck do not annotate
type: AnnotationProperty
comment: Term not to be used for direct annotation
sub property of: subset_property

gocheck obsoletion candidate
type: AnnotationProperty
comment: Terms planned for obsoletion
sub property of: subset_property

goslim agr
type: AnnotationProperty
comment: AGR slim
sub property of: subset_property

goslim aspergillus
type: AnnotationProperty
comment: Aspergillus GO slim
sub property of: subset_property

goslim candida
type: AnnotationProperty
comment: Candida GO slim
sub property of: subset_property

goslim chembl
type: AnnotationProperty
comment: ChEMBL protein targets summary
sub property of: subset_property

goslim drosophila
type: AnnotationProperty
comment: Drosophila GO slim
sub property of: subset_property

goslim euk cellular processes ribbon
type: AnnotationProperty
comment: GO ribbon for eukaroytic cellular processes
sub property of: subset_property

goslim flybase ribbon
type: AnnotationProperty
comment: Insecta GO ribbon slim
sub property of: subset_property

goslim generic
type: AnnotationProperty
comment: Generic GO slim
sub property of: subset_property

goslim metagenomics
type: AnnotationProperty
comment: Metagenomics GO slim
sub property of: subset_property

goslim mouse
type: AnnotationProperty
comment: Mouse GO slim
sub property of: subset_property

goslim pir
type: AnnotationProperty
comment: PIR GO slim
sub property of: subset_property

goslim plant
type: AnnotationProperty
comment: Plant GO slim
sub property of: subset_property

goslim plant ribbon
type: AnnotationProperty
comment: Plant GO ribbon
sub property of: subset_property

goslim pombe
type: AnnotationProperty
comment: Fission yeast GO slim
sub property of: subset_property

goslim prokaryote
type: AnnotationProperty
comment: GO subset for prokaryotes
sub property of: subset_property

goslim prokaryote ribbon
type: AnnotationProperty
comment: Prokaryote GO ribbon slim
sub property of: subset_property

goslim synapse
type: AnnotationProperty
comment: synapse GO slim
sub property of: subset_property

goslim virus
type: AnnotationProperty
comment: GO subset for viruses
sub property of: subset_property

goslim yeast
type: AnnotationProperty
comment: Yeast GO slim
sub property of: subset_property

label approved by the SynGO project
type: AnnotationProperty
sub property of: synonym_type_property

Systematic synonym
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
database_cross_reference: BFO:0000050
has_obo_namespace: external
id: part_of
shorthand: part_of

has part
type: ObjectProperty
type: TransitiveProperty
database_cross_reference: BFO:0000051
has_obo_namespace: external
id: has_part
shorthand: has_part

occurs in
type: ObjectProperty
property chain axiom: part of
database_cross_reference: BFO:0000066
has_obo_namespace: external
id: occurs_in
shorthand: occurs_in

starts during
type: ObjectProperty
database_cross_reference: RO:0002091
has_obo_namespace: external
id: starts_during
shorthand: starts_during

happens during
type: ObjectProperty
sub property of: ends during
type: TransitiveProperty
database_cross_reference: RO:0002092
has_obo_namespace: external
id: happens_during
shorthand: happens_during

ends during
type: ObjectProperty
database_cross_reference: RO:0002093
has_obo_namespace: external
id: ends_during
shorthand: ends_during

regulates
type: ObjectProperty
type: TransitiveProperty
database_cross_reference: RO:0002211
has_obo_namespace: external
id: regulates
shorthand: regulates

negatively regulates
type: ObjectProperty
sub property of: regulates
database_cross_reference: RO:0002212
has_obo_namespace: external
id: negatively_regulates
shorthand: negatively_regulates

positively regulates
type: ObjectProperty
sub property of: regulates
property chain axiom: negatively regulates
database_cross_reference: RO:0002213
has_obo_namespace: external
id: positively_regulates
shorthand: positively_regulates

nucleotide-excision repair complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: Any complex formed of proteins that act in nucleotide-excision repair.
has_narrow_synonym: UvrB-UvrC complex
has_narrow_synonym: UvrBC complex
has_obo_namespace: cellular_component
id: GO:0000109
in_subset: goslim pir
comment: Note that process information is included in the term and definition for the purpose of describing and distinguishing the complex.

Axiom
annotated source: nucleotide-excision repair complex
annotated property: definition
annotated target: Any complex formed of proteins that act in nucleotide-excision repair.
database_cross_reference: PMID:10915862

Axiom
annotated source: nucleotide-excision repair complex
annotated property: has_narrow_synonym
annotated target: UvrB-UvrC complex
database_cross_reference: PMID:12145219

Axiom
annotated source: nucleotide-excision repair complex
annotated property: has_narrow_synonym
annotated target: UvrBC complex
database_cross_reference: GOC:bhm
database_cross_reference: PMID:12145219

flocculation
type: Class
subclass of: cell adhesion
subclass of: biological process involved in intraspecies interaction between organisms
definition: The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs.
term tracker item: https://github.com/geneontology/go-ontology/issues/18785
term tracker item: https://github.com/geneontology/go-ontology/issues/20192
created by: bf
creation date: 2012-07-11T01:30:40Z
has_alternative_id: GO:0000501
has_alternative_id: GO:0032128
has_alternative_id: GO:0036281
has_alternative_id: GO:0036282
has_alternative_id: GO:0043689
has_alternative_id: GO:0043690
database_cross_reference: Wikipedia:Flocculation
has_exact_synonym: cell-cell adhesion involved in flocculation
has_narrow_synonym: cell-cell adhesion involved in flocculation via cell wall protein-carbohydrate interaction
has_narrow_synonym: co-flocculation
has_narrow_synonym: coflocculation
has_narrow_synonym: coflocculation via lectin-mannose interaction
has_narrow_synonym: coflocculation via protein-carbohydrate interaction
has_obo_namespace: biological_process
has_related_synonym: flocculation via cell wall protein-carbohydrate interaction
has_related_synonym: flocculation via extracellular polymer
id: GO:0000128
in_subset: goslim pir
comment: The word floc derives from the Latin word floccus, which means a tuft of wool.

Axiom
annotated source: flocculation
annotated property: has_narrow_synonym
annotated target: co-flocculation
database_cross_reference: PMID:10689163

Axiom
annotated source: flocculation
annotated property: has_narrow_synonym
annotated target: coflocculation via lectin-mannose interaction
database_cross_reference: PMID:11693916

Axiom
annotated source: flocculation
annotated property: definition
annotated target: The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs.
database_cross_reference: GOC:jl
database_cross_reference: GOC:vw
database_cross_reference: PMID:11472912
database_cross_reference: PMID:21114594
database_cross_reference: PMID:8740415

polarisome
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
subclass of: Restriction
  on property: part of
  some values from: site of polarized growth
definition: Protein complex that plays a role in determining cell polarity by directing the localized assembly of actin filaments at polarization sites; in Saccharomyces the polarisome includes Bni1p, Spa2p, Pea2p, and Bud6p.
has_obo_namespace: cellular_component
id: GO:0000133
in_subset: goslim pir

Axiom
annotated source: polarisome
annotated property: definition
annotated target: Protein complex that plays a role in determining cell polarity by directing the localized assembly of actin filaments at polarization sites; in Saccharomyces the polarisome includes Bni1p, Spa2p, Pea2p, and Bud6p.
database_cross_reference: PMID:14734532
database_cross_reference: PMID:14998522
database_cross_reference: PMID:9632790

ubiquitin ligase complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.
has_obo_namespace: cellular_component
id: GO:0000151
in_subset: goslim pir

Axiom
annotated source: ubiquitin ligase complex
annotated property: definition
annotated target: A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.
database_cross_reference: GOC:jh2
database_cross_reference: PMID:9529603

nucleotide binding
type: Class
subclass of: binding
definition: Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
has_obo_namespace: molecular_function
id: GO:0000166
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: nucleotide binding
annotated property: definition
annotated target: Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0198547684

exosome (RNase complex)
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.
has_exact_synonym: exosome (ribonucleasease complex)
has_exact_synonym: exosome multienzyme ribonuclease complex
has_obo_namespace: cellular_component
id: GO:0000178
in_subset: goslim pir
comment: Note that this term should not be confused with 'exosome' used in the context of vesicles released from multivesicular bodies.

Axiom
annotated source: exosome (RNase complex)
annotated property: definition
annotated target: A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.
database_cross_reference: PMID:17174896
database_cross_reference: PMID:20531386
database_cross_reference: PMID:26726035

nuclear division
type: Class
subclass of: organelle fission
definition: The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
has_obo_namespace: biological_process
has_related_synonym: karyokinesis
id: GO:0000280
in_subset: goslim pir

Axiom
annotated source: nuclear division
annotated property: definition
annotated target: The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
database_cross_reference: GOC:mah

cyclin-dependent protein kinase holoenzyme complex
type: Class
subclass of: protein-containing complex
definition: Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.
has_exact_synonym: CDK holoenzyme
has_obo_namespace: cellular_component
id: GO:0000307
in_subset: goslim pir

Axiom
annotated source: cyclin-dependent protein kinase holoenzyme complex
annotated property: definition
annotated target: Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.
database_cross_reference: GOC:krc
database_cross_reference: PMID:11602261

transcription export complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans.
has_exact_synonym: TREX complex
has_obo_namespace: cellular_component
id: GO:0000346
in_subset: goslim pir

Axiom
annotated source: transcription export complex
annotated property: definition
annotated target: The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans.
database_cross_reference: GOC:krc
database_cross_reference: PMID:11979277

THO complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1p, Tho2p, Thp1p, and Mft1p, while the human complex is composed of 7 subunits.
has_obo_namespace: cellular_component
id: GO:0000347
in_subset: goslim pir

Axiom
annotated source: THO complex
annotated property: definition
annotated target: The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1p, Tho2p, Thp1p, and Mft1p, while the human complex is composed of 7 subunits.
database_cross_reference: GOC:krc
database_cross_reference: PMID:11060033
database_cross_reference: PMID:11979277
database_cross_reference: PMID:16983072

RNA splicing, via transesterification reactions
type: Class
subclass of: RNA processing
definition: Splicing of RNA via a series of two transesterification reactions.
has_alternative_id: GO:0000385
has_alternative_id: GO:0031202
has_obo_namespace: biological_process
has_related_synonym: RNA splicing factor activity, transesterification mechanism
has_related_synonym: pre-mRNA splicing factor activity
has_related_synonym: spliceosomal catalysis
id: GO:0000375
in_subset: goslim pir
comment: Note that nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism.

Axiom
annotated source: RNA splicing, via transesterification reactions
annotated property: definition
annotated target: Splicing of RNA via a series of two transesterification reactions.
database_cross_reference: GOC:krc

Axiom
annotated source: RNA splicing, via transesterification reactions
annotated property: has_related_synonym
annotated target: RNA splicing factor activity, transesterification mechanism
database_cross_reference: GOC:krc
database_cross_reference: GOC:mah

Axiom
annotated source: RNA splicing, via transesterification reactions
annotated property: has_related_synonym
annotated target: pre-mRNA splicing factor activity
database_cross_reference: GOC:krc
database_cross_reference: GOC:mah

transcription factor TFIIH core complex
type: Class
subclass of: transcription regulator complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
has_alternative_id: GO:0000441
has_exact_synonym: SSL2-core TFIIH complex
has_exact_synonym: core TFIIH complex
has_obo_namespace: cellular_component
id: GO:0000439
in_subset: goslim pir

Axiom
annotated source: transcription factor TFIIH core complex
annotated property: definition
annotated target: The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
database_cross_reference: GOC:ew
database_cross_reference: GOC:krc
database_cross_reference: PMID:14500720
database_cross_reference: PMID:17215295
database_cross_reference: PMID:22308316
database_cross_reference: PMID:22572993
database_cross_reference: PMID:23028141
database_cross_reference: PMID:7813015

proteasome complex
type: Class
subclass of: protein-containing complex
definition: A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
has_exact_synonym: proteasome
has_narrow_synonym: 26S proteasome
has_obo_namespace: cellular_component
id: GO:0000502
in_subset: goslim pir

Axiom
annotated source: proteasome complex
annotated property: definition
annotated target: A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
database_cross_reference: GOC:rb
database_cross_reference: Wikipedia:Proteasome

Axiom
annotated source: proteasome complex
annotated property: has_exact_synonym
annotated target: proteasome
database_cross_reference: GOC:cjm

conjugation with cellular fusion
type: Class
subclass of: reproductive process
subclass of: Restriction
  on property: has part
  some values from: membrane organization
definition: A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
has_alternative_id: GO:0007322
has_alternative_id: GO:0007333
has_alternative_id: GO:0030461
has_alternative_id: GO:0030477
database_cross_reference: Wikipedia:Conjugation
has_obo_namespace: biological_process
has_related_synonym: cell fusion
has_related_synonym: mating
id: GO:0000747
in_subset: goslim candida
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim yeast

Axiom
annotated source: conjugation with cellular fusion
annotated property: definition
annotated target: A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
database_cross_reference: GOC:elh

kinetochore
type: Class
subclass of: intracellular non-membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
term tracker item: https://github.com/geneontology/go-ontology/issues/21126
term tracker item: https://github.com/geneontology/go-ontology/issues/23605
has_alternative_id: GO:0000777
has_alternative_id: GO:0000778
has_alternative_id: GO:0005699
has_alternative_id: GO:0031617
database_cross_reference: Wikipedia:Kinetochore
has_exact_synonym: condensed chromosome kinetochore
has_exact_synonym: condensed nuclear chromosome kinetochore
has_narrow_synonym: NMS complex
has_obo_namespace: cellular_component
id: GO:0000776
in_subset: goslim pir
comment: Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore.

Axiom
annotated source: kinetochore
annotated property: definition
annotated target: A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
database_cross_reference: GOC:elh

telomere cap complex
type: Class
subclass of: protein-DNA complex
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome.
has_obo_namespace: cellular_component
id: GO:0000782
in_subset: goslim pir
comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome.

Axiom
annotated source: telomere cap complex
annotated property: definition
annotated target: A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome.
database_cross_reference: GOC:elh

nucleosome
type: Class
subclass of: protein-DNA complex
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
has_alternative_id: GO:0000787
has_alternative_id: GO:0000788
has_alternative_id: GO:0005718
database_cross_reference: Wikipedia:Nucleosome
has_narrow_synonym: cytoplasmic nucleosome
has_narrow_synonym: nuclear nucleosome
has_obo_namespace: cellular_component
id: GO:0000786
in_subset: goslim pir

Axiom
annotated source: nucleosome
annotated property: definition
annotated target: A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
database_cross_reference: GOC:elh

condensin complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A multisubunit protein complex that plays a central role in chromosome condensation in meiosis and mitosis.
term tracker item: https://github.com/geneontology/go-ontology/issues/12832
has_alternative_id: GO:0000797
has_alternative_id: GO:0000799
has_alternative_id: GO:0005676
has_alternative_id: GO:0008620
has_alternative_id: GO:0008621
has_alternative_id: GO:0061814
has_narrow_synonym: 13S condensin complex
has_narrow_synonym: 8S condensin complex
has_narrow_synonym: Smc2-Smc4 complex
has_narrow_synonym: condensin I complex
has_narrow_synonym: condensin core heterodimer
has_narrow_synonym: nuclear condensin complex
has_obo_namespace: cellular_component
has_related_synonym: SMC complex
id: GO:0000796
in_subset: goslim pir

Axiom
annotated source: condensin complex
annotated property: definition
annotated target: A multisubunit protein complex that plays a central role in chromosome condensation in meiosis and mitosis.
database_cross_reference: GOC:elh
database_cross_reference: PMID:17268547
database_cross_reference: PMID:21795393

origin recognition complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A multisubunit complex that is located at the replication origins of a chromosome.
database_cross_reference: Wikipedia:Origin_recognition_complex
has_exact_synonym: ORC
has_exact_synonym: origin of replication recognition complex
has_obo_namespace: cellular_component
id: GO:0000808
in_subset: goslim pir

Axiom
annotated source: origin recognition complex
annotated property: definition
annotated target: A multisubunit complex that is located at the replication origins of a chromosome.
database_cross_reference: GOC:elh

gamma-tubulin complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoskeleton
definition: A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species.
has_obo_namespace: cellular_component
id: GO:0000930
in_subset: goslim pir

Axiom
annotated source: gamma-tubulin complex
annotated property: definition
annotated target: A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species.
database_cross_reference: GOC:clt
database_cross_reference: PMID:12134075

radial spoke
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: axoneme
definition: Protein complex that links the outer microtubule doublet of a 9+2 type ciliary or flagellar axoneme with the sheath that surrounds the central pair of microtubules. Composed of a stalk that attaches to each doublet microtubule and a globular structure (spoke head) that projects toward the central pair of microtubules.
term tracker item: https://github.com/geneontology/go-ontology/issues/25321
database_cross_reference: Wikipedia:Radial_spoke
has_obo_namespace: cellular_component
id: GO:0001534
in_subset: goslim pir
comment: Radial spokes are involved in some types of beating motions of the cilium. The radial spoke is usually a T-shaped structure comprised of a short base that attaches to the A-microtubule of an axonemal outer microtubule doublet (MTD) of a cilium, an elongated stalk, a neck complex, and an orthogonal head structure that extends perpendicularly towards the inner sheath and the central pair (CP) microtubules. Groups of radial spokes (RSs) repeat along the MTD with regular spacing. In most organisms, each group of radial spokes is comprised of a triplet of spokes: RS1, RS2, and RS3. In some organisms (e.g. Chlamydomonas and Sarcophaga bullata), each group contains a doublet of radial spokes: RS1 and RS2, while RS3 is represented only as a stump (referred to as RS3S) attached to the A-microtubule but lacking the rest of the stalk structure and entirely lacking the head structure.

Axiom
annotated source: radial spoke
annotated property: definition
annotated target: Protein complex that links the outer microtubule doublet of a 9+2 type ciliary or flagellar axoneme with the sheath that surrounds the central pair of microtubules. Composed of a stalk that attaches to each doublet microtubule and a globular structure (spoke head) that projects toward the central pair of microtubules.
database_cross_reference: GOC:krc
database_cross_reference: ISBN:0124325653
database_cross_reference: PMID:22118931
database_cross_reference: PMID:25694453
database_cross_reference: PMID:34871179
database_cross_reference: PMID:9450971

Axiom
annotated source: radial spoke
annotated property: comment
annotated target: Radial spokes are involved in some types of beating motions of the cilium. The radial spoke is usually a T-shaped structure comprised of a short base that attaches to the A-microtubule of an axonemal outer microtubule doublet (MTD) of a cilium, an elongated stalk, a neck complex, and an orthogonal head structure that extends perpendicularly towards the inner sheath and the central pair (CP) microtubules. Groups of radial spokes (RSs) repeat along the MTD with regular spacing. In most organisms, each group of radial spokes is comprised of a triplet of spokes: RS1, RS2, and RS3. In some organisms (e.g. Chlamydomonas and Sarcophaga bullata), each group contains a doublet of radial spokes: RS1 and RS2, while RS3 is represented only as a stump (referred to as RS3S) attached to the A-microtubule but lacking the rest of the stalk structure and entirely lacking the head structure.
database_cross_reference: GOC:krc
database_cross_reference: PMID:25694453
database_cross_reference: PMID:34871179
database_cross_reference: PMID:9450971

cell activation
type: Class
subclass of: multicellular organismal process
definition: A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell.
term tracker item: https://github.com/geneontology/go-ontology/issues/24416
has_obo_namespace: biological_process
id: GO:0001775
in_subset: goslim pir

Axiom
annotated source: cell activation
annotated property: definition
annotated target: A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell.
database_cross_reference: GOC:mgi_curators

cytokine production
type: Class
subclass of: macromolecule biosynthetic process
subclass of: multicellular organismal process
definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
term tracker item: https://github.com/geneontology/go-ontology/issues/19116
has_alternative_id: GO:0042032
has_alternative_id: GO:0042089
has_alternative_id: GO:0042107
has_alternative_id: GO:0050663
has_narrow_synonym: cytokine biosynthetic process
has_narrow_synonym: cytokine metabolic process
has_narrow_synonym: cytokine secretion
has_narrow_synonym: interferon production
has_narrow_synonym: interferon secretion
has_narrow_synonym: interleukin production
has_narrow_synonym: interleukin secretion
has_obo_namespace: biological_process
id: GO:0001816
in_subset: gocheck do not annotate
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.

Axiom
annotated source: cytokine production
annotated property: definition
annotated target: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

Axiom
annotated source: cytokine production
annotated property: has_narrow_synonym
annotated target: interferon production
database_cross_reference: GOC:add
database_cross_reference: GOC:mah

Axiom
annotated source: cytokine production
annotated property: has_narrow_synonym
annotated target: interferon secretion
database_cross_reference: GOC:add
database_cross_reference: GOC:mah

Axiom
annotated source: cytokine production
annotated property: has_narrow_synonym
annotated target: interleukin production
database_cross_reference: GOC:add
database_cross_reference: GOC:mah
database_cross_reference: http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F

Axiom
annotated source: cytokine production
annotated property: has_narrow_synonym
annotated target: interleukin secretion
database_cross_reference: GOC:add
database_cross_reference: GOC:mah
database_cross_reference: http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F

nucleoside binding
type: Class
subclass of: binding
definition: Binding to a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
has_obo_namespace: molecular_function
id: GO:0001882
in_subset: goslim pir

Axiom
annotated source: nucleoside binding
annotated property: definition
annotated target: Binding to a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
database_cross_reference: GOC:hjd

cell killing
type: Class
subclass of: biological_process
definition: Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
has_obo_namespace: biological_process
has_related_synonym: necrosis
id: GO:0001906
in_subset: goslim pir

Axiom
annotated source: cell killing
annotated property: definition
annotated target: Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
database_cross_reference: GOC:add

photoreceptor inner segment
type: Class
subclass of: cellular anatomical structure
definition: The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
has_obo_namespace: cellular_component
id: GO:0001917
in_subset: goslim pir

Axiom
annotated source: photoreceptor inner segment
annotated property: definition
annotated target: The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
database_cross_reference: GOC:add
database_cross_reference: PMID:12019563

nucleobase binding
type: Class
subclass of: binding
definition: Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases.
has_obo_namespace: molecular_function
id: GO:0002054
in_subset: goslim pir

Axiom
annotated source: nucleobase binding
annotated property: definition
annotated target: Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases.
database_cross_reference: GOC:hjd

immune system process
type: Class
subclass of: biological_process
definition: Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
database_cross_reference: Wikipedia:Immune_system
has_obo_namespace: biological_process
id: GO:0002376
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501).

Axiom
annotated source: immune system process
annotated property: definition
annotated target: Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
database_cross_reference: GOC:add
database_cross_reference: GO_REF:0000022

molecular_function
type: Class
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
has_alternative_id: GO:0005554
has_exact_synonym: molecular function
has_obo_namespace: molecular_function
id: GO:0003674
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.

Axiom
annotated source: molecular_function
annotated property: definition
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
database_cross_reference: GOC:pdt

nucleic acid binding
type: Class
subclass of: binding
definition: Binding to a nucleic acid.
has_alternative_id: GO:0000496
has_narrow_synonym: base pairing
has_obo_namespace: molecular_function
id: GO:0003676
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: nucleic acid binding
annotated property: definition
annotated target: Binding to a nucleic acid.
database_cross_reference: GOC:jl

chromatin binding
type: Class
subclass of: binding
definition: Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
has_narrow_synonym: lamin/chromatin binding
has_narrow_synonym: microtubule/chromatin interaction
has_narrow_synonym: nuclear membrane vesicle binding to chromatin
has_obo_namespace: molecular_function
id: GO:0003682
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast

Axiom
annotated source: chromatin binding
annotated property: definition
annotated target: Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732
database_cross_reference: PMID:20404130

cytoskeletal motor activity
type: Class
subclass of: molecular_function
definition: Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force).
term tracker item: https://github.com/geneontology/go-ontology/issues/19590
term tracker item: https://github.com/geneontology/go-ontology/issues/21756
has_broad_synonym: motor activity
database_cross_reference: Reactome:R-HSA-1861595
has_obo_namespace: molecular_function
id: GO:0003774
in_subset: goslim candida
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: cytoskeletal motor activity
annotated property: definition
annotated target: Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force).
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw
database_cross_reference: PMID:11242086
database_cross_reference: PMID:29716949

Extension of pseudopodia by myosin-X in a PI3K dependent manner
type: Axiom
annotated source: cytoskeletal motor activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1861595

antigen binding
type: Class
subclass of: binding
definition: Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell.
term tracker item: https://github.com/geneontology/go-ontology/issues/25644
has_narrow_synonym: B cell receptor activity
has_narrow_synonym: MHC activity
has_narrow_synonym: major histocompatibility complex activity
has_narrow_synonym: major histocompatibility complex antigen display activity
has_narrow_synonym: opsonin activity
has_obo_namespace: molecular_function
has_related_synonym: antibody activity
id: GO:0003823
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: antigen binding
annotated property: definition
annotated target: Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732
database_cross_reference: ISBN:0721662544

catalytic activity
type: Class
subclass of: molecular_function
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
database_cross_reference: Wikipedia:Enzyme
has_exact_synonym: enzyme activity
has_obo_namespace: molecular_function
id: GO:0003824
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: catalytic activity
annotated property: definition
annotated target: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
database_cross_reference: GOC:vw
database_cross_reference: ISBN:0198506732

Axiom
annotated source: catalytic activity
annotated property: has_exact_synonym
annotated target: enzyme activity
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

glycogen debranching enzyme activity
type: Class
subclass of: catalytic activity
subclass of: Restriction
  on property: part of
  some values from: polysaccharide metabolic process
subclass of: Restriction
  on property: part of
  some values from: energy reserve metabolic process
definition: Catalysis of the cleavage of branch points in branched glycogen polymers.
has_obo_namespace: molecular_function
id: GO:0004133
in_subset: goslim pir

Axiom
annotated source: glycogen debranching enzyme activity
annotated property: definition
annotated target: Catalysis of the cleavage of branch points in branched glycogen polymers.
database_cross_reference: ISBN:0198506732

helicase activity
type: Class
subclass of: catalytic activity
subclass of: Restriction
  on property: has part
  some values from: hydrolase activity
definition: Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
term tracker item: https://github.com/geneontology/go-ontology/issues/21393
has_alternative_id: GO:0008026
database_cross_reference: Reactome:R-HSA-169461
database_cross_reference: Reactome:R-HSA-169468
database_cross_reference: Reactome:R-HSA-5686410
database_cross_reference: Reactome:R-HSA-5690996
has_exact_synonym: ATP-dependent helicase activity
has_obo_namespace: molecular_function
id: GO:0004386
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim pir
in_subset: goslim yeast
comment: Note that most helicases catalyze processive duplex unwinding.

Axiom
annotated source: helicase activity
annotated property: definition
annotated target: Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
database_cross_reference: GOC:jl

MCM8 mediated fork unwinding
type: Axiom
annotated source: helicase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-169461

MCM2-7 mediated fork unwinding
type: Axiom
annotated source: helicase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-169468

BLM mediates dissolution of double Holliday junction
type: Axiom
annotated source: helicase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5686410

ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA
type: Axiom
annotated source: helicase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5690996

monooxygenase activity
type: Class
subclass of: oxidoreductase activity
definition: Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
database_cross_reference: Reactome:R-HSA-143468
database_cross_reference: Reactome:R-HSA-156526
database_cross_reference: Reactome:R-HSA-211882
database_cross_reference: Reactome:R-HSA-211904
database_cross_reference: Reactome:R-HSA-211910
database_cross_reference: Reactome:R-HSA-211919
database_cross_reference: Reactome:R-HSA-211924
database_cross_reference: Reactome:R-HSA-211929
database_cross_reference: Reactome:R-HSA-211948
database_cross_reference: Reactome:R-HSA-211959
database_cross_reference: Reactome:R-HSA-211960
database_cross_reference: Reactome:R-HSA-211962
database_cross_reference: Reactome:R-HSA-211968
database_cross_reference: Reactome:R-HSA-211988
database_cross_reference: Reactome:R-HSA-211991
database_cross_reference: Reactome:R-HSA-212004
database_cross_reference: Reactome:R-HSA-212005
database_cross_reference: Reactome:R-HSA-213175
database_cross_reference: Reactome:R-HSA-215526
database_cross_reference: Reactome:R-HSA-2161795
database_cross_reference: Reactome:R-HSA-2161814
database_cross_reference: Reactome:R-HSA-2161890
database_cross_reference: Reactome:R-HSA-2161899
database_cross_reference: Reactome:R-HSA-2161940
database_cross_reference: Reactome:R-HSA-2162191
database_cross_reference: Reactome:R-HSA-217258
database_cross_reference: Reactome:R-HSA-5423647
database_cross_reference: Reactome:R-HSA-5423664
database_cross_reference: Reactome:R-HSA-5423672
database_cross_reference: Reactome:R-HSA-5423678
database_cross_reference: Reactome:R-HSA-5602242
database_cross_reference: Reactome:R-HSA-5602272
database_cross_reference: Reactome:R-HSA-5602295
database_cross_reference: Reactome:R-HSA-5605147
database_cross_reference: Reactome:R-HSA-5662662
database_cross_reference: Reactome:R-HSA-5662692
database_cross_reference: Reactome:R-HSA-5663050
database_cross_reference: Reactome:R-HSA-76354
database_cross_reference: Reactome:R-HSA-76373
database_cross_reference: Reactome:R-HSA-76386
database_cross_reference: Reactome:R-HSA-76397
database_cross_reference: Reactome:R-HSA-76416
database_cross_reference: Reactome:R-HSA-76426
database_cross_reference: Reactome:R-HSA-76434
database_cross_reference: Reactome:R-HSA-76456
database_cross_reference: Reactome:R-HSA-76466
database_cross_reference: Reactome:R-HSA-76472
database_cross_reference: Reactome:R-HSA-76475
database_cross_reference: Reactome:R-HSA-8865107
database_cross_reference: Reactome:R-HSA-9018874
database_cross_reference: Reactome:R-HSA-9027042
database_cross_reference: Reactome:R-HSA-9027043
database_cross_reference: Reactome:R-HSA-9027044
database_cross_reference: Reactome:R-HSA-9027302
database_cross_reference: Reactome:R-HSA-9027321
database_cross_reference: Reactome:R-HSA-9037761
database_cross_reference: Reactome:R-HSA-9749986
database_cross_reference: Reactome:R-HSA-9750016
database_cross_reference: Reactome:R-HSA-9753285
database_cross_reference: Reactome:R-HSA-9756138
database_cross_reference: Reactome:R-HSA-9756162
database_cross_reference: Reactome:R-HSA-9756169
database_cross_reference: Reactome:R-HSA-9756180
has_obo_namespace: molecular_function
has_related_synonym: hydroxylase activity
id: GO:0004497
in_subset: goslim pir

Arachidonic acid is epoxidated to 8,9/11,12/14,15-EET by CYP(5)
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2161899

Arachidonic acid is hydroxylated to 20-HETE by CYP(3)
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2161940

Unknown enzyme hydroxylates DMPhOH
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2162191

FMO2:FAD:Mg2+ S-oxidises MTZ
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-217258

CYP2A13 oxidises AFM1 to AFM1E
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5423647

CYP3A4,5 hydroxylates AFB1 to AFQ1
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5423664

CYP1A2, 3A4 oxidise AFB1 to AFNBO
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5423672

CYP1A2 hydroxylates AFB1 to AFM1
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5423678

Defective CYP2U1 does not omega-hydroxylate ARA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5602242

Defective CYP4F22 does not 20-hydroxylate TrXA3
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5602272

CYP4F22 20-hydroxylates TrXA3
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5602295

Defective CYP1B1 does not 4-hydroxylate EST17b
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5605147

Tyrosinase oxidises tyrosine to dopaquinone
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5662662

Dopa is oxidized to dopaquinone by TYR
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5662692

DHI and DHICA polymerize forming eumelanin
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5663050

Vinyl chloride is oxidized to 2-Chloroethylene oxide
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76354

N-hydroxylation of 4-aminobiphenyl
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76373

CYP1A2 S-demethylates 6MMP
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76386

Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI)
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76397

Benzene is hydroxylated to phenol
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76416

N-atom dealkylation of caffeine
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76426

Dehalogenation of carbon tetrachloride to form a free radical
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76434

O-atom dealkylation of dextromethorphan
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76456

CYP4A11 12-hydroxylates DDCX
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76466

Ethylene is oxidized to Ethylene oxide by CYP1A1
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76472

Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-76475

MICAL1 produces NADP+, H2O2
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8865107

CYP monooxygenates EPA to 18(S)-HpEPE
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9018874

CPY4 -oxidises 14(S)-HDHA to MaR-L1
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9027042

CYPs hydroxylate DHA to 14(R)-HDHA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9027043

CYP4 -oxidises 14(R)-HDHA to MaR-L2
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9027044

CYP2E1 oxidises 14(S)-HDHA to 14(S),21(R)-diHDHA and 14(S),21(S)-diHDHA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9027302

CYP2E1 oxidises 14(R)-HDHA to 14(R),21(R)-diHDHA and 14(R),21(S)-diHDHA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9027321

CYP1, CYP2 hydroxylate (N)PD1 to 22-OH-(N)PD1
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9037761

CYP2,3 cytochromes hydroxylate ST to 2,3-DHBA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9749986

CYP2,3 cytochromes hydroxylate ST to 2,5-DHBA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9750016

CYP2E1 monooxygenates APAP to NAPQI
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9753285

CYP3A4 monooxygenates ATVL to 2-OH-ATVL
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9756138

CYP3A4 monooxygenates ATV to 4-OH-ATV
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9756162

CYP3A4 monooxygenates ATV to 2-OH-ATV
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9756169

CYP3A4 monooxygenates ATVL to 4-OH-ATVL
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9756180

Axiom
annotated source: monooxygenase activity
annotated property: has_related_synonym
annotated target: hydroxylase activity
database_cross_reference: GOC:mah
database_cross_reference: GOC:vk

Axiom
annotated source: monooxygenase activity
annotated property: definition
annotated target: Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
database_cross_reference: ISBN:0198506732

MEOS oxidizes ethanol to acetaldehyde
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-143468

CYP1A2,3A4,3A5,2A13 oxidise AFB1 to AFXBO
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-156526

CYP3A7 can 6beta-hydroxylate testosterone
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211882

CYP4F12 18-hydroxylates ARA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211904

CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211910

CYP4F8 19-hydroxylates PGH2
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211919

CYP4B1 12-hydroxylates ARA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211924

CYP2C19 5-hydroxylates omeprazole
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211929

CYP3A4 can N-demethylate loperamide
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211948

CYP3A43 6b-hydroxylates TEST
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211959

CYP2U1 19-hydroxylates ARA
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211960

CYP4F11 16-hydroxylates 3OH-PALM
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211962

CYP2W1 oxidises INDOL
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211968

CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211988

Cyclophosphamide is 4-hydroxylated by CYP2B6
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-211991

CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-212004

CYP2F1 dehydrogenates 3-methylindole
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-212005

CYP3A4,5 oxidise AFB1 to AFXBO
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-213175

CYP4F3 20-hydroxylates LTB4
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-215526

Arachidonic acid is hydroxylated to 16/17/18-HETE by CYP(1)
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2161795

Arachidonic acid is hydroxylated to 19-HETE by CYP(2)
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2161814

Arachidonic acid is epoxidated to 5,6-EET by CYP(4)
type: Axiom
annotated source: monooxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2161890

transposase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element.
has_alternative_id: GO:0004804
has_narrow_synonym: P-element encoded transposase activity
has_obo_namespace: molecular_function
id: GO:0004803
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: transposase activity
annotated property: definition
annotated target: Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element.
database_cross_reference: GOC:bm
database_cross_reference: ISBN:0198506732

structural molecule activity
type: Class
subclass of: molecular_function
definition: The action of a molecule that contributes to the structural integrity of a complex.
term tracker item: https://github.com/geneontology/go-ontology/issues/24130
has_obo_namespace: molecular_function
id: GO:0005198
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: structural molecule activity
annotated property: definition
annotated target: The action of a molecule that contributes to the structural integrity of a complex.
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw

transporter activity
type: Class
subclass of: molecular_function
definition: Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells.
term tracker item: https://github.com/geneontology/go-ontology/issues/27621
has_alternative_id: GO:0005478
has_obo_namespace: molecular_function
has_related_synonym: carrier
id: GO:0005215
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.

Axiom
annotated source: transporter activity
annotated property: definition
annotated target: Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dgf

binding
type: Class
subclass of: molecular_function
definition: The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
database_cross_reference: Wikipedia:Binding_(molecular)
has_narrow_synonym: ligand
has_obo_namespace: molecular_function
id: GO:0005488
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: binding
annotated property: definition
annotated target: The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
database_cross_reference: GOC:ceb
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0198506732

steroid binding
type: Class
subclass of: lipid binding
definition: Binding to a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
has_obo_namespace: molecular_function
id: GO:0005496
in_subset: goslim pir

Axiom
annotated source: steroid binding
annotated property: definition
annotated target: Binding to a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732

protein binding
type: Class
subclass of: binding
definition: Binding to a protein.
has_alternative_id: GO:0001948
has_alternative_id: GO:0045308
database_cross_reference: Reactome:R-HSA-9866132
has_exact_synonym: protein amino acid binding
has_narrow_synonym: glycoprotein binding
has_obo_namespace: molecular_function
id: GO:0005515
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: protein binding
annotated property: definition
annotated target: Binding to a protein.
database_cross_reference: GOC:go_curators

Intermediate II binds CYC1, UQCRC1, UQCRC2, UQCRH
type: Axiom
annotated source: protein binding
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9866132

odorant binding
type: Class
subclass of: binding
definition: Binding to an odorant, any substance capable of stimulating the sense of smell.
has_obo_namespace: molecular_function
id: GO:0005549
in_subset: goslim pir

Axiom
annotated source: odorant binding
annotated property: definition
annotated target: Binding to an odorant, any substance capable of stimulating the sense of smell.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0721662544

cellular_component
type: Class
definition: A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
term tracker item: https://github.com/geneontology/go-ontology/issues/17729
has_alternative_id: GO:0008372
database_cross_reference: NIF_Subcellular:sao1337158144
has_exact_synonym: cell or subcellular entity
has_exact_synonym: cellular component
has_obo_namespace: cellular_component
has_related_synonym: subcellular entity
id: GO:0005575
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

Axiom
annotated source: cellular_component
annotated property: definition
annotated target: A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
database_cross_reference: GOC:pdt

Axiom
annotated source: cellular_component
annotated property: has_related_synonym
annotated target: subcellular entity
database_cross_reference: NIF_Subcellular:nlx_subcell_100315

extracellular region
type: Class
subclass of: cellular anatomical structure
definition: The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
database_cross_reference: Wikipedia:Extracellular
has_exact_synonym: extracellular
has_obo_namespace: cellular_component
id: GO:0005576
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast
comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.

Axiom
annotated source: extracellular region
annotated property: definition
annotated target: The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
database_cross_reference: GOC:go_curators

cell wall
type: Class
subclass of: external encapsulating structure
definition: The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
term tracker item: https://github.com/geneontology/go-ontology/issues/21669
database_cross_reference: Wikipedia:Cell_wall
has_obo_namespace: cellular_component
id: GO:0005618
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast
comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).

Axiom
annotated source: cell wall
annotated property: definition
annotated target: The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
database_cross_reference: GOC:giardia
database_cross_reference: ISBN:0198547684
database_cross_reference: PMID:15134259
database_cross_reference: Wikipedia:Microbial_cyst

nucleus
type: Class
subclass of: intracellular membrane-bounded organelle
definition: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
database_cross_reference: NIF_Subcellular:sao1702920020
database_cross_reference: Wikipedia:Cell_nucleus
has_exact_synonym: cell nucleus
has_narrow_synonym: horsetail nucleus
has_obo_namespace: cellular_component
id: GO:0005634
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast

Axiom
annotated source: nucleus
annotated property: definition
annotated target: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
database_cross_reference: GOC:go_curators

Axiom
annotated source: nucleus
annotated property: has_narrow_synonym
annotated target: horsetail nucleus
database_cross_reference: GOC:al
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw
database_cross_reference: PMID:15030757

nuclear pore
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: A protein complex providing a discrete opening in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
has_alternative_id: GO:0005644
database_cross_reference: NIF_Subcellular:sao220861693
database_cross_reference: Wikipedia:Nuclear_pore
has_exact_synonym: NPC
has_exact_synonym: nuclear pore complex
has_exact_synonym: nucleopore
has_narrow_synonym: nuclear pore membrane protein
has_obo_namespace: cellular_component
id: GO:0005643
in_subset: goslim pir

Axiom
annotated source: nuclear pore
annotated property: definition
annotated target: A protein complex providing a discrete opening in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
database_cross_reference: ISBN:0198547684

Axiom
annotated source: nuclear pore
annotated property: has_exact_synonym
annotated target: nucleopore
database_cross_reference: GOC:al
database_cross_reference: PMID:7603572

DNA replication factor C complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.
has_exact_synonym: RFC complex
has_exact_synonym: activator 1 complex
has_obo_namespace: cellular_component
id: GO:0005663
in_subset: goslim pir

Axiom
annotated source: DNA replication factor C complex
annotated property: definition
annotated target: A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.
database_cross_reference: PMID:14614842
database_cross_reference: PMID:14646196
database_cross_reference: PMID:16172520

transcription regulator complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
created by: jl
creation date: 2013-08-28T12:11:37Z
has_alternative_id: GO:0044797
has_alternative_id: GO:0044798
has_obo_namespace: cellular_component
has_related_synonym: cytoplasmic transcription factor complex
has_related_synonym: nuclear transcription factor complex
has_related_synonym: transcription factor complex
id: GO:0005667
in_subset: goslim pir

Axiom
annotated source: transcription regulator complex
annotated property: definition
annotated target: A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
database_cross_reference: GOC:jl

spliceosomal complex
type: Class
subclass of: ribonucleoprotein complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.
has_broad_synonym: spliceosome
database_cross_reference: Wikipedia:Spliceosome
has_exact_synonym: spliceosome complex
has_obo_namespace: cellular_component
id: GO:0005681
in_subset: goslim pir

Axiom
annotated source: spliceosomal complex
annotated property: definition
annotated target: Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.
database_cross_reference: GOC:editors
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0198547684
database_cross_reference: PMID:19239890

chromosome
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
database_cross_reference: Wikipedia:Chromosome
has_narrow_synonym: interphase chromosome
has_narrow_synonym: prophase chromosome
has_obo_namespace: cellular_component
has_related_synonym: chromatid
id: GO:0005694
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast
comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.

Axiom
annotated source: chromosome
annotated property: definition
annotated target: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
database_cross_reference: ISBN:0198547684

telomerase holoenzyme complex
type: Class
subclass of: ribonucleoprotein complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits.
has_obo_namespace: cellular_component
id: GO:0005697
in_subset: goslim pir

Axiom
annotated source: telomerase holoenzyme complex
annotated property: definition
annotated target: Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits.
database_cross_reference: PMID:11884619

nucleolus
type: Class
subclass of: intracellular non-membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
database_cross_reference: NIF_Subcellular:sao1820400233
database_cross_reference: Wikipedia:Nucleolus
has_obo_namespace: cellular_component
id: GO:0005730
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast

Axiom
annotated source: nucleolus
annotated property: definition
annotated target: A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
database_cross_reference: ISBN:0198506732

sno(s)RNA-containing ribonucleoprotein complex
type: Class
subclass of: ribonucleoprotein complex
definition: A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family and associated proteins. Many are involved in a step of processing of rRNA molecules: cleavage, 2'-O-methylation, or pseudouridylation, but other RNA types can be targets as well. The majority fall into one of two classes, box C/D type or box H/ACA type, which are conserved across eukaryotes and archaea. Other members include the telomerase RNA and the ribonuclease MRP RNA.
term tracker item: https://github.com/geneontology/go-ontology/issues/20416
has_narrow_synonym: sRNP
has_narrow_synonym: small nucleolar ribonucleoprotein
has_narrow_synonym: small nucleolar ribonucleoprotein complex
has_narrow_synonym: small ribonucleoprotein
has_narrow_synonym: small ribonucleoprotein protein complex
has_narrow_synonym: snoRNP
has_obo_namespace: cellular_component
id: GO:0005732
in_subset: goslim pir
comment: Note that 'nucleolar' in the name acronym 'snoRNA' is part of the RNA family designation 'small nucleolar', and does not reflect the location of the complex. Both box C/D type and box H/ACA RNAs are found in Archaea (where they are referred to as sRNAs) as well as in Eukaryota. In eukaryotes, box H/ACA RNAs are found in both nucleolar-localized snoRNP complexes and in Cajal body-localized scaRNP complexes.

Axiom
annotated source: sno(s)RNA-containing ribonucleoprotein complex
annotated property: definition
annotated target: A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family and associated proteins. Many are involved in a step of processing of rRNA molecules: cleavage, 2'-O-methylation, or pseudouridylation, but other RNA types can be targets as well. The majority fall into one of two classes, box C/D type or box H/ACA type, which are conserved across eukaryotes and archaea. Other members include the telomerase RNA and the ribonuclease MRP RNA.
database_cross_reference: GOC:krc
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0879695897
database_cross_reference: PMID:17284456

cytoplasm
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
term tracker item: https://github.com/geneontology/go-ontology/issues/23023
database_cross_reference: Wikipedia:Cytoplasm
has_obo_namespace: cellular_component
id: GO:0005737
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: cytoplasm
annotated property: definition
annotated target: The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
database_cross_reference: ISBN:0198547684

mitochondrion
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
database_cross_reference: NIF_Subcellular:sao1860313010
database_cross_reference: Wikipedia:Mitochondrion
has_exact_synonym: mitochondria
has_obo_namespace: cellular_component
id: GO:0005739
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)

Axiom
annotated source: mitochondrion
annotated property: definition
annotated target: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
database_cross_reference: GOC:giardia
database_cross_reference: ISBN:0198506732

TIM23 mitochondrial import inner membrane translocase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: mitochondrion
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor.
term tracker item: https://github.com/geneontology/go-ontology/issues/21246
has_broad_synonym: mitochondrial inner membrane translocase complex
has_exact_synonym: Tim23 complex
has_exact_synonym: mitochondrial inner membrane pre-sequence translocase complex
has_exact_synonym: mitochondrial inner membrane presequence translocase complex
has_obo_namespace: cellular_component
id: GO:0005744
in_subset: goslim pir
comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'.

Axiom
annotated source: TIM23 mitochondrial import inner membrane translocase complex
annotated property: definition
annotated target: The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor.
database_cross_reference: PMID:27554484
database_cross_reference: PMID:8851659

endosome
type: Class
subclass of: vesicle
subclass of: intracellular membrane-bounded organelle
definition: A vacuole to which materials ingested by endocytosis are delivered.
database_cross_reference: NIF_Subcellular:sao1720343330
database_cross_reference: Wikipedia:Endosome
has_obo_namespace: cellular_component
id: GO:0005768
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: endosome
annotated property: definition
annotated target: A vacuole to which materials ingested by endocytosis are delivered.
database_cross_reference: ISBN:0198506732
database_cross_reference: PMID:19696797

vacuole
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
database_cross_reference: Wikipedia:Vacuole
has_obo_namespace: cellular_component
has_related_synonym: vacuolar carboxypeptidase Y
id: GO:0005773
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast

Axiom
annotated source: vacuole
annotated property: definition
annotated target: A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
database_cross_reference: GOC:mtg_sensu
database_cross_reference: ISBN:0198506732

endoplasmic reticulum
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
database_cross_reference: NIF_Subcellular:sao1036339110
database_cross_reference: Wikipedia:Endoplasmic_reticulum
has_exact_synonym: ER
has_obo_namespace: cellular_component
id: GO:0005783
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast

Axiom
annotated source: endoplasmic reticulum
annotated property: definition
annotated target: The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
database_cross_reference: ISBN:0198506732

Golgi apparatus
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
has_broad_synonym: Golgi
database_cross_reference: NIF_Subcellular:sao451912436
database_cross_reference: Wikipedia:Golgi_apparatus
has_exact_synonym: Golgi complex
has_narrow_synonym: Golgi ribbon
has_obo_namespace: cellular_component
id: GO:0005794
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.

Axiom
annotated source: Golgi apparatus
annotated property: definition
annotated target: A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
database_cross_reference: ISBN:0198506732

centrosome
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cytoskeleton
subclass of: Restriction
  on property: has part
  some values from: intracellular non-membrane-bounded organelle
definition: A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
database_cross_reference: Wikipedia:Centrosome
has_obo_namespace: cellular_component
id: GO:0005813
in_subset: goslim pir

Axiom
annotated source: centrosome
annotated property: definition
annotated target: A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0198547684

fatty acid synthase complex
type: Class
subclass of: protein-containing complex
definition: A multienzyme complex that catalyses the synthesis of fatty acids from acetyl CoA.
has_alternative_id: GO:0031373
has_alternative_id: GO:0031374
database_cross_reference: Wikipedia:Fatty_acid_synthetase_complex
has_exact_synonym: FAS complex
has_exact_synonym: cytosolic FAS complex
has_exact_synonym: cytosolic fatty acid synthase complex
has_exact_synonym: cytosolic type I FAS complex
has_exact_synonym: cytosolic type I fatty acid synthase complex
has_exact_synonym: fatty acid synthetase complex
has_obo_namespace: cellular_component
has_related_synonym: holo-[acyl-carrier-protein] synthase complex
id: GO:0005835
in_subset: goslim pir

Axiom
annotated source: fatty acid synthase complex
annotated property: definition
annotated target: A multienzyme complex that catalyses the synthesis of fatty acids from acetyl CoA.
database_cross_reference: GOC:pde
database_cross_reference: GOC:sgd_curators
database_cross_reference: ISBN:0716746840

ribosome
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
has_alternative_id: GO:0033279
database_cross_reference: NIF_Subcellular:sao1429207766
database_cross_reference: Wikipedia:Ribosome
has_narrow_synonym: free ribosome
has_narrow_synonym: membrane bound ribosome
has_obo_namespace: cellular_component
has_related_synonym: ribosomal RNA
id: GO:0005840
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: ribosome
annotated property: definition
annotated target: An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
database_cross_reference: ISBN:0198506732

Axiom
annotated source: ribosome
annotated property: has_narrow_synonym
annotated target: free ribosome
database_cross_reference: NIF_Subcellular:sao1139385046

Axiom
annotated source: ribosome
annotated property: has_narrow_synonym
annotated target: membrane bound ribosome
database_cross_reference: NIF_Subcellular:sao1291545653

mRNA cleavage factor complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
has_obo_namespace: cellular_component
id: GO:0005849
in_subset: goslim pir

Axiom
annotated source: mRNA cleavage factor complex
annotated property: definition
annotated target: Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
database_cross_reference: GOC:mah
database_cross_reference: PMID:10357856

cytoskeleton
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
database_cross_reference: Wikipedia:Cytoskeleton
has_obo_namespace: cellular_component
id: GO:0005856
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: cytoskeleton
annotated property: definition
annotated target: A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
database_cross_reference: GOC:mah
database_cross_reference: PMID:16959967
database_cross_reference: PMID:27419875

voltage-gated calcium channel complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.
has_exact_synonym: voltage gated calcium channel complex
has_exact_synonym: voltage-dependent calcium channel complex
has_exact_synonym: voltage-sensitive calcium channel complex
has_obo_namespace: cellular_component
id: GO:0005891
in_subset: goslim pir

Axiom
annotated source: voltage-gated calcium channel complex
annotated property: definition
annotated target: A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.
database_cross_reference: GOC:mah

microvillus
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
database_cross_reference: NIF_Subcellular:sao671419673
database_cross_reference: Wikipedia:Microvillus
has_obo_namespace: cellular_component
has_related_synonym: microvilli
id: GO:0005902
in_subset: goslim pir
comment: Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta.

Axiom
annotated source: microvillus
annotated property: definition
annotated target: Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
database_cross_reference: ISBN:0815316194

Axiom
annotated source: microvillus
annotated property: has_related_synonym
annotated target: microvilli
database_cross_reference: NIF_Subcellular:sao671419673

brush border
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: has part
  some values from: microvillus
definition: The dense covering of microvilli on the apical surface of an epithelial cell in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
database_cross_reference: Wikipedia:Brush_border
has_obo_namespace: cellular_component
id: GO:0005903
in_subset: goslim pir

Axiom
annotated source: brush border
annotated property: definition
annotated target: The dense covering of microvilli on the apical surface of an epithelial cell in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
database_cross_reference: GOC:sl
database_cross_reference: ISBN:0815316194

cilium
type: Class
subclass of: cell projection
subclass of: organelle
subclass of: Restriction
  on property: has part
  some values from: membrane
subclass of: Restriction
  on property: has part
  some values from: intraciliary transport particle
definition: A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
has_alternative_id: GO:0072372
database_cross_reference: FMA:67181
database_cross_reference: NIF_Subcellular:sao787716553
database_cross_reference: Wikipedia:Cilium
has_exact_synonym: eukaryotic flagellum
has_exact_synonym: microtubule-based flagellum
has_narrow_synonym: primary cilium
has_obo_namespace: cellular_component
has_related_synonym: flagellum
id: GO:0005929
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.

Axiom
annotated source: cilium
annotated property: definition
annotated target: A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
database_cross_reference: GOC:cilia
database_cross_reference: GOC:curators
database_cross_reference: GOC:kmv
database_cross_reference: GOC:vw
database_cross_reference: ISBN:0198547684
database_cross_reference: PMID:16824949
database_cross_reference: PMID:17009929
database_cross_reference: PMID:20144998

axoneme
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
subclass of: Restriction
  on property: part of
  some values from: cytoskeleton
subclass of: Restriction
  on property: part of
  some values from: cilium
definition: The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
has_alternative_id: GO:0035085
has_alternative_id: GO:0035086
database_cross_reference: Wikipedia:Axoneme
has_exact_synonym: ciliary axoneme
has_exact_synonym: cilium axoneme
has_exact_synonym: flagellar axoneme
has_exact_synonym: flagellum axoneme
has_obo_namespace: cellular_component
id: GO:0005930
in_subset: goslim pir
comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane.

Axiom
annotated source: axoneme
annotated property: definition
annotated target: The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
database_cross_reference: GOC:bf
database_cross_reference: GOC:cilia
database_cross_reference: ISBN:0198547684

cellular bud
type: Class
subclass of: cellular anatomical structure
definition: A protuberance from a cell of an organism that reproduces by budding, which will grow larger and become a separate daughter cell after nuclear division, cytokinesis, and cell wall formation (when appropriate). The daughter cell may completely separate from the mother cell, or the mother and daughter cells may remain associated.
has_obo_namespace: cellular_component
id: GO:0005933
in_subset: goslim candida
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: cellular bud
annotated property: definition
annotated target: A protuberance from a cell of an organism that reproduces by budding, which will grow larger and become a separate daughter cell after nuclear division, cytokinesis, and cell wall formation (when appropriate). The daughter cell may completely separate from the mother cell, or the mother and daughter cells may remain associated.
database_cross_reference: GOC:sgd_curators

mating projection
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: The projection formed by unicellular fungi in response to mating pheromone.
has_narrow_synonym: conjugation tube
has_narrow_synonym: shmoo
has_obo_namespace: cellular_component
id: GO:0005937
in_subset: goslim pir

Axiom
annotated source: mating projection
annotated property: definition
annotated target: The projection formed by unicellular fungi in response to mating pheromone.
database_cross_reference: GOC:mcc

phosphatidylinositol 3-kinase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too.
has_exact_synonym: 1-phosphatidylinositol 3-kinase complex
has_exact_synonym: PI3K complex
has_exact_synonym: phosphoinositide 3-kinase complex
has_narrow_synonym: PI3-kinase p85-subunit alpha- PI3-kinase p110 complex
has_narrow_synonym: PIK3C3-PIK3R4 complex
has_narrow_synonym: PIK3CA-PIK3R1 complex
has_obo_namespace: cellular_component
id: GO:0005942
in_subset: goslim pir
comment: For discussion of membrane association, please see https://sourceforge.net/p/geneontology/ontology-requests/11559/

Axiom
annotated source: phosphatidylinositol 3-kinase complex
annotated property: definition
annotated target: A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too.
database_cross_reference: GOC:bf
database_cross_reference: PMID:24587488

Axiom
annotated source: phosphatidylinositol 3-kinase complex
annotated property: has_narrow_synonym
annotated target: PI3-kinase p85-subunit alpha- PI3-kinase p110 complex
database_cross_reference: CORUM:2575

Axiom
annotated source: phosphatidylinositol 3-kinase complex
annotated property: has_narrow_synonym
annotated target: PIK3C3-PIK3R4 complex
database_cross_reference: CORUM:429

Axiom
annotated source: phosphatidylinositol 3-kinase complex
annotated property: has_narrow_synonym
annotated target: PIK3CA-PIK3R1 complex
database_cross_reference: CORUM:439

glycine cleavage complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.
term tracker item: https://github.com/geneontology/go-ontology/issues/28865
has_alternative_id: GO:0005961
has_alternative_id: GO:0070015
database_cross_reference: Wikipedia:Glycine_decarboxylase_complex
has_exact_synonym: glycine cleavage system
has_exact_synonym: glycine decarboxylase complex
has_exact_synonym: glycine dehydrogenase (decarboxylating) complex
has_exact_synonym: glycine synthase complex
has_obo_namespace: cellular_component
has_related_synonym: glycine dehydrogenase complex (decarboxylating)
id: GO:0005960
in_subset: goslim pir

Axiom
annotated source: glycine cleavage complex
annotated property: definition
annotated target: A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.
database_cross_reference: GOC:mah
database_cross_reference: MetaCyc:GCVMULTI-CPLX

carbohydrate metabolic process
type: Class
subclass of: primary metabolic process
definition: The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
term tracker item: https://github.com/geneontology/go-ontology/issues/22880
created by: jl
creation date: 2012-10-23T15:40:34Z
has_alternative_id: GO:0044261
has_alternative_id: GO:0044723
database_cross_reference: Wikipedia:Carbohydrate_metabolism
has_exact_synonym: carbohydrate metabolism
has_obo_namespace: biological_process
id: GO:0005975
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: carbohydrate metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0198506732

polysaccharide metabolic process
type: Class
subclass of: carbohydrate metabolic process
subclass of: macromolecule metabolic process
definition: The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
has_alternative_id: GO:0044263
has_exact_synonym: polysaccharide metabolism
has_narrow_synonym: glycan metabolic process
has_narrow_synonym: glycan metabolism
has_narrow_synonym: multicellular organismal polysaccharide metabolic process
has_obo_namespace: biological_process
id: GO:0005976
in_subset: goslim pir

Axiom
annotated source: polysaccharide metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
database_cross_reference: ISBN:0198547684

alcohol metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom.
has_exact_synonym: alcohol metabolism
has_obo_namespace: biological_process
id: GO:0006066
in_subset: goslim drosophila
in_subset: goslim pir

Axiom
annotated source: alcohol metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom.
database_cross_reference: ISBN:0198506732

cellular aldehyde metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells.
has_exact_synonym: aldehyde metabolism
has_exact_synonym: alkanal metabolic process
has_exact_synonym: alkanal metabolism
has_obo_namespace: biological_process
id: GO:0006081
in_subset: goslim pir

Axiom
annotated source: cellular aldehyde metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells.
database_cross_reference: GOC:go_curators
database_cross_reference: ISBN:0198506732

organic acid metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
has_exact_synonym: organic acid metabolism
has_obo_namespace: biological_process
id: GO:0006082
in_subset: goslim pir

Axiom
annotated source: organic acid metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
database_cross_reference: ISBN:0198506732

generation of precursor metabolites and energy
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
has_broad_synonym: energy pathways
has_obo_namespace: biological_process
has_related_synonym: intermediary metabolism
has_related_synonym: metabolic energy generation
id: GO:0006091
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: generation of precursor metabolites and energy
annotated property: definition
annotated target: The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
database_cross_reference: GOC:jl

Axiom
annotated source: generation of precursor metabolites and energy
annotated property: has_related_synonym
annotated target: intermediary metabolism
database_cross_reference: GOC:mah

energy reserve metabolic process
type: Class
subclass of: generation of precursor metabolites and energy
definition: The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
has_exact_synonym: energy reserve metabolism
has_obo_namespace: biological_process
id: GO:0006112
in_subset: goslim pir

Axiom
annotated source: energy reserve metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
database_cross_reference: GOC:mah

fermentation
type: Class
subclass of: generation of precursor metabolites and energy
definition: The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
database_cross_reference: MetaCyc:FERMENTATION-PWY
database_cross_reference: Wikipedia:Fermentation_(biochemistry)
has_obo_namespace: biological_process
id: GO:0006113
in_subset: goslim pir

Axiom
annotated source: fermentation
annotated property: definition
annotated target: The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
database_cross_reference: GOC:curators
database_cross_reference: ISBN:0201090910
database_cross_reference: MetaCyc:Fermentation

oxidative phosphorylation
type: Class
subclass of: cellular respiration
subclass of: Restriction
  on property: has part
  some values from: nucleotide metabolic process
definition: The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
database_cross_reference: Wikipedia:Oxidative_phosphorylation
has_exact_synonym: respiratory-chain phosphorylation
has_obo_namespace: biological_process
id: GO:0006119
in_subset: goslim pir

Axiom
annotated source: oxidative phosphorylation
annotated property: definition
annotated target: The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
database_cross_reference: ISBN:0198506732
database_cross_reference: ISBN:0471331309

nucleobase-containing compound metabolic process
type: Class
subclass of: primary metabolic process
definition: Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
has_alternative_id: GO:0055134
has_exact_synonym: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
has_exact_synonym: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
has_exact_synonym: nucleobase, nucleoside, nucleotide and nucleic acid metabolism
has_obo_namespace: biological_process
has_related_synonym: nucleobase, nucleoside and nucleotide metabolic process
has_related_synonym: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
id: GO:0006139
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: nucleobase-containing compound metabolic process
annotated property: definition
annotated target: Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
database_cross_reference: GOC:ai

Axiom
annotated source: nucleobase-containing compound metabolic process
annotated property: has_related_synonym
annotated target: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

DNA metabolic process
type: Class
subclass of: nucleobase-containing compound metabolic process
subclass of: macromolecule metabolic process
definition: Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
has_alternative_id: GO:0055132
has_exact_synonym: DNA metabolism
has_exact_synonym: cellular DNA metabolism
has_obo_namespace: biological_process
id: GO:0006259
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: DNA metabolic process
annotated property: definition
annotated target: Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
database_cross_reference: ISBN:0198506732

DNA replication
type: Class
subclass of: DNA metabolic process
subclass of: Restriction
  on property: has part
  some values from: DNA metabolic process
subclass of: Restriction
  on property: has part
  some values from: macromolecule biosynthetic process
definition: The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
term tracker item: https://github.com/geneontology/go-ontology/issues/10596
has_alternative_id: GO:0055133
database_cross_reference: Wikipedia:DNA_replication
has_obo_namespace: biological_process
id: GO:0006260
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim yeast
comment: DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.

Axiom
annotated source: DNA replication
annotated property: definition
annotated target: The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
database_cross_reference: GOC:mah

DNA ligation
type: Class
subclass of: DNA metabolic process
definition: The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
has_obo_namespace: biological_process
id: GO:0006266
in_subset: goslim pir

Axiom
annotated source: DNA ligation
annotated property: definition
annotated target: The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
database_cross_reference: ISBN:0815316194

plasmid maintenance
type: Class
subclass of: biological_process
definition: The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
has_obo_namespace: biological_process
id: GO:0006276
in_subset: goslim pir

Axiom
annotated source: plasmid maintenance
annotated property: definition
annotated target: The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
database_cross_reference: GOC:ai

DNA repair
type: Class
subclass of: DNA metabolic process
subclass of: response to stimulus
definition: The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
database_cross_reference: Wikipedia:DNA_repair
has_obo_namespace: biological_process
id: GO:0006281
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: DNA repair
annotated property: definition
annotated target: The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
database_cross_reference: PMID:11563486

DNA modification
type: Class
subclass of: DNA metabolic process
subclass of: macromolecule modification
definition: The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
has_obo_namespace: biological_process
id: GO:0006304
in_subset: goslim pir

Axiom
annotated source: DNA modification
annotated property: definition
annotated target: The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
database_cross_reference: GOC:jl
database_cross_reference: GOC:ma

DNA-templated transcription
type: Class
subclass of: macromolecule biosynthetic process
subclass of: RNA metabolic process
subclass of: Restriction
  on property: part of
  some values from: macromolecule biosynthetic process
definition: The synthesis of an RNA transcript from a DNA template.
term tracker item: https://github.com/geneontology/go-ontology/issues/14854
term tracker item: https://github.com/geneontology/go-ontology/issues/16737
term tracker item: https://github.com/geneontology/go-ontology/issues/22258
term tracker item: https://github.com/geneontology/go-ontology/issues/22555
has_alternative_id: GO:0001121
has_alternative_id: GO:0006350
has_alternative_id: GO:0061018
has_alternative_id: GO:0061022
has_broad_synonym: cellular transcription
has_broad_synonym: transcription
database_cross_reference: Wikipedia:Transcription_(genetics)
has_exact_synonym: DNA-dependent transcription
has_exact_synonym: transcription, DNA-dependent
has_exact_synonym: transcription, DNA-templated
has_narrow_synonym: bacterial transcription
has_narrow_synonym: transcription from bacterial-type RNA polymerase promoter
has_obo_namespace: biological_process
id: GO:0006351
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: DNA-templated transcription
annotated property: definition
annotated target: The synthesis of an RNA transcript from a DNA template.
database_cross_reference: GOC:jl
database_cross_reference: GOC:txnOH

Axiom
annotated source: DNA-templated transcription
annotated property: has_exact_synonym
annotated target: transcription, DNA-dependent
database_cross_reference: GOC:txnOH

DNA-templated transcription elongation
type: Class
subclass of: macromolecule biosynthetic process
subclass of: RNA metabolic process
subclass of: Restriction
  on property: part of
  some values from: DNA-templated transcription
definition: The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
term tracker item: https://github.com/geneontology/go-ontology/issues/23386
has_alternative_id: GO:0001124
has_broad_synonym: RNA elongation
has_exact_synonym: DNA-dependent transcription, elongation
has_exact_synonym: DNA-templated transcription, elongation
has_exact_synonym: transcription elongation, DNA-dependent
has_exact_synonym: transcriptional elongation, DNA-dependent
has_narrow_synonym: RNA elongation from bacterial-type RNA polymerase promoter
has_narrow_synonym: transcription elongation from bacterial-type RNA polymerase promoter
has_obo_namespace: biological_process
id: GO:0006354
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: DNA-templated transcription elongation
annotated property: definition
annotated target: The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
database_cross_reference: GOC:mah
database_cross_reference: GOC:txnOH
database_cross_reference: PMID:15020047
database_cross_reference: PMID:18280161

Axiom
annotated source: DNA-templated transcription elongation
annotated property: has_exact_synonym
annotated target: DNA-dependent transcription, elongation
database_cross_reference: GOC:txnOH

Axiom
annotated source: DNA-templated transcription elongation
annotated property: has_exact_synonym
annotated target: transcription elongation, DNA-dependent
database_cross_reference: GOC:jh2

RNA processing
type: Class
subclass of: primary metabolic process
subclass of: Restriction
  on property: part of
  some values from: macromolecule biosynthetic process
subclass of: Restriction
  on property: part of
  some values from: RNA metabolic process
definition: Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
has_alternative_id: GO:0006394
database_cross_reference: Wikipedia:Post-transcriptional_modification
has_obo_namespace: biological_process
id: GO:0006396
in_subset: goslim drosophila
in_subset: goslim pir

Axiom
annotated source: RNA processing
annotated property: definition
annotated target: Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
database_cross_reference: GOC:mah

translation
type: Class
subclass of: macromolecule biosynthetic process
subclass of: protein metabolic process
subclass of: Restriction
  on property: has part
  some values from: macromolecule biosynthetic process
definition: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
has_alternative_id: GO:0006416
has_alternative_id: GO:0006453
has_alternative_id: GO:0043037
database_cross_reference: Wikipedia:Translation_(genetics)
has_exact_synonym: protein anabolism
has_exact_synonym: protein biosynthesis
has_exact_synonym: protein biosynthetic process
has_exact_synonym: protein formation
has_exact_synonym: protein synthesis
has_exact_synonym: protein translation
has_obo_namespace: biological_process
id: GO:0006412
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: translation
annotated property: definition
annotated target: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
database_cross_reference: GOC:go_curators

protein folding
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: part of
  some values from: protein maturation
definition: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
term tracker item: https://github.com/geneontology/go-ontology/issues/25673
has_alternative_id: GO:0007022
has_alternative_id: GO:0007024
has_alternative_id: GO:0007025
database_cross_reference: Wikipedia:Protein_folding
has_narrow_synonym: alpha-tubulin folding
has_narrow_synonym: beta-tubulin folding
has_narrow_synonym: chaperonin-mediated tubulin folding
has_obo_namespace: biological_process
has_related_synonym: chaperone activity
has_related_synonym: chaperonin ATPase activity
has_related_synonym: co-chaperone activity
has_related_synonym: co-chaperonin activity
has_related_synonym: glycoprotein-specific chaperone activity
has_related_synonym: non-chaperonin molecular chaperone ATPase activity
has_related_synonym: protein complex assembly, multichaperone pathway
id: GO:0006457
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: protein folding
annotated property: definition
annotated target: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:rb

Axiom
annotated source: protein folding
annotated property: has_narrow_synonym
annotated target: alpha-tubulin folding
database_cross_reference: GOC:mah

Axiom
annotated source: protein folding
annotated property: has_narrow_synonym
annotated target: beta-tubulin folding
database_cross_reference: GOC:mah

Axiom
annotated source: protein folding
annotated property: has_narrow_synonym
annotated target: chaperonin-mediated tubulin folding
database_cross_reference: GOC:mah

proteolysis
type: Class
subclass of: protein metabolic process
definition: The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
database_cross_reference: Wikipedia:Proteolysis
has_exact_synonym: peptidolysis
has_narrow_synonym: ATP-dependent proteolysis
has_obo_namespace: biological_process
id: GO:0006508
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
comment: This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing.

Axiom
annotated source: proteolysis
annotated property: definition
annotated target: The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
database_cross_reference: GOC:bf
database_cross_reference: GOC:mah

Axiom
annotated source: proteolysis
annotated property: has_narrow_synonym
annotated target: ATP-dependent proteolysis
database_cross_reference: GOC:mah

peptide metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
has_exact_synonym: peptide metabolism
has_obo_namespace: biological_process
id: GO:0006518
in_subset: goslim pir

Axiom
annotated source: peptide metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
database_cross_reference: GOC:go_curators

amino acid metabolic process
type: Class
subclass of: primary metabolic process
definition: The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
term tracker item: https://github.com/geneontology/go-ontology/issues/17904
has_alternative_id: GO:0006519
has_exact_synonym: cellular amino acid metabolic process
has_exact_synonym: cellular amino acid metabolism
has_obo_namespace: biological_process
has_related_synonym: amino acid and derivative metabolism
has_related_synonym: cellular amino acid and derivative metabolic process
id: GO:0006520
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: amino acid metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
database_cross_reference: ISBN:0198506732

lipid metabolic process
type: Class
subclass of: primary metabolic process
definition: The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
database_cross_reference: Wikipedia:Lipid_metabolism
has_exact_synonym: lipid metabolism
has_obo_namespace: biological_process
id: GO:0006629
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: lipid metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
database_cross_reference: GOC:ma

glycerol ether metabolic process
type: Class
subclass of: ether metabolic process
definition: The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
has_exact_synonym: glycerol ether metabolism
has_obo_namespace: biological_process
id: GO:0006662
in_subset: goslim pir

Axiom
annotated source: glycerol ether metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
database_cross_reference: GOC:ai
database_cross_reference: ISBN:0198506732

one-carbon metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
has_alternative_id: GO:0019753
has_alternative_id: GO:0019754
database_cross_reference: UM-BBD_pathwayID:C1cyc
has_exact_synonym: one carbon metabolic process
has_exact_synonym: one carbon metabolism
has_exact_synonym: one-carbon metabolism
has_exact_synonym: one-carbon transfer metabolic process
has_exact_synonym: one-carbon transfer metabolism
has_obo_namespace: biological_process
id: GO:0006730
in_subset: goslim pir

Axiom
annotated source: one-carbon metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
database_cross_reference: GOC:hjd
database_cross_reference: GOC:mah
database_cross_reference: GOC:pde

Axiom
annotated source: one-carbon metabolic process
annotated property: has_exact_synonym
annotated target: one carbon metabolic process
database_cross_reference: GOC:mah

Axiom
annotated source: one-carbon metabolic process
annotated property: has_exact_synonym
annotated target: one carbon metabolism
database_cross_reference: GOC:mah

Axiom
annotated source: one-carbon metabolic process
annotated property: has_exact_synonym
annotated target: one-carbon metabolism
database_cross_reference: GOC:mah

Axiom
annotated source: one-carbon metabolic process
annotated property: has_exact_synonym
annotated target: one-carbon transfer metabolic process
database_cross_reference: GOC:mah

Axiom
annotated source: one-carbon metabolic process
annotated property: has_exact_synonym
annotated target: one-carbon transfer metabolism
database_cross_reference: GOC:mah

vitamin metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.
has_exact_synonym: vitamin metabolism
has_obo_namespace: biological_process
id: GO:0006766
in_subset: goslim candida
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim yeast

Axiom
annotated source: vitamin metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.
database_cross_reference: GOC:ai

sulfur compound metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
database_cross_reference: Wikipedia:Sulfur_metabolism
has_exact_synonym: sulfur metabolism
has_exact_synonym: sulphur metabolic process
has_exact_synonym: sulphur metabolism
has_obo_namespace: biological_process
id: GO:0006790
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote

Axiom
annotated source: sulfur compound metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
database_cross_reference: GOC:ai

phosphorus metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus.
has_exact_synonym: phosphorus metabolism
has_obo_namespace: biological_process
id: GO:0006793
in_subset: goslim pir

Axiom
annotated source: phosphorus metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus.
database_cross_reference: GOC:ai

xenobiotic metabolic process
type: Class
subclass of: metabolic process
subclass of: Restriction
  on property: part of
  some values from: response to stimulus
definition: The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
term tracker item: https://github.com/geneontology/go-ontology/issues/19460
has_alternative_id: GO:0017144
database_cross_reference: Wikipedia:Drug_metabolism
database_cross_reference: Wikipedia:Xenobiotic_metabolism
has_exact_synonym: xenobiotic metabolism
has_obo_namespace: biological_process
has_related_synonym: drug metabolic process
has_related_synonym: drug metabolism
id: GO:0006805
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: xenobiotic metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
database_cross_reference: GOC:cab2
database_cross_reference: GOC:krc

transport
type: Class
subclass of: establishment of localization
definition: The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
term tracker item: https://github.com/geneontology/go-ontology/issues/20292
created by: jl
creation date: 2012-12-13T16:25:32Z
has_alternative_id: GO:0015457
has_alternative_id: GO:0015460
has_alternative_id: GO:0044765
has_obo_namespace: biological_process
has_related_synonym: single-organism transport
id: GO:0006810
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.

Axiom
annotated source: transport
annotated property: definition
annotated target: The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
database_cross_reference: GOC:dos
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

monoatomic ion transport
type: Class
subclass of: transport
definition: The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
has_broad_synonym: ion transport
has_obo_namespace: biological_process
id: GO:0006811
in_subset: goslim drosophila
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: monoatomic ion transport
annotated property: definition
annotated target: The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
database_cross_reference: GOC:ai

neurotransmitter transport
type: Class
subclass of: transport
definition: The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
has_narrow_synonym: sodium:neurotransmitter transport
has_obo_namespace: biological_process
id: GO:0006836
in_subset: goslim pir

Axiom
annotated source: neurotransmitter transport
annotated property: definition
annotated target: The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
database_cross_reference: GOC:ai

amino acid transport
type: Class
subclass of: transport
definition: The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_alternative_id: GO:0006866
has_obo_namespace: biological_process
id: GO:0006865
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: amino acid transport
annotated property: definition
annotated target: The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

lipid transport
type: Class
subclass of: transport
subclass of: Restriction
  on property: part of
  some values from: localization
definition: The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
has_obo_namespace: biological_process
id: GO:0006869
in_subset: goslim drosophila
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: lipid transport
annotated property: definition
annotated target: The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
database_cross_reference: ISBN:0198506732

autophagy
type: Class
subclass of: metabolic process
subclass of: Restriction
  on property: has part
  some values from: transport
definition: The cellular catabolic process in which cells digest cellular materials, such as organelles and other macromolecular constituents, or non-self materials such as intracellular pathogens. Autophagy serves to provide essential nutrients under conditions of cellular stress; or can remodel intracellular structures during cell differentiation.
term tracker item: https://github.com/geneontology/go-ontology/issues/25541
has_alternative_id: GO:0016238
database_cross_reference: Wikipedia:Autophagy_(cellular)
has_obo_namespace: biological_process
id: GO:0006914
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe

Axiom
annotated source: autophagy
annotated property: definition
annotated target: The cellular catabolic process in which cells digest cellular materials, such as organelles and other macromolecular constituents, or non-self materials such as intracellular pathogens. Autophagy serves to provide essential nutrients under conditions of cellular stress; or can remodel intracellular structures during cell differentiation.
database_cross_reference: GOC:autophagy
database_cross_reference: ISBN:0198547684
database_cross_reference: PMID:11099404
database_cross_reference: PMID:29455577
database_cross_reference: PMID:9412464

muscle contraction
type: Class
subclass of: multicellular organismal process
definition: A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
database_cross_reference: Wikipedia:Muscle_contraction
has_obo_namespace: biological_process
id: GO:0006936
in_subset: goslim pir

Axiom
annotated source: muscle contraction
annotated property: definition
annotated target: A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
database_cross_reference: GOC:ef
database_cross_reference: GOC:mtg_muscle
database_cross_reference: ISBN:0198506732

syncytium formation
type: Class
subclass of: developmental process
subclass of: Restriction
  on property: part of
  some values from: developmental process
definition: The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.
has_obo_namespace: biological_process
id: GO:0006949
in_subset: goslim pir

Axiom
annotated source: syncytium formation
annotated property: definition
annotated target: The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.
database_cross_reference: ISBN:0198506732

organelle organization
type: Class
subclass of: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
created by: jl
creation date: 2013-12-19T15:25:51Z
has_alternative_id: GO:1902589
has_exact_synonym: organelle organisation
has_exact_synonym: single organism organelle organization
has_obo_namespace: biological_process
has_related_synonym: organelle organization and biogenesis
has_related_synonym: single-organism organelle organization
id: GO:0006996
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: organelle organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
database_cross_reference: GOC:mah

Axiom
annotated source: organelle organization
annotated property: has_exact_synonym
annotated target: single organism organelle organization
database_cross_reference: GOC:TermGenie

Axiom
annotated source: organelle organization
annotated property: has_related_synonym
annotated target: organelle organization and biogenesis
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

nucleus organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
has_alternative_id: GO:0048287
has_exact_synonym: nuclear organisation
has_exact_synonym: nuclear organization
has_obo_namespace: biological_process
has_related_synonym: nuclear morphology
has_related_synonym: nuclear organization and biogenesis
has_related_synonym: nucleus organization and biogenesis
id: GO:0006997
in_subset: goslim candida
in_subset: goslim drosophila
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: nucleus organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
database_cross_reference: GOC:dph
database_cross_reference: GOC:ems
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: nucleus organization
annotated property: has_related_synonym
annotated target: nuclear organization and biogenesis
database_cross_reference: GOC:mah

Axiom
annotated source: nucleus organization
annotated property: has_related_synonym
annotated target: nucleus organization and biogenesis
database_cross_reference: GOC:mah

mitochondrion organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
has_exact_synonym: mitochondria organization
has_exact_synonym: mitochondrial biogenesis
has_exact_synonym: mitochondrial organization
has_exact_synonym: mitochondrion biogenesis
has_exact_synonym: mitochondrion organisation
has_obo_namespace: biological_process
has_related_synonym: mitochondrion morphogenesis
has_related_synonym: mitochondrion organization and biogenesis
id: GO:0007005
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim yeast

Axiom
annotated source: mitochondrion organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah
database_cross_reference: GOC:sgd_curators
database_cross_reference: PMID:9786946

Axiom
annotated source: mitochondrion organization
annotated property: has_exact_synonym
annotated target: mitochondria organization
database_cross_reference: GOC:mah

Axiom
annotated source: mitochondrion organization
annotated property: has_exact_synonym
annotated target: mitochondrion organisation
database_cross_reference: GOC:mah

cytoplasm organization
type: Class
subclass of: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
has_exact_synonym: cytoplasm organisation
has_obo_namespace: biological_process
has_related_synonym: cytoplasm organization and biogenesis
id: GO:0007028
in_subset: goslim pir

Axiom
annotated source: cytoplasm organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
database_cross_reference: GOC:curators
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: cytoplasm organization
annotated property: has_related_synonym
annotated target: cytoplasm organization and biogenesis
database_cross_reference: GOC:mah

endoplasmic reticulum organization
type: Class
subclass of: organelle organization
subclass of: Restriction
  on property: part of
  some values from: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum.
has_exact_synonym: ER organisation
has_exact_synonym: endoplasmic reticulum organisation
has_obo_namespace: biological_process
has_related_synonym: ER organization and biogenesis
has_related_synonym: endoplasmic reticulum morphology
has_related_synonym: endoplasmic reticulum organization and biogenesis
id: GO:0007029
in_subset: goslim pir

Axiom
annotated source: endoplasmic reticulum organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum.
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: endoplasmic reticulum organization
annotated property: has_related_synonym
annotated target: ER organization and biogenesis
database_cross_reference: GOC:mah

Axiom
annotated source: endoplasmic reticulum organization
annotated property: has_related_synonym
annotated target: endoplasmic reticulum organization and biogenesis
database_cross_reference: GOC:mah

Golgi organization
type: Class
subclass of: organelle organization
subclass of: Restriction
  on property: part of
  some values from: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
has_exact_synonym: Golgi apparatus organization
has_exact_synonym: Golgi organisation
has_obo_namespace: biological_process
has_related_synonym: Golgi organization and biogenesis
id: GO:0007030
in_subset: goslim pir

Axiom
annotated source: Golgi organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: Golgi organization
annotated property: has_related_synonym
annotated target: Golgi organization and biogenesis
database_cross_reference: GOC:mah

peroxisome organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
has_exact_synonym: peroxisome organisation
has_obo_namespace: biological_process
has_related_synonym: peroxisome organization and biogenesis
id: GO:0007031
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim yeast

Axiom
annotated source: peroxisome organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
database_cross_reference: GOC:mah

Axiom
annotated source: peroxisome organization
annotated property: has_related_synonym
annotated target: peroxisome organization and biogenesis
database_cross_reference: GOC:mah

endosome organization
type: Class
subclass of: vesicle organization
subclass of: Restriction
  on property: part of
  some values from: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
has_exact_synonym: endosome organisation
has_obo_namespace: biological_process
has_related_synonym: endosome organization and biogenesis
id: GO:0007032
in_subset: goslim pir

Axiom
annotated source: endosome organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: endosome organization
annotated property: has_related_synonym
annotated target: endosome organization and biogenesis
database_cross_reference: GOC:mah

vacuole organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.
has_alternative_id: GO:0044086
has_exact_synonym: vacuole organisation
has_narrow_synonym: vacuolar assembly
has_obo_namespace: biological_process
has_related_synonym: vacuole biogenesis
has_related_synonym: vacuole organization and biogenesis
id: GO:0007033
in_subset: goslim drosophila
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: vacuole organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.
database_cross_reference: GOC:mah

Axiom
annotated source: vacuole organization
annotated property: has_narrow_synonym
annotated target: vacuolar assembly
database_cross_reference: GOC:mah

Axiom
annotated source: vacuole organization
annotated property: has_related_synonym
annotated target: vacuole biogenesis
database_cross_reference: GOC:mah

Axiom
annotated source: vacuole organization
annotated property: has_related_synonym
annotated target: vacuole organization and biogenesis
database_cross_reference: GOC:mah

cell cycle
type: Class
subclass of: biological_process
definition: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
database_cross_reference: Wikipedia:Cell_cycle
has_exact_synonym: cell-division cycle
has_obo_namespace: biological_process
id: GO:0007049
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: cell cycle
annotated property: definition
annotated target: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:mtg_cell_cycle

chromosome segregation
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: part of
  some values from: cell cycle
definition: The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
database_cross_reference: Wikipedia:Chromosome_segregation
has_exact_synonym: chromosome division
has_obo_namespace: biological_process
has_related_synonym: chromosome transmission
id: GO:0007059
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: chromosome segregation
annotated property: definition
annotated target: The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah
database_cross_reference: GOC:mtg_cell_cycle
database_cross_reference: GOC:vw

cell communication
type: Class
subclass of: biological_process
definition: Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
database_cross_reference: Wikipedia:Cell_signaling
has_obo_namespace: biological_process
id: GO:0007154
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: cell communication
annotated property: definition
annotated target: Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
database_cross_reference: GOC:mah

cell adhesion
type: Class
subclass of: biological_process
definition: The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
created by: dos
creation date: 2014-04-15T15:59:10Z
has_alternative_id: GO:0098602
database_cross_reference: Wikipedia:Cell_adhesion
has_obo_namespace: biological_process
has_related_synonym: cell adhesion molecule activity
has_related_synonym: single organism cell adhesion
id: GO:0007155
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote

Axiom
annotated source: cell adhesion
annotated property: definition
annotated target: The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
database_cross_reference: GOC:hb
database_cross_reference: GOC:pf

digestion
type: Class
subclass of: multicellular organismal process
definition: The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
database_cross_reference: Wikipedia:Digestion
has_obo_namespace: biological_process
id: GO:0007586
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: digestion
annotated property: definition
annotated target: The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
database_cross_reference: GOC:isa_complete
database_cross_reference: ISBN:0198506732

excretion
type: Class
subclass of: multicellular organismal process
definition: The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
term tracker item: https://github.com/geneontology/go-ontology/issues/22368
database_cross_reference: Wikipedia:Excretion
has_obo_namespace: biological_process
id: GO:0007588
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: excretion
annotated property: definition
annotated target: The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
database_cross_reference: ISBN:0192801023

blood circulation
type: Class
subclass of: multicellular organismal process
definition: The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
has_alternative_id: GO:0070261
has_obo_namespace: biological_process
has_related_synonym: hemolymph circulation
id: GO:0008015
in_subset: goslim pir

Axiom
annotated source: blood circulation
annotated property: definition
annotated target: The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
database_cross_reference: GOC:mtg_heart
database_cross_reference: ISBN:0192800825

transcription elongation factor complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.
has_obo_namespace: cellular_component
id: GO:0008023
in_subset: goslim pir

Axiom
annotated source: transcription elongation factor complex
annotated property: definition
annotated target: Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.
database_cross_reference: GOC:jl

cell recognition
type: Class
subclass of: biological_process
definition: The process in which a cell in an organism interprets its surroundings.
has_exact_synonym: recognition of surroundings by cell
has_obo_namespace: biological_process
id: GO:0008037
in_subset: goslim pir

Axiom
annotated source: cell recognition
annotated property: definition
annotated target: The process in which a cell in an organism interprets its surroundings.
database_cross_reference: GOC:go_curators

biological_process
type: Class
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
term tracker item: https://github.com/geneontology/go-ontology/issues/24968
created by: jl
creation date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
database_cross_reference: Wikipedia:Biological_process
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_obo_namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
database_cross_reference: GOC:pdt

metabolic process
type: Class
subclass of: biological_process
disjoint with: localization
definition: A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
term tracker item: https://github.com/geneontology/go-ontology/issues/28932
created by: jl
creation date: 2012-10-17T15:46:40Z
has_alternative_id: GO:0044236
has_alternative_id: GO:0044710
database_cross_reference: Wikipedia:Metabolism
has_exact_synonym: metabolism
has_obo_namespace: biological_process
id: GO:0008152
in_subset: gocheck do not annotate
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim prokaryote ribbon
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.

Axiom
annotated source: metabolic process
annotated property: definition
annotated target: A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.
database_cross_reference: GOC:go_curators
database_cross_reference: ISBN:0198547684

peptidase activity
type: Class
subclass of: hydrolase activity
definition: Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
has_alternative_id: GO:0070010
has_alternative_id: GO:0070011
database_cross_reference: EC:3.4.-.-
database_cross_reference: Reactome:R-HSA-205112
database_cross_reference: Reactome:R-HSA-3000243
database_cross_reference: Reactome:R-HSA-3000263
database_cross_reference: Reactome:R-HSA-3065958
database_cross_reference: Reactome:R-HSA-3065959
database_cross_reference: Reactome:R-HSA-3139027
database_cross_reference: Reactome:R-HSA-376149
database_cross_reference: Reactome:R-HSA-4167501
database_cross_reference: Reactome:R-HSA-448678
database_cross_reference: Reactome:R-HSA-5655483
database_cross_reference: Reactome:R-HSA-5684864
database_cross_reference: Reactome:R-HSA-5685902
database_cross_reference: Reactome:R-HSA-6803060
has_exact_synonym: hydrolase, acting on peptide bonds
has_exact_synonym: peptide hydrolase activity
has_exact_synonym: protease activity
has_narrow_synonym: peptidase activity, acting on D-amino acid peptides
has_narrow_synonym: peptidase activity, acting on L-amino acid peptides
has_narrow_synonym: proteinase activity
has_obo_namespace: molecular_function
id: GO:0008233
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: peptidase activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0815332181

gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-205112

Unknown lysosomal protease degrades CBLIF:RCbl to release Cbl
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3000243

TCN2:RCbl is degraded to release RCbl
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3000263

An unknown protease degrades ACACA
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3065958

An unknown protease degrades hCBXs
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3065959

Maturation of HIV Virion
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3139027

Proteolytic processing of SLIT
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-376149

An unknown protease degrades ACACB
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-4167501

CTSG cleaves CASP1(1-404)
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-448678

USP1 autocleavage
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5655483

NAPSA, CTSH, PGA3-5 cleave pro-SFTPB
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5684864

NAPSA, CTSH, PGA3-5 cleave pro-SFTPC
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5685902

DCD(63-110) is processed to DCD(63-109)
type: Axiom
annotated source: peptidase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6803060

cohesin complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3).
has_alternative_id: GO:0000798
has_alternative_id: GO:0008279
has_alternative_id: GO:0008280
has_alternative_id: GO:0043222
has_exact_synonym: SMC/kleisin ring complex
has_narrow_synonym: 14S cohesin
has_narrow_synonym: 9S cohesin
has_narrow_synonym: Smc1-Smc3 complex
has_obo_namespace: cellular_component
has_related_synonym: SMC complex
has_related_synonym: cohesin core heterodimer
has_related_synonym: nuclear cohesin complex
id: GO:0008278
in_subset: goslim pir

Axiom
annotated source: cohesin complex
annotated property: definition
annotated target: A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3).
database_cross_reference: GOC:jl
database_cross_reference: GOC:sp
database_cross_reference: GOC:vw
database_cross_reference: PMID:9887095

cell population proliferation
type: Class
subclass of: biological_process
definition: The multiplication or reproduction of cells, resulting in the expansion of a cell population.
has_obo_namespace: biological_process
has_related_synonym: cell proliferation
id: GO:0008283
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.

Axiom
annotated source: cell population proliferation
annotated property: definition
annotated target: The multiplication or reproduction of cells, resulting in the expansion of a cell population.
database_cross_reference: GOC:mah
database_cross_reference: GOC:mb

protein serine/threonine phosphatase complex
type: Class
subclass of: protein-containing complex
definition: A complex, normally consisting of a catalytic and a regulatory subunit, which catalyzes the removal of a phosphate group from a serine or threonine residue of a protein.
has_obo_namespace: cellular_component
id: GO:0008287
in_subset: goslim pir

Axiom
annotated source: protein serine/threonine phosphatase complex
annotated property: definition
annotated target: A complex, normally consisting of a catalytic and a regulatory subunit, which catalyzes the removal of a phosphate group from a serine or threonine residue of a protein.
database_cross_reference: GOC:bf

lipid binding
type: Class
subclass of: binding
definition: Binding to a lipid.
has_obo_namespace: molecular_function
id: GO:0008289
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: lipid binding
annotated property: definition
annotated target: Binding to a lipid.
database_cross_reference: GOC:ai

F-actin capping protein complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoskeleton
definition: A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments.
has_obo_namespace: cellular_component
id: GO:0008290
in_subset: goslim pir

Axiom
annotated source: F-actin capping protein complex
annotated property: definition
annotated target: A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments.
database_cross_reference: GOC:go_curators
database_cross_reference: ISBN:0198599560

ubiquitin-like modifier activating enzyme activity
type: Class
subclass of: ligase activity
subclass of: Restriction
  on property: has part
  some values from: hydrolase activity
definition: Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
term tracker item: https://github.com/geneontology/go-ontology/issues/14208
has_alternative_id: GO:0008642
has_narrow_synonym: small protein activating enzyme activity
has_obo_namespace: molecular_function
id: GO:0008641
in_subset: goslim pir

Axiom
annotated source: ubiquitin-like modifier activating enzyme activity
annotated property: definition
annotated target: Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

carbohydrate transport
type: Class
subclass of: transport
definition: The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
has_alternative_id: GO:0006861
has_alternative_id: GO:0008644
has_narrow_synonym: sugar transport
has_obo_namespace: biological_process
id: GO:0008643
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: carbohydrate transport
annotated property: definition
annotated target: The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
database_cross_reference: GOC:ai

pyrimidine-containing compound salvage
type: Class
subclass of: nucleobase-containing compound metabolic process
subclass of: cellular metabolic compound salvage
definition: Any process that generates a pyrimidine-containing compound, a nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.
has_obo_namespace: biological_process
has_related_synonym: pyrimidine salvage
id: GO:0008655
in_subset: goslim pir

Axiom
annotated source: pyrimidine-containing compound salvage
annotated property: definition
annotated target: Any process that generates a pyrimidine-containing compound, a nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.
database_cross_reference: GOC:jl

integrase activity
type: Class
subclass of: catalytic activity
subclass of: Restriction
  on property: part of
  some values from: DNA integration
definition: Catalysis of the integration of one DNA segment into another.
database_cross_reference: Reactome:R-HSA-164523
has_obo_namespace: molecular_function
id: GO:0008907
in_subset: goslim pir

Axiom
annotated source: integrase activity
annotated property: definition
annotated target: Catalysis of the integration of one DNA segment into another.
database_cross_reference: GOC:mah

Transesterification to connect viral DNA 3' ends to host DNA 5' ends
type: Axiom
annotated source: integrase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-164523

site-specific recombinase activity
type: Class
subclass of: integrase activity
definition: Catalysis of the formation of new phosphodiester bonds between a pair of short, unique target DNA sequences.
term tracker item: https://github.com/geneontology/go-ontology/issues/22264
term tracker item: https://github.com/geneontology/go-ontology/issues/3917
has_exact_synonym: RecA-family recombinase activity
has_obo_namespace: molecular_function
id: GO:0009009
in_subset: goslim pir
comment: Note that this term is not a child of 'recombinase activity ; GO:0000150' because the latter represents activities that do not break or form phosphodiester bonds.

Axiom
annotated source: site-specific recombinase activity
annotated property: definition
annotated target: Catalysis of the formation of new phosphodiester bonds between a pair of short, unique target DNA sequences.
database_cross_reference: GOC:elh
database_cross_reference: PMID:6286142

electron transfer activity
type: Class
subclass of: molecular_function
definition: A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
term tracker item: https://github.com/geneontology/go-ontology/issues/21334
term tracker item: https://github.com/geneontology/go-ontology/issues/26572
has_alternative_id: GO:0009053
has_alternative_id: GO:0009054
database_cross_reference: Reactome:R-HSA-169260
database_cross_reference: Reactome:R-HSA-2564826
has_narrow_synonym: electron acceptor activity
has_narrow_synonym: electron donor activity
has_obo_namespace: molecular_function
has_related_synonym: electron carrier
has_related_synonym: electron transporter activity
id: GO:0009055
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: electron transfer activity
annotated property: definition
annotated target: A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
database_cross_reference: Wikipedia:Electron_transfer

Reducing equivalents from beta-oxidation of fatty acids transfer to ETF
type: Axiom
annotated source: electron transfer activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-169260

4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold
type: Axiom
annotated source: electron transfer activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2564826

macromolecule catabolic process
type: Class
subclass of: macromolecule metabolic process
definition: The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
has_alternative_id: GO:0043285
has_alternative_id: GO:0044266
has_exact_synonym: biopolymer catabolic process
has_exact_synonym: macromolecule breakdown
has_exact_synonym: macromolecule catabolism
has_exact_synonym: macromolecule degradation
has_narrow_synonym: multicellular organismal macromolecule catabolic process
has_obo_namespace: biological_process
has_related_synonym: cellular macromolecule catabolic process
has_related_synonym: cellular macromolecule catabolism
has_related_synonym: cellular macromolecule degradation
id: GO:0009057
in_subset: goslim pir

Axiom
annotated source: macromolecule catabolic process
annotated property: definition
annotated target: The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
database_cross_reference: GOC:mah

Axiom
annotated source: macromolecule catabolic process
annotated property: has_exact_synonym
annotated target: biopolymer catabolic process
database_cross_reference: GOC:mtg_chebi_dec09

macromolecule biosynthetic process
type: Class
subclass of: macromolecule metabolic process
definition: The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
term tracker item: https://github.com/geneontology/go-ontology/issues/15249
term tracker item: https://github.com/geneontology/go-ontology/issues/25418
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
has_alternative_id: GO:0043284
has_exact_synonym: biopolymer biosynthetic process
has_exact_synonym: macromolecule anabolism
has_exact_synonym: macromolecule biosynthesis
has_exact_synonym: macromolecule formation
has_exact_synonym: macromolecule synthesis
has_obo_namespace: biological_process
id: GO:0009059
in_subset: gocheck do not annotate
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: macromolecule biosynthetic process
annotated property: definition
annotated target: The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
database_cross_reference: GOC:mah

Axiom
annotated source: macromolecule biosynthetic process
annotated property: has_exact_synonym
annotated target: biopolymer biosynthetic process
database_cross_reference: GOC:mtg_chebi_dec09

nucleoside metabolic process
type: Class
subclass of: nucleobase-containing compound metabolic process
definition: The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
has_exact_synonym: nucleoside metabolism
has_obo_namespace: biological_process
id: GO:0009116
in_subset: goslim pir

Axiom
annotated source: nucleoside metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
database_cross_reference: GOC:ma

nucleotide metabolic process
type: Class
subclass of: nucleobase-containing compound metabolic process
subclass of: phosphorus metabolic process
definition: The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
has_exact_synonym: nucleotide metabolism
has_obo_namespace: biological_process
id: GO:0009117
in_subset: goslim pir

Axiom
annotated source: nucleotide metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
database_cross_reference: GOC:ma

nucleotide-sugar metabolic process
type: Class
subclass of: nucleobase-containing compound metabolic process
subclass of: phosphorus metabolic process
definition: The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.
term tracker item: https://github.com/geneontology/go-ontology/issues/14587
has_exact_synonym: nucleotide-sugar metabolism
has_obo_namespace: biological_process
id: GO:0009225
in_subset: goslim pir

Axiom
annotated source: nucleotide-sugar metabolic process
annotated property: definition
annotated target: The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.
database_cross_reference: ISBN:0198506732

bacterial-type flagellum
type: Class
subclass of: cell projection
subclass of: organelle
definition: A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
database_cross_reference: Wikipedia:Flagellum#Bacterial
has_exact_synonym: flagellin-based flagellum
has_obo_namespace: cellular_component
id: GO:0009288
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: bacterial-type flagellum
annotated property: definition
annotated target: A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
database_cross_reference: GOC:cilia
database_cross_reference: GOC:jh2
database_cross_reference: GOC:krc
database_cross_reference: GOC:mtg_sensu
database_cross_reference: PMID:7787060
database_cross_reference: Wikipedia:Flagellum#Bacterial

pilus
type: Class
subclass of: cell projection
definition: A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.
database_cross_reference: Wikipedia:Pilus
has_exact_synonym: fimbria
has_exact_synonym: fimbriae
has_exact_synonym: fimbrium
has_exact_synonym: pili
has_obo_namespace: cellular_component
id: GO:0009289
in_subset: goslim pir

Axiom
annotated source: pilus
annotated property: definition
annotated target: A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.
database_cross_reference: GOC:pamgo_curators
database_cross_reference: PMID:28496159

unidirectional conjugation
type: Class
subclass of: horizontal gene transfer
definition: The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells. Some or all of the chromosome(s) of the donor cell is transferred into the recipient cell.
database_cross_reference: Wikipedia:Bacterial_conjugation
has_obo_namespace: biological_process
has_related_synonym: bacterial conjugation
id: GO:0009291
in_subset: goslim pir
comment: Unidirectional conjugation is not a type of not sexual reproduction, since no exchange of gamete occurs and no generation of a new organism: instead an existing organism is transformed.

Axiom
annotated source: unidirectional conjugation
annotated property: definition
annotated target: The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells. Some or all of the chromosome(s) of the donor cell is transferred into the recipient cell.
database_cross_reference: Wikipedia:Bacterial_conjugation

horizontal gene transfer
type: Class
subclass of: biological_process
definition: The introduction of genetic information into a cell to create a genetically different individual, without production of new individuals.
term tracker item: https://github.com/geneontology/go-ontology/issues/22952
has_broad_synonym: genetic exchange
has_exact_synonym: genetic transfer
has_exact_synonym: lateral gene transfer
has_obo_namespace: biological_process
id: GO:0009292
in_subset: goslim pir

Axiom
annotated source: horizontal gene transfer
annotated property: definition
annotated target: The introduction of genetic information into a cell to create a genetically different individual, without production of new individuals.
database_cross_reference: PMID:26184597

amine metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
created by: jl
creation date: 2009-07-15T11:55:44Z
has_alternative_id: GO:0044106
has_exact_synonym: amine metabolism
has_exact_synonym: cellular amine metabolic process
has_obo_namespace: biological_process
id: GO:0009308
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: amine metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732

acetyl-CoA carboxylase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.
has_exact_synonym: ACCase complex
has_obo_namespace: cellular_component
id: GO:0009317
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: acetyl-CoA carboxylase complex
annotated property: definition
annotated target: A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah
database_cross_reference: PMID:12121720

endopeptidase Clp complex
type: Class
subclass of: protein-containing complex
definition: A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form.
has_obo_namespace: cellular_component
id: GO:0009368
in_subset: goslim pir

Axiom
annotated source: endopeptidase Clp complex
annotated property: definition
annotated target: A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form.
database_cross_reference: GOC:mah
database_cross_reference: PMID:11352464

quorum sensing
type: Class
subclass of: cell communication
subclass of: regulation of biological process
subclass of: detection of stimulus
definition: The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
term tracker item: https://github.com/geneontology/go-ontology/issues/17730
term tracker item: https://github.com/geneontology/go-ontology/issues/18018
term tracker item: https://github.com/geneontology/go-ontology/issues/18061
has_alternative_id: GO:0010699
has_alternative_id: GO:0060247
database_cross_reference: Wikipedia:Quorum_sensing
has_exact_synonym: quorum sensing system
has_obo_namespace: biological_process
has_related_synonym: cell-cell signaling involved in quorum sensing
has_related_synonym: detection of cell density by secreted molecule
id: GO:0009372
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: quorum sensing
annotated property: definition
annotated target: The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
database_cross_reference: GOC:krc
database_cross_reference: GOC:mlg
database_cross_reference: PMID:10607620
database_cross_reference: PMID:15716452
database_cross_reference: PMID:16497924
database_cross_reference: PMID:16630813
database_cross_reference: PMID:8288518

toxin metabolic process
type: Class
subclass of: secondary metabolic process
definition: The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
has_exact_synonym: toxin metabolism
has_obo_namespace: biological_process
id: GO:0009404
in_subset: goslim pir

Axiom
annotated source: toxin metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
database_cross_reference: GOC:cab2

photosystem
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: thylakoid
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A complex located in a photosynthetic membrane that consists of a photoreaction center associated with accessory pigments and electron carriers. Examples of this component are found in Arabidopsis thaliana and in photosynthetic bacterial and archaeal species.
has_alternative_id: GO:0030090
database_cross_reference: Wikipedia:Photosystem
has_narrow_synonym: reaction center
has_narrow_synonym: reaction centre
has_obo_namespace: cellular_component
id: GO:0009521
in_subset: goslim pir

Axiom
annotated source: photosystem
annotated property: definition
annotated target: A complex located in a photosynthetic membrane that consists of a photoreaction center associated with accessory pigments and electron carriers. Examples of this component are found in Arabidopsis thaliana and in photosynthetic bacterial and archaeal species.
database_cross_reference: GOC:ds
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0140514031
database_cross_reference: PMID:9821949

plastid
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
database_cross_reference: Wikipedia:Plastid
has_obo_namespace: cellular_component
id: GO:0009536
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: plastid
annotated property: definition
annotated target: Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198547684

thylakoid
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
term tracker item: https://github.com/geneontology/go-ontology/issues/13958
database_cross_reference: Wikipedia:Thylakoid
has_obo_namespace: cellular_component
has_related_synonym: photosynthetic membrane
id: GO:0009579
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
comment: A thylakoid is not considered an organelle, but some thylakoids are part of organelles.

Axiom
annotated source: thylakoid
annotated property: definition
annotated target: A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
database_cross_reference: GOC:ds
database_cross_reference: GOC:mtg_sensu
database_cross_reference: ISBN:0198506732

plastid organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plastid.
has_exact_synonym: plastid organisation
has_obo_namespace: biological_process
has_related_synonym: plastid organization and biogenesis
id: GO:0009657
in_subset: goslim pir

Axiom
annotated source: plastid organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plastid.
database_cross_reference: GOC:mah

Axiom
annotated source: plastid organization
annotated property: has_related_synonym
annotated target: plastid organization and biogenesis
database_cross_reference: GOC:mah

hormone transport
type: Class
subclass of: transport
subclass of: regulation of biological quality
definition: The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
id: GO:0009914
in_subset: goslim pir

Axiom
annotated source: hormone transport
annotated property: definition
annotated target: The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:tb

cyclase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of a ring closure reaction.
has_obo_namespace: molecular_function
id: GO:0009975
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim prokaryote

Axiom
annotated source: cyclase activity
annotated property: definition
annotated target: Catalysis of a ring closure reaction.
database_cross_reference: ISBN:0198547684

cell surface
type: Class
subclass of: cellular anatomical structure
definition: The external part of the cell wall and/or plasma membrane.
has_alternative_id: GO:0009928
has_alternative_id: GO:0009929
has_exact_synonym: cell associated
has_exact_synonym: cell bound
has_obo_namespace: cellular_component
id: GO:0009986
in_subset: goslim pir
comment: Note that this term is intended to annotate gene products that are attached (integrated or loosely bound) to the plasma membrane or cell wall.

Axiom
annotated source: cell surface
annotated property: definition
annotated target: The external part of the cell wall and/or plasma membrane.
database_cross_reference: GOC:jl
database_cross_reference: GOC:mtg_sensu
database_cross_reference: GOC:sm

stomatal movement
type: Class
subclass of: biological_process
definition: The process of opening or closing of stomata, which is directly related to the stomatal conductance (measuring rate of passage of either water vapor or carbon dioxide (CO2) through stomata).
has_obo_namespace: biological_process
id: GO:0010118
in_subset: goslim pir

Axiom
annotated source: stomatal movement
annotated property: definition
annotated target: The process of opening or closing of stomata, which is directly related to the stomatal conductance (measuring rate of passage of either water vapor or carbon dioxide (CO2) through stomata).
database_cross_reference: GOC:sm

mucilage metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving mucilage, a gelatinous substance secreted by plants.
has_exact_synonym: mucilage metabolism
has_obo_namespace: biological_process
id: GO:0010191
in_subset: goslim pir

Axiom
annotated source: mucilage metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving mucilage, a gelatinous substance secreted by plants.
database_cross_reference: GOC:sm

pyrophosphate-dependent phosphofructokinase complex
type: Class
subclass of: protein-containing complex
definition: Heterodimeric complex that catalyzes the pyrophosphate-dependent phosphorylation of D-fructose 6-phosphate into D-fructose 1,6-bisphosphate.
has_obo_namespace: cellular_component
has_related_synonym: PFK complex
id: GO:0010316
in_subset: goslim pir

Axiom
annotated source: pyrophosphate-dependent phosphofructokinase complex
annotated property: definition
annotated target: Heterodimeric complex that catalyzes the pyrophosphate-dependent phosphorylation of D-fructose 6-phosphate into D-fructose 1,6-bisphosphate.
database_cross_reference: PMID:2170409

protein transport
type: Class
subclass of: transport
subclass of: cellular localization
definition: The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_alternative_id: GO:0015831
has_narrow_synonym: enzyme transport
has_obo_namespace: biological_process
id: GO:0015031
in_subset: goslim chembl
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: protein transport
annotated property: definition
annotated target: The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

DNA integration
type: Class
subclass of: DNA metabolic process
definition: The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome.
has_obo_namespace: biological_process
id: GO:0015074
in_subset: goslim pir

Axiom
annotated source: DNA integration
annotated property: definition
annotated target: The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome.
database_cross_reference: GOC:mah

gas transport
type: Class
subclass of: transport
definition: The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
id: GO:0015669
in_subset: goslim pir

Axiom
annotated source: gas transport
annotated property: definition
annotated target: The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

polyol transmembrane transport
type: Class
subclass of: transport
definition: The directed movement of polyols, any polyhydric alcohol, across a membrane.
has_obo_namespace: biological_process
id: GO:0015791
in_subset: goslim pir

Axiom
annotated source: polyol transmembrane transport
annotated property: definition
annotated target: The directed movement of polyols, any polyhydric alcohol, across a membrane.
database_cross_reference: GOC:ai

peptide transport
type: Class
subclass of: amide transport
definition: The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
id: GO:0015833
in_subset: goslim pir

Axiom
annotated source: peptide transport
annotated property: definition
annotated target: The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

peptidoglycan transport
type: Class
subclass of: transport
definition: The directed movement of peptidoglycans, a class of glycoconjugates found in bacterial cell walls, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_exact_synonym: murein transport
has_obo_namespace: biological_process
id: GO:0015835
in_subset: goslim pir

Axiom
annotated source: peptidoglycan transport
annotated property: definition
annotated target: The directed movement of peptidoglycans, a class of glycoconjugates found in bacterial cell walls, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

amine transport
type: Class
subclass of: transport
definition: The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
has_related_synonym: amine/polyamine transport
id: GO:0015837
in_subset: goslim pir

Axiom
annotated source: amine transport
annotated property: definition
annotated target: The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai
database_cross_reference: ISBN:0198506732

organic acid transport
type: Class
subclass of: transport
definition: The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
id: GO:0015849
in_subset: goslim pir

Axiom
annotated source: organic acid transport
annotated property: definition
annotated target: The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: ISBN:0198506732

siderophore transport
type: Class
subclass of: monoatomic ion transport
definition: The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_alternative_id: GO:0015892
has_exact_synonym: iron-siderophore transport
has_exact_synonym: siderophore-iron transport
has_narrow_synonym: iron-siderochrome transport
has_narrow_synonym: siderochrome transport
has_obo_namespace: biological_process
id: GO:0015891
in_subset: goslim pir

Axiom
annotated source: siderophore transport
annotated property: definition
annotated target: The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

lipopolysaccharide transport
type: Class
subclass of: lipid transport
definition: The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
term tracker item: https://github.com/geneontology/go-ontology/issues/23034
has_alternative_id: GO:0015921
has_exact_synonym: LPS transport
has_narrow_synonym: LPS export
has_narrow_synonym: lipopolysaccharide export
has_obo_namespace: biological_process
id: GO:0015920
in_subset: goslim pir

Axiom
annotated source: lipopolysaccharide transport
annotated property: definition
annotated target: The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
database_cross_reference: GOC:ai

nucleobase-containing compound transport
type: Class
subclass of: transport
definition: The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
has_related_synonym: nucleobase, nucleoside, nucleotide and nucleic acid transport
id: GO:0015931
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: nucleobase-containing compound transport
annotated property: definition
annotated target: The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

Axiom
annotated source: nucleobase-containing compound transport
annotated property: has_related_synonym
annotated target: nucleobase, nucleoside, nucleotide and nucleic acid transport
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

small ribosomal subunit
type: Class
subclass of: ribonucleoprotein complex
subclass of: Restriction
  on property: part of
  some values from: ribosome
definition: The smaller of the two subunits of a ribosome.
has_exact_synonym: ribosomal small subunit
has_obo_namespace: cellular_component
id: GO:0015935
in_subset: goslim pir

Axiom
annotated source: small ribosomal subunit
annotated property: definition
annotated target: The smaller of the two subunits of a ribosome.
database_cross_reference: GOC:mah

methanogenesis
type: Class
subclass of: cellular alkane metabolic process
subclass of: cellular respiration
definition: The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
database_cross_reference: UM-BBD_pathwayID:meth
database_cross_reference: Wikipedia:Methanogenesis
has_exact_synonym: methane biosynthesis
has_exact_synonym: methane biosynthetic process
has_obo_namespace: biological_process
id: GO:0015948
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: methanogenesis
annotated property: definition
annotated target: The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
database_cross_reference: GOC:ai

nucleobase-containing small molecule interconversion
type: Class
subclass of: nucleobase-containing compound metabolic process
definition: The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
has_obo_namespace: biological_process
id: GO:0015949
in_subset: goslim pir

Axiom
annotated source: nucleobase-containing small molecule interconversion
annotated property: definition
annotated target: The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0306444747
database_cross_reference: ISBN:0471394831

carbon utilization
type: Class
subclass of: response to stimulus
definition: A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism.
has_alternative_id: GO:0015978
database_cross_reference: Wikipedia:Heterotroph
has_exact_synonym: carbon utilization by utilization of organic compounds
has_exact_synonym: heterotrophy
has_obo_namespace: biological_process
id: GO:0015976
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: carbon utilization
annotated property: definition
annotated target: A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism.
database_cross_reference: GOC:mah
database_cross_reference: GOC:mlg

Axiom
annotated source: carbon utilization
annotated property: has_exact_synonym
annotated target: carbon utilization by utilization of organic compounds
database_cross_reference: GOC:mah

photosynthesis
type: Class
subclass of: metabolic process
definition: The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
database_cross_reference: Wikipedia:Photosynthesis
has_obo_namespace: biological_process
id: GO:0015979
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: photosynthesis
annotated property: definition
annotated target: The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
database_cross_reference: ISBN:0198547684

dystrophin-associated glycoprotein complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A multiprotein complex that forms a strong mechanical link between the cytoskeleton and extracellular matrix; typical of, but not confined to, muscle cells. The complex is composed of transmembrane, cytoplasmic, and extracellular proteins, including dystrophin, sarcoglycans, dystroglycan, dystrobrevins, syntrophins, sarcospan, caveolin-3, and NO synthase.
has_exact_synonym: DGC
has_exact_synonym: dystrophin glycoprotein complex
has_obo_namespace: cellular_component
id: GO:0016010
in_subset: goslim pir

Axiom
annotated source: dystrophin-associated glycoprotein complex
annotated property: definition
annotated target: A multiprotein complex that forms a strong mechanical link between the cytoskeleton and extracellular matrix; typical of, but not confined to, muscle cells. The complex is composed of transmembrane, cytoplasmic, and extracellular proteins, including dystrophin, sarcoglycans, dystroglycan, dystrobrevins, syntrophins, sarcospan, caveolin-3, and NO synthase.
database_cross_reference: PMID:15117830
database_cross_reference: PMID:16710609

membrane
type: Class
subclass of: cellular anatomical structure
definition: A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
creation date: 2014-03-06T11:37:54Z
has_alternative_id: GO:0016021
has_alternative_id: GO:0098589
has_alternative_id: GO:0098805
database_cross_reference: Wikipedia:Biological_membrane
database_cross_reference: Wikipedia:Transmembrane_protein
has_narrow_synonym: integral component of membrane
has_narrow_synonym: integral to membrane
has_narrow_synonym: membrane region
has_narrow_synonym: region of membrane
has_narrow_synonym: whole membrane
has_obo_namespace: cellular_component
has_related_synonym: transmembrane
id: GO:0016020
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast

Axiom
annotated source: membrane
annotated property: definition
annotated target: A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
database_cross_reference: GOC:dos
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0815316194

Axiom
annotated source: membrane
annotated property: has_related_synonym
annotated target: transmembrane
database_cross_reference: GOC:mah

rhabdomere
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: The specialized microvilli-containing organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction.
has_obo_namespace: cellular_component
id: GO:0016028
in_subset: goslim pir

Axiom
annotated source: rhabdomere
annotated property: definition
annotated target: The specialized microvilli-containing organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction.
database_cross_reference: GOC:hb
database_cross_reference: GOC:sart
database_cross_reference: PMID:8646774

viral process
type: Class
subclass of: biological_process
definition: A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
has_alternative_id: GO:0022415
database_cross_reference: Wikipedia:Viral_life_cycle
has_exact_synonym: virus process
has_obo_namespace: biological_process
has_related_synonym: viral infection
has_related_synonym: virulence
id: GO:0016032
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim virus
comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.

Axiom
annotated source: viral process
annotated property: definition
annotated target: A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: viral process
annotated property: has_exact_synonym
annotated target: virus process
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

cellular component organization
type: Class
subclass of: biological_process
definition: A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
has_alternative_id: GO:0044235
has_alternative_id: GO:0071842
has_exact_synonym: cell organisation
has_exact_synonym: cellular component organisation at cellular level
has_exact_synonym: cellular component organisation in other organism
has_exact_synonym: cellular component organization at cellular level
has_exact_synonym: cellular component organization in other organism
has_obo_namespace: biological_process
has_related_synonym: cell organization and biogenesis
id: GO:0016043
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: cellular component organization
annotated property: definition
annotated target: A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
database_cross_reference: GOC:ai
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_exact_synonym
annotated target: cellular component organisation at cellular level
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_exact_synonym
annotated target: cellular component organisation in other organism
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_related_synonym
annotated target: cell organization and biogenesis
database_cross_reference: GOC:mah

cell growth
type: Class
subclass of: growth
definition: The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
has_alternative_id: GO:0048591
has_exact_synonym: cellular growth
has_exact_synonym: growth of cell
has_obo_namespace: biological_process
has_related_synonym: cell expansion
has_related_synonym: metabolic process resulting in cell growth
has_related_synonym: metabolism resulting in cell growth
has_related_synonym: non-developmental cell growth
has_related_synonym: non-developmental growth of a unicellular organism
id: GO:0016049
in_subset: gocheck do not annotate
in_subset: goslim drosophila
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: cell growth
annotated property: definition
annotated target: The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
database_cross_reference: GOC:ai

Axiom
annotated source: cell growth
annotated property: has_related_synonym
annotated target: non-developmental cell growth
database_cross_reference: GOC:mah

Axiom
annotated source: cell growth
annotated property: has_related_synonym
annotated target: non-developmental growth of a unicellular organism
database_cross_reference: GOC:mah

vesicle organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
has_exact_synonym: vesicle organisation
has_obo_namespace: biological_process
has_related_synonym: vesicle organization and biogenesis
id: GO:0016050
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: vesicle organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
database_cross_reference: GOC:mah

Axiom
annotated source: vesicle organization
annotated property: has_related_synonym
annotated target: vesicle organization and biogenesis
database_cross_reference: GOC:mah

RNA metabolic process
type: Class
subclass of: nucleobase-containing compound metabolic process
subclass of: macromolecule metabolic process
definition: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
has_exact_synonym: RNA metabolism
has_obo_namespace: biological_process
id: GO:0016070
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim euk cellular processes ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim prokaryote

Axiom
annotated source: RNA metabolic process
annotated property: definition
annotated target: The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
database_cross_reference: ISBN:0198506732

vesicle-mediated transport
type: Class
subclass of: transport
definition: A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
term tracker item: https://github.com/geneontology/go-ontology/issues/25421
has_alternative_id: GO:0006899
has_exact_synonym: vesicle transport
has_exact_synonym: vesicular transport
has_narrow_synonym: nonselective vesicle transport
has_obo_namespace: biological_process
has_related_synonym: protein sorting along secretory pathway
has_related_synonym: vesicle trafficking
id: GO:0016192
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe

Axiom
annotated source: vesicle-mediated transport
annotated property: definition
annotated target: A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
database_cross_reference: GOC:ai
database_cross_reference: GOC:mah
database_cross_reference: ISBN:08789310662000

Axiom
annotated source: vesicle-mediated transport
annotated property: has_exact_synonym
annotated target: vesicular transport
database_cross_reference: GOC:mah

antioxidant activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: part of
  some values from: response to stimulus
definition: Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
has_obo_namespace: molecular_function
id: GO:0016209
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: antioxidant activity
annotated property: definition
annotated target: Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
database_cross_reference: ISBN:0198506732

proton-transporting two-sector ATPase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible.
term tracker item: https://github.com/geneontology/go-ontology/issues/15936
term tracker item: https://github.com/geneontology/go-ontology/issues/28017
has_exact_synonym: hydrogen-transporting two-sector ATPase complex
has_obo_namespace: cellular_component
has_related_synonym: vacuolar hydrogen-transporting ATPase
id: GO:0016469
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: proton-transporting two-sector ATPase complex
annotated property: definition
annotated target: A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0716743663
database_cross_reference: PMID:16691483

sodium ion-transporting two-sector ATPase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of sodium ions across a membrane. The complex comprises a membrane sector (F0 or V0) that carries out ion transport and a cytoplasmic compartment sector (F1 or V1) that catalyzes ATP synthesis or hydrolysis.
has_exact_synonym: sodium-transporting two-sector ATPase complex
has_obo_namespace: cellular_component
id: GO:0016472
in_subset: goslim pir

Axiom
annotated source: sodium ion-transporting two-sector ATPase complex
annotated property: definition
annotated target: A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of sodium ions across a membrane. The complex comprises a membrane sector (F0 or V0) that carries out ion transport and a cytoplasmic compartment sector (F1 or V1) that catalyzes ATP synthesis or hydrolysis.
database_cross_reference: GOC:mah
database_cross_reference: PMID:14656431

oxidoreductase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
database_cross_reference: EC:1.-.-.-
database_cross_reference: Reactome:R-HSA-1614362
database_cross_reference: Reactome:R-HSA-209921
database_cross_reference: Reactome:R-HSA-209960
database_cross_reference: Reactome:R-HSA-390425
database_cross_reference: Reactome:R-HSA-390438
database_cross_reference: Reactome:R-HSA-5662660
database_cross_reference: Reactome:R-HSA-8878581
database_cross_reference: Reactome:R-HSA-8936442
database_cross_reference: Reactome:R-HSA-9020249
database_cross_reference: Reactome:R-HSA-9020260
database_cross_reference: Reactome:R-HSA-9024624
database_cross_reference: Reactome:R-HSA-9024630
database_cross_reference: Reactome:R-HSA-9025007
database_cross_reference: Reactome:R-HSA-9026001
database_cross_reference: Reactome:R-HSA-9026917
database_cross_reference: Reactome:R-HSA-9027033
database_cross_reference: Reactome:R-HSA-9693722
database_cross_reference: Reactome:R-HSA-9759549
has_exact_synonym: redox activity
has_narrow_synonym: oxidoreductase activity, acting on other substrates
has_obo_namespace: molecular_function
id: GO:0016491
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: oxidoreductase activity
annotated property: definition
annotated target: Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
database_cross_reference: EC:1.-.-.-

SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1614362

Monoiodinated tyrosine can be deiodinated
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-209921

Diiodinated tyrosine can be deiodinated
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-209960

FAR1 reduces PalmCoA to HXOL
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-390425

FAR2 reduces PalmCoA to HXOL
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-390438

Dopachrome is transformed to DHICA by DCT
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5662660

TYRP1 oxidises DHICA to IQCA
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8878581

MARC1,MARC2 reduce N-hydroxylated compounds
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8936442

Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9020249

Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9020260

Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9024624

Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9024630

Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9025007

Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9026001

Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9026917

Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9027033

Unknown sepiapterin synthase transforms PTHP to sepiapterin
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9693722

Cob(I)alamin bound to MMACHC is oxidized to cob(II)alamin
type: Axiom
annotated source: oxidoreductase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9759549

metallochaperone activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: has part
  some values from: ion binding
definition: Binding to and delivering metal ions to a target protein.
has_obo_namespace: molecular_function
id: GO:0016530
in_subset: goslim pir

Axiom
annotated source: metallochaperone activity
annotated property: definition
annotated target: Binding to and delivering metal ions to a target protein.
database_cross_reference: PMID:11739376

RNA polymerase II, holoenzyme
type: Class
subclass of: RNA polymerase complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
has_exact_synonym: DNA-directed RNA polymerase II, holoenzyme
has_obo_namespace: cellular_component
id: GO:0016591
in_subset: goslim pir

Axiom
annotated source: RNA polymerase II, holoenzyme
annotated property: definition
annotated target: A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
database_cross_reference: GOC:jl
database_cross_reference: GOC:krc
database_cross_reference: PMID:16858867
database_cross_reference: Wikipedia:Rna_polymerase_ii

amino acid binding
type: Class
subclass of: binding
definition: Binding to an amino acid, organic acids containing one or more amino substituents.
has_obo_namespace: molecular_function
id: GO:0016597
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: amino acid binding
annotated property: definition
annotated target: Binding to an amino acid, organic acids containing one or more amino substituents.
database_cross_reference: GOC:ai

nitrogenase complex
type: Class
subclass of: protein-containing complex
definition: An enzyme complex composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase is tetrameric with an alpha2-beta2 structure and nitrogenase reductase is a homodimer, and both are associated with metal ions, which differ between species. Both proteins are required for the enzyme activity of the complex, the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen.
term tracker item: https://github.com/geneontology/go-ontology/issues/21246
has_obo_namespace: cellular_component
id: GO:0016610
in_subset: goslim pir

Axiom
annotated source: nitrogenase complex
annotated property: definition
annotated target: An enzyme complex composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase is tetrameric with an alpha2-beta2 structure and nitrogenase reductase is a homodimer, and both are associated with metal ions, which differ between species. Both proteins are required for the enzyme activity of the complex, the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen.
database_cross_reference: PMID:10852721

transferase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
database_cross_reference: EC:2.-.-.-
database_cross_reference: Reactome:R-HSA-1483089
database_cross_reference: Reactome:R-HSA-1483186
database_cross_reference: Reactome:R-HSA-5668414
database_cross_reference: Reactome:R-HSA-8868783
has_obo_namespace: molecular_function
id: GO:0016740
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: transferase activity
annotated property: definition
annotated target: Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
database_cross_reference: EC:2.-.-.-

PE is converted to PS by PTDSS2
type: Axiom
annotated source: transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1483089

PC is converted to PS by PTDSS1
type: Axiom
annotated source: transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1483186

TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
type: Axiom
annotated source: transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5668414

TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
type: Axiom
annotated source: transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8868783

hydrolase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
database_cross_reference: EC:3.-.-.-
database_cross_reference: Reactome:R-HSA-1236938
database_cross_reference: Reactome:R-HSA-2029475
database_cross_reference: Reactome:R-HSA-5694583
database_cross_reference: Reactome:R-HSA-5695964
database_cross_reference: Reactome:R-HSA-6786190
database_cross_reference: Reactome:R-HSA-6788295
database_cross_reference: Reactome:R-HSA-8938314
database_cross_reference: Reactome:R-HSA-8952137
has_obo_namespace: molecular_function
id: GO:0016787
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: hydrolase activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
database_cross_reference: ISBN:0198506732

Partial proteolysis of antigen in phagolysosomes
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1236938

Production of AA by iPLA2 upon FCGR activation
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-2029475

ABHD4 hydrolyses NAPE
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5694583

ABHD14B hydrolyses PNPB
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5695964

CMBL hydrolyses OM to OLMS
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6786190

HDHD1:Mg2+ dephosphorylates PURIDP
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788295

ENPPs hydrolyse CoA-SH to PPANT, PAP
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8938314

Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate
type: Axiom
annotated source: hydrolase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-8952137

lyase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
database_cross_reference: EC:4.-.-.-
database_cross_reference: Reactome:R-HSA-5696408
database_cross_reference: Reactome:R-HSA-6782895
has_obo_namespace: molecular_function
id: GO:0016829
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: lyase activity
annotated property: definition
annotated target: Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
database_cross_reference: EC:4.-.-.-

PXLP-K278-PHYKPL tetramer hydrolyses 5PHL
type: Axiom
annotated source: lyase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5696408

TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe)
type: Axiom
annotated source: lyase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6782895

isomerase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
database_cross_reference: EC:5.-.-.-
database_cross_reference: Reactome:R-HSA-6787623
has_narrow_synonym: other isomerase activity
has_obo_namespace: molecular_function
id: GO:0016853
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: isomerase activity
annotated property: definition
annotated target: Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
database_cross_reference: ISBN:0198506732

TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal
type: Axiom
annotated source: isomerase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6787623

ligase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
term tracker item: https://github.com/geneontology/go-ontology/issues/19380
database_cross_reference: EC:6.-.-.-
has_exact_synonym: synthetase activity
has_obo_namespace: molecular_function
id: GO:0016874
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: ligase activity
annotated property: definition
annotated target: Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
database_cross_reference: EC:6.-.-.-

Axiom
annotated source: ligase activity
annotated property: has_exact_synonym
annotated target: synthetase activity
database_cross_reference: GOC:jh2

insulin-like growth factor binding protein complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: extracellular region
definition: A complex of proteins which includes the insulin-like growth factor (IGF) and a number of IGF-binding proteins. The complex plays a role in growth and development.
has_exact_synonym: IGF binding protein complex
has_obo_namespace: cellular_component
id: GO:0016942
in_subset: goslim pir

Axiom
annotated source: insulin-like growth factor binding protein complex
annotated property: definition
annotated target: A complex of proteins which includes the insulin-like growth factor (IGF) and a number of IGF-binding proteins. The complex plays a role in growth and development.
database_cross_reference: GOC:jl

transcription repressor complex
type: Class
subclass of: transcription regulator complex
definition: A protein complex that possesses activity that prevents or downregulates transcription.
created by: tb
creation date: 2014-05-09T13:23:51Z
has_alternative_id: GO:0090568
has_alternative_id: GO:0090569
has_exact_synonym: transcription factor inhibitor complex
has_exact_synonym: transcriptional repressor complex
has_obo_namespace: cellular_component
has_related_synonym: cytoplasmic transcriptional repressor complex
has_related_synonym: nuclear transcriptional repressor complex
id: GO:0017053
in_subset: goslim pir

Axiom
annotated source: transcription repressor complex
annotated property: definition
annotated target: A protein complex that possesses activity that prevents or downregulates transcription.
database_cross_reference: GOC:mah

Axiom
annotated source: transcription repressor complex
annotated property: has_exact_synonym
annotated target: transcription factor inhibitor complex
database_cross_reference: GOC:bhm

ether metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving organic ethers, any anhydride of the general formula R1-O-R2, formed between two identical or nonidentical organic hydroxy compounds.
has_exact_synonym: ether metabolism
has_exact_synonym: organic ether metabolic process
has_exact_synonym: organic ether metabolism
has_obo_namespace: biological_process
id: GO:0018904
in_subset: goslim pir

Axiom
annotated source: ether metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving organic ethers, any anhydride of the general formula R1-O-R2, formed between two identical or nonidentical organic hydroxy compounds.
database_cross_reference: GOC:pr
database_cross_reference: ISBN:0198506732

organometal metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving organometals, any metal-containing organic compound, especially one in which the metal atom is linked directly to one of more carbon atoms.
has_exact_synonym: organometal metabolism
has_obo_namespace: biological_process
id: GO:0018942
in_subset: goslim pir

Axiom
annotated source: organometal metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving organometals, any metal-containing organic compound, especially one in which the metal atom is linked directly to one of more carbon atoms.
database_cross_reference: ISBN:0198506732

deacetylase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the hydrolysis of an acetyl group from a substrate molecule.
term tracker item: https://github.com/geneontology/go-ontology/issues/28920
database_cross_reference: EC:2.3.1.-
database_cross_reference: EC:3.1.1.-
database_cross_reference: EC:3.5.1.-
database_cross_reference: Reactome:R-HSA-5689000
has_obo_namespace: molecular_function
id: GO:0019213
in_subset: goslim pir

Axiom
annotated source: deacetylase activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of an acetyl group from a substrate molecule.
database_cross_reference: GOC:jl

AADAC deacetylates PHEN
type: Axiom
annotated source: deacetylase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5689000

deaminase activity
type: Class
subclass of: hydrolase activity
definition: Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH3/NH2R).
database_cross_reference: Reactome:R-HSA-74241
database_cross_reference: Reactome:R-HSA-9014641
database_cross_reference: Reactome:R-HSA-9734745
database_cross_reference: Reactome:R-HSA-9754964
has_obo_namespace: molecular_function
id: GO:0019239
in_subset: goslim pir

Axiom
annotated source: deaminase activity
annotated property: definition
annotated target: Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH3/NH2R).
database_cross_reference: GOC:jl

ADA catalyzes the deamination of (deoxy)adenosine
type: Axiom
annotated source: deaminase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-74241

HRSP12 deaminates 2AA to 2OBUTA
type: Axiom
annotated source: deaminase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9014641

Defective ADA does not deaminate (deoxy)adenosine
type: Axiom
annotated source: deaminase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9734745

ADA deamidates RBV
type: Axiom
annotated source: deaminase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-9754964

protein metabolic process
type: Class
subclass of: macromolecule metabolic process
subclass of: primary metabolic process
definition: The chemical reactions and pathways involving a protein. Includes protein modification.
term tracker item: https://github.com/geneontology/go-ontology/issues/23112
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
has_alternative_id: GO:0006411
has_alternative_id: GO:0044267
has_alternative_id: GO:0044268
database_cross_reference: Wikipedia:Protein_metabolism
has_exact_synonym: cellular protein metabolic process
has_exact_synonym: cellular protein metabolism
has_exact_synonym: protein metabolic process and modification
has_exact_synonym: protein metabolism
has_exact_synonym: protein metabolism and modification
has_narrow_synonym: multicellular organismal protein metabolic process
has_obo_namespace: biological_process
id: GO:0019538
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: protein metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a protein. Includes protein modification.
database_cross_reference: GOC:ma

secondary metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.
database_cross_reference: Wikipedia:Secondary_metabolism
has_exact_synonym: secondary metabolism
has_exact_synonym: secondary metabolite metabolic process
has_exact_synonym: secondary metabolite metabolism
has_obo_namespace: biological_process
id: GO:0019748
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe

Axiom
annotated source: secondary metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.
database_cross_reference: GOC:go_curators

ubiquitin-like protein transferase activity
type: Class
subclass of: transferase activity
definition: Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y = Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.
term tracker item: https://github.com/geneontology/go-ontology/issues/24697
has_alternative_id: GO:0008639
has_alternative_id: GO:0008640
has_broad_synonym: E2
database_cross_reference: Reactome:R-HSA-5678490
database_cross_reference: Reactome:R-HSA-688137
has_exact_synonym: small conjugating protein transferase activity
has_narrow_synonym: small conjugating protein ligase activity
has_narrow_synonym: small protein conjugating enzyme activity
has_narrow_synonym: ubiquitin-like conjugating enzyme activity
has_narrow_synonym: ubiquitin-like-protein ligase activity
has_obo_namespace: molecular_function
has_related_synonym: E3
id: GO:0019787
in_subset: goslim drosophila
in_subset: goslim pir

Axiom
annotated source: ubiquitin-like protein transferase activity
annotated property: definition
annotated target: Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y = Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.
database_cross_reference: GOC:mah
database_cross_reference: GOC:rn
database_cross_reference: PMID:10806345
database_cross_reference: PMID:10884686

ATG16L1 complex transfers LC3 from ATG3 to PE
type: Axiom
annotated source: ubiquitin-like protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-5678490

RIP2 is K63 polyubiquitinated
type: Axiom
annotated source: ubiquitin-like protein transferase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-688137

Axiom
annotated source: ubiquitin-like protein transferase activity
annotated property: has_exact_synonym
annotated target: small conjugating protein transferase activity
database_cross_reference: GOC:dph

Axiom
annotated source: ubiquitin-like protein transferase activity
annotated property: has_narrow_synonym
annotated target: small conjugating protein ligase activity
database_cross_reference: GOC:dph

Axiom
annotated source: ubiquitin-like protein transferase activity
annotated property: has_related_synonym
annotated target: E3
database_cross_reference: GOC:dph

immunoglobulin complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
has_narrow_synonym: antibody
has_obo_namespace: cellular_component
id: GO:0019814
in_subset: goslim pir
comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.

Axiom
annotated source: immunoglobulin complex
annotated property: definition
annotated target: A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
database_cross_reference: GOC:add
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0781765196

oxygen binding
type: Class
subclass of: binding
definition: Binding to oxygen (O2).
has_narrow_synonym: cytochrome P450
has_obo_namespace: molecular_function
has_related_synonym: cytochrome P450 activity
id: GO:0019825
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: oxygen binding
annotated property: definition
annotated target: Binding to oxygen (O2).
database_cross_reference: GOC:jl

isoprenoid binding
type: Class
subclass of: lipid binding
definition: Binding to an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
has_obo_namespace: molecular_function
id: GO:0019840
in_subset: goslim pir

Axiom
annotated source: isoprenoid binding
annotated property: definition
annotated target: Binding to an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
database_cross_reference: GOC:jl

vitamin binding
type: Class
subclass of: binding
definition: Binding to a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
has_obo_namespace: molecular_function
id: GO:0019842
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: vitamin binding
annotated property: definition
annotated target: Binding to a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
database_cross_reference: GOC:ai

glycosome
type: Class
subclass of: microbody
definition: A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
database_cross_reference: Wikipedia:Glycosome
has_obo_namespace: cellular_component
id: GO:0020015
in_subset: goslim pir

Axiom
annotated source: glycosome
annotated property: definition
annotated target: A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
database_cross_reference: GOC:mb

acidocalcisome
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: An electron-dense acidic membrane-bounded organelle which contains a matrix of pyrophosphate and polyphosphates with bound calcium and other cations.
has_exact_synonym: metachromatic granule
has_exact_synonym: volutin granule
has_obo_namespace: cellular_component
has_related_synonym: polyphosphate vacuole
id: GO:0020022
in_subset: goslim pir

Axiom
annotated source: acidocalcisome
annotated property: definition
annotated target: An electron-dense acidic membrane-bounded organelle which contains a matrix of pyrophosphate and polyphosphates with bound calcium and other cations.
database_cross_reference: GOC:mb

Axiom
annotated source: acidocalcisome
annotated property: has_exact_synonym
annotated target: metachromatic granule
database_cross_reference: PMID:15738951

Axiom
annotated source: acidocalcisome
annotated property: has_exact_synonym
annotated target: volutin granule
database_cross_reference: PMID:15738951

Axiom
annotated source: acidocalcisome
annotated property: has_related_synonym
annotated target: polyphosphate vacuole
database_cross_reference: PMID:15738951

membrane docking
type: Class
subclass of: biological_process
definition: The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.
has_obo_namespace: biological_process
id: GO:0022406
in_subset: goslim pir

Axiom
annotated source: membrane docking
annotated property: definition
annotated target: The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.
database_cross_reference: GOC:isa_complete
database_cross_reference: PMID:27875684

cellular component disassembly
type: Class
subclass of: cellular component organization
disjoint with: cellular component assembly
definition: A cellular process that results in the breakdown of a cellular component.
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
has_alternative_id: GO:0071845
has_exact_synonym: cell structure disassembly
has_exact_synonym: cellular component disassembly at cellular level
has_obo_namespace: biological_process
id: GO:0022411
in_subset: gocheck do not annotate
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: cellular component disassembly
annotated property: definition
annotated target: A cellular process that results in the breakdown of a cellular component.
database_cross_reference: GOC:isa_complete

reproductive process
type: Class
subclass of: biological_process
definition: A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
term tracker item: https://github.com/geneontology/go-ontology/issues/27054
created by: jl
creation date: 2012-09-19T15:56:06Z
has_alternative_id: GO:0044702
database_cross_reference: Wikipedia:Reproduction
has_obo_namespace: biological_process
has_related_synonym: single organism reproductive process
id: GO:0022414
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: reproductive process
annotated property: definition
annotated target: A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete

cellular component assembly
type: Class
subclass of: cellular component organization
subclass of: Restriction
  on property: part of
  some values from: cellular component biogenesis
definition: The aggregation, arrangement and bonding together of a cellular component.
has_alternative_id: GO:0071844
has_exact_synonym: cell structure assembly
has_exact_synonym: cellular component assembly at cellular level
has_obo_namespace: biological_process
id: GO:0022607
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim pir

Axiom
annotated source: cellular component assembly
annotated property: definition
annotated target: The aggregation, arrangement and bonding together of a cellular component.
database_cross_reference: GOC:isa_complete

electron transport chain
type: Class
subclass of: generation of precursor metabolites and energy
definition: A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors.
term tracker item: https://github.com/geneontology/go-ontology/issues/21455
database_cross_reference: Wikipedia:Electron_transport_chain
has_obo_namespace: biological_process
id: GO:0022900
in_subset: goslim pir

Axiom
annotated source: electron transport chain
annotated property: definition
annotated target: A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors.
database_cross_reference: GOC:mtg_electron_transport

light-harvesting complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center.
database_cross_reference: Wikipedia:Light-harvesting_complex
has_obo_namespace: cellular_component
has_related_synonym: antenna complex
id: GO:0030076
in_subset: goslim pir

Axiom
annotated source: light-harvesting complex
annotated property: definition
annotated target: A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center.
database_cross_reference: GOC:lr

glycocalyx
type: Class
subclass of: external encapsulating structure
definition: A carbohydrate rich layer at the outermost periphery of a cell.
database_cross_reference: Wikipedia:Glycocalyx
has_obo_namespace: cellular_component
id: GO:0030112
in_subset: goslim pir

Axiom
annotated source: glycocalyx
annotated property: definition
annotated target: A carbohydrate rich layer at the outermost periphery of a cell.
database_cross_reference: GOC:krc
database_cross_reference: GOC:mlg
database_cross_reference: ISBN:0815316208
database_cross_reference: PMID:28876829

S-layer
type: Class
subclass of: external encapsulating structure
definition: A crystalline protein layer surrounding some bacteria.
database_cross_reference: Wikipedia:S-layer
has_obo_namespace: cellular_component
id: GO:0030115
in_subset: goslim pir

Axiom
annotated source: S-layer
annotated property: definition
annotated target: A crystalline protein layer surrounding some bacteria.
database_cross_reference: GOC:mlg
database_cross_reference: ISBN:0815108893

AP-type membrane coat adaptor complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
subclass of: Restriction
  on property: part of
  some values from: membrane
subclass of: Restriction
  on property: part of
  some values from: protein-containing complex
definition: Any of several heterotetrameric complexes that link clathrin (or another coat-forming molecule, as hypothesized for AP-3 and AP-4) to a membrane surface; they are found on coated pits and coated vesicles, and mediate sorting of cargo proteins into vesicles. Each AP complex contains two large (a beta and one of either an alpha, gamma, delta, or epsilon) subunits (110-130 kDa), a medium (mu) subunit (approximately 50 kDa), and a small (sigma) subunit (15-20 kDa).
has_obo_namespace: cellular_component
has_related_synonym: clathrin adaptor
id: GO:0030119
in_subset: goslim pir

Axiom
annotated source: AP-type membrane coat adaptor complex
annotated property: definition
annotated target: Any of several heterotetrameric complexes that link clathrin (or another coat-forming molecule, as hypothesized for AP-3 and AP-4) to a membrane surface; they are found on coated pits and coated vesicles, and mediate sorting of cargo proteins into vesicles. Each AP complex contains two large (a beta and one of either an alpha, gamma, delta, or epsilon) subunits (110-130 kDa), a medium (mu) subunit (approximately 50 kDa), and a small (sigma) subunit (15-20 kDa).
database_cross_reference: GOC:mah
database_cross_reference: PMID:10611976
database_cross_reference: PMID:15473838

filopodium
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
has_alternative_id: GO:0030028
database_cross_reference: NIF_Subcellular:sao1046371754
database_cross_reference: Wikipedia:Filopodia
has_obo_namespace: cellular_component
id: GO:0030175
in_subset: goslim pir
comment: A filopodium may be approximately 0.1 um wide, 5-10 um long, and up to 50 um long in axon growth cones; contain a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward. Note that filopodia on dendritic shafts are distinct from other types of filopodia (even those found in dendritic growth cones) and may react differently to stimuli, as shown in PMID:12904473.

Axiom
annotated source: filopodium
annotated property: definition
annotated target: Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
database_cross_reference: GOC:mah
database_cross_reference: GOC:pr
database_cross_reference: ISBN:0815316194

enzyme regulator activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: has part
  some values from: protein binding
subclass of: Restriction
  on property: regulates
  some values from: catalytic activity
definition: Binds to and modulates the activity of an enzyme.
has_alternative_id: GO:0010576
has_exact_synonym: catalytic regulator activity
has_exact_synonym: enzyme modulator
has_narrow_synonym: metalloenzyme regulator activity
has_obo_namespace: molecular_function
id: GO:0030234
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
comment: This term should only be used in cases when the regulator directly interacts with the enzyme.

Axiom
annotated source: enzyme regulator activity
annotated property: definition
annotated target: Binds to and modulates the activity of an enzyme.
database_cross_reference: GOC:dph
database_cross_reference: GOC:mah
database_cross_reference: GOC:tb

Axiom
annotated source: enzyme regulator activity
annotated property: has_exact_synonym
annotated target: catalytic regulator activity
database_cross_reference: GOC:dph

carbohydrate binding
type: Class
subclass of: binding
definition: Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
has_alternative_id: GO:0005529
has_exact_synonym: sugar binding
has_obo_namespace: molecular_function
has_related_synonym: selectin
id: GO:0030246
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: carbohydrate binding
annotated property: definition
annotated target: Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
database_cross_reference: GOC:mah

external encapsulating structure
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
has_obo_namespace: cellular_component
id: GO:0030312
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
comment: The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.

Axiom
annotated source: external encapsulating structure
annotated property: definition
annotated target: A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
database_cross_reference: GOC:go_curators

cell envelope
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
database_cross_reference: Wikipedia:Cell_envelope
has_obo_namespace: cellular_component
id: GO:0030313
in_subset: goslim pir

Axiom
annotated source: cell envelope
annotated property: definition
annotated target: An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
database_cross_reference: GOC:ds
database_cross_reference: GOC:mlg
database_cross_reference: http://pathmicro.med.sc.edu/fox/cell_envelope.htm

site of polarized growth
type: Class
subclass of: cellular anatomical structure
definition: Any part of a cell where non-isotropic growth takes place.
has_alternative_id: GO:0000134
has_alternative_id: GO:0030483
has_obo_namespace: cellular_component
id: GO:0030427
in_subset: goslim candida
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: site of polarized growth
annotated property: definition
annotated target: Any part of a cell where non-isotropic growth takes place.
database_cross_reference: GOC:mah

cell septum
type: Class
subclass of: cellular anatomical structure
definition: A structure composed of peptidoglycan and often chitin in addition to other materials. It usually forms perpendicular to the long axis of a cell or hypha and grows centripetally from the cell wall to the center of the cell and often functions in the compartmentalization of a cell into two daughter cells.
has_broad_synonym: septum
has_exact_synonym: cross wall
has_obo_namespace: cellular_component
id: GO:0030428
in_subset: goslim pir

Axiom
annotated source: cell septum
annotated property: definition
annotated target: A structure composed of peptidoglycan and often chitin in addition to other materials. It usually forms perpendicular to the long axis of a cell or hypha and grows centripetally from the cell wall to the center of the cell and often functions in the compartmentalization of a cell into two daughter cells.
database_cross_reference: GOC:clt
database_cross_reference: ISBN:0471940526

sleep
type: Class
subclass of: multicellular organismal process
definition: Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.
database_cross_reference: Wikipedia:Sleep
has_obo_namespace: biological_process
has_related_synonym: diapause
has_related_synonym: dormancy
has_related_synonym: lethargus
id: GO:0030431
in_subset: goslim pir

Axiom
annotated source: sleep
annotated property: definition
annotated target: Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain.
database_cross_reference: ISBN:0192800981

midbody
type: Class
subclass of: cellular anatomical structure
definition: A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
database_cross_reference: Wikipedia:Midbody_(cell_biology)
has_obo_namespace: cellular_component
id: GO:0030496
in_subset: goslim pir

Axiom
annotated source: midbody
annotated property: definition
annotated target: A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
database_cross_reference: ISBN:0815316194

small nuclear ribonucleoprotein complex
type: Class
subclass of: ribonucleoprotein complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: A ribonucleoprotein complex that contains at least one RNA of the small nuclear RNA (snRNA) class and as well as its associated proteins. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP, U4/U6 snRNP, or 7SK snRNP. Many, of these complexes become part of the spliceosome involved in splicing of nuclear mRNAs. Others are involved in regulation of transcription elongation or 3'-end processing of replication-dependent histone pre-mRNAs.
database_cross_reference: Wikipedia:SnRNP
has_exact_synonym: small nuclear ribonucleoprotein
has_exact_synonym: snRNP
has_obo_namespace: cellular_component
id: GO:0030532
in_subset: goslim pir

Axiom
annotated source: small nuclear ribonucleoprotein complex
annotated property: definition
annotated target: A ribonucleoprotein complex that contains at least one RNA of the small nuclear RNA (snRNA) class and as well as its associated proteins. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP, U4/U6 snRNP, or 7SK snRNP. Many, of these complexes become part of the spliceosome involved in splicing of nuclear mRNAs. Others are involved in regulation of transcription elongation or 3'-end processing of replication-dependent histone pre-mRNAs.
database_cross_reference: GOC:krc
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0879695897

ribonuclease P complex
type: Class
subclass of: ribonucleoprotein complex
definition: A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs.
has_exact_synonym: RNase P complex
has_obo_namespace: cellular_component
id: GO:0030677
in_subset: goslim pir
comment: Note that chloroplasts possess a complex that is called 'RNase P' because it catalyzes pre-tRNA cleavage, but the chloroplast complex appears not to contain RNA.

Axiom
annotated source: ribonuclease P complex
annotated property: definition
annotated target: A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs.
database_cross_reference: GOC:mah
database_cross_reference: PMID:12045094

preribosome
type: Class
subclass of: ribonucleoprotein complex
definition: Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis.
has_obo_namespace: cellular_component
id: GO:0030684
in_subset: goslim pir

Axiom
annotated source: preribosome
annotated property: definition
annotated target: Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis.
database_cross_reference: PMID:10567516

Noc complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: Any of several heterodimers containing one or two Noc proteins, associated with preribosomal complexes; involved in ribosome biogenesis.
has_obo_namespace: cellular_component
id: GO:0030689
in_subset: goslim pir
comment: Noc complexes exhibit a dynamic intranuclear location; consider also annotating to 'nucleolus ; GO:0005730' and/or 'nucleoplasm ; GO:0005654'. Note that the definition uses Saccharomyces gene product names because this complex has only been described in Saccharomyces cerevisiae and no other names have yet arisen; the term nevertheless can be used for analogous complexes in other eukaryotes, and the definition can be changed if better wording is found.

Axiom
annotated source: Noc complex
annotated property: definition
annotated target: Any of several heterodimers containing one or two Noc proteins, associated with preribosomal complexes; involved in ribosome biogenesis.
database_cross_reference: PMID:12446671

RNA polymerase complex
type: Class
subclass of: protein-containing complex
definition: Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits.
has_exact_synonym: multisubunit RNA polymerase
has_obo_namespace: cellular_component
id: GO:0030880
in_subset: goslim pir

Axiom
annotated source: RNA polymerase complex
annotated property: definition
annotated target: Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits.
database_cross_reference: GOC:mah

replisome
type: Class
subclass of: protein-DNA complex
subclass of: Restriction
  on property: part of
  some values from: chromosome
subclass of: Restriction
  on property: has part
  some values from: DNA helicase complex
subclass of: Restriction
  on property: has part
  some values from: DNA polymerase complex
definition: A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins.
database_cross_reference: Wikipedia:Replisome
has_obo_namespace: cellular_component
has_related_synonym: DNA synthesome complex
has_related_synonym: RC complex
has_related_synonym: replication-competent complex
id: GO:0030894
in_subset: goslim pir

Axiom
annotated source: replisome
annotated property: definition
annotated target: A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins.
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw

Axiom
annotated source: replisome
annotated property: has_related_synonym
annotated target: DNA synthesome complex
database_cross_reference: CORUM:1001

Axiom
annotated source: replisome
annotated property: has_related_synonym
annotated target: RC complex
database_cross_reference: CORUM:309
database_cross_reference: PMID:12006500

Axiom
annotated source: replisome
annotated property: has_related_synonym
annotated target: replication-competent complex
database_cross_reference: CORUM:309
database_cross_reference: PMID:12006500

retromer complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.
has_obo_namespace: cellular_component
id: GO:0030904
in_subset: goslim pir

Axiom
annotated source: retromer complex
annotated property: definition
annotated target: A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.
database_cross_reference: GOC:bf
database_cross_reference: PMID:26220253
database_cross_reference: PMID:27385586
database_cross_reference: PMID:9700157

ADPG pyrophosphorylase complex
type: Class
subclass of: protein-containing complex
definition: Complex that possesses ADPG pyrophosphorylase activity. In all organisms where it has been found, the complex is a tetramer. In bacteria, it is a homotetramer. In plants, the complex is a heterotetramer composed small and large subunits.
has_obo_namespace: cellular_component
id: GO:0030929
in_subset: goslim pir

Axiom
annotated source: ADPG pyrophosphorylase complex
annotated property: definition
annotated target: Complex that possesses ADPG pyrophosphorylase activity. In all organisms where it has been found, the complex is a tetramer. In bacteria, it is a homotetramer. In plants, the complex is a heterotetramer composed small and large subunits.
database_cross_reference: GOC:tb
database_cross_reference: PMID:9680965

NADH dehydrogenase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyzes the transfer of a pair of electrons from NADH to a quinone.
has_alternative_id: GO:0030025
has_alternative_id: GO:0030966
has_alternative_id: GO:0031675
has_alternative_id: GO:0031677
has_alternative_id: GO:0031678
has_alternative_id: GO:0045280
database_cross_reference: Wikipedia:NADH_dehydrogenase
has_narrow_synonym: NADH dehydrogenase complex (plastoquinone)
has_narrow_synonym: NADH dehydrogenase complex (quinone)
has_narrow_synonym: NADH dehydrogenase complex (ubiquinone)
has_narrow_synonym: NADH:plastoquinone reductase complex
has_narrow_synonym: plastid NADH dehydrogenase complex (plastoquinone)
has_obo_namespace: cellular_component
id: GO:0030964
in_subset: goslim pir
comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function possessed by this complex is represented by the molecular function term 'NADH dehydrogenase (quinone) activity ; GO:0050136'.

Axiom
annotated source: NADH dehydrogenase complex
annotated property: definition
annotated target: An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyzes the transfer of a pair of electrons from NADH to a quinone.
database_cross_reference: GOC:mah

intraciliary transport particle
type: Class
subclass of: protein-containing complex
definition: A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.
has_exact_synonym: intraflagellar transport complex
has_exact_synonym: intraflagellar transport particle
has_obo_namespace: cellular_component
has_related_synonym: IFT complex
id: GO:0030990
in_subset: goslim pir
comment: Note that we deem cilia and microtubule-based flagella to be equivalent.

Axiom
annotated source: intraciliary transport particle
annotated property: definition
annotated target: A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.
database_cross_reference: GOC:cilia
database_cross_reference: GOC:kmv
database_cross_reference: PMID:14570576
database_cross_reference: PMID:22118932
database_cross_reference: PMID:23945166

extracellular matrix
type: Class
subclass of: external encapsulating structure
definition: A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
has_alternative_id: GO:0005578
database_cross_reference: NIF_Subcellular:nlx_subcell_20090513
database_cross_reference: Wikipedia:Extracellular_matrix
has_exact_synonym: proteinaceous extracellular matrix
has_narrow_synonym: matrisome
has_obo_namespace: cellular_component
id: GO:0031012
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim prokaryote

Axiom
annotated source: extracellular matrix
annotated property: definition
annotated target: A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
database_cross_reference: GOC:BHF
database_cross_reference: GOC:mah
database_cross_reference: GOC:rph
database_cross_reference: NIF_Subcellular:nlx_subcell_20090513
database_cross_reference: PMID:21123617
database_cross_reference: PMID:28089324

microtubule organizing center organization
type: Class
subclass of: cellular component organization
subclass of: Restriction
  on property: part of
  some values from: organelle organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow.
has_exact_synonym: microtubule organising center organisation
has_obo_namespace: biological_process
has_related_synonym: microtubule organizing center organization and biogenesis
id: GO:0031023
in_subset: goslim pir

Axiom
annotated source: microtubule organizing center organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow.
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: microtubule organizing center organization
annotated property: has_related_synonym
annotated target: microtubule organizing center organization and biogenesis
database_cross_reference: GOC:mah

glutamate synthase complex
type: Class
subclass of: protein-containing complex
definition: A complex that possesses glutamate synthase activity.
has_obo_namespace: cellular_component
id: GO:0031026
in_subset: goslim pir

Axiom
annotated source: glutamate synthase complex
annotated property: definition
annotated target: A complex that possesses glutamate synthase activity.
database_cross_reference: GOC:mah

programmed DNA elimination
type: Class
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: macromolecule biosynthetic process
subclass of: Restriction
  on property: negatively regulates
  some values from: macromolecule biosynthetic process
definition: A process in which genomic fragments or entire chromosomes are eliminated from somatic cells or from micronuclei of ciliates. This process occurs in the developing macronucleus (anlage) of a ciliate, as well as in other species, including vertebrates and is an irreversible mechanism of gene silencing.
term tracker item: https://github.com/geneontology/go-ontology/issues/22815
has_obo_namespace: biological_process
id: GO:0031049
in_subset: goslim pir

Axiom
annotated source: programmed DNA elimination
annotated property: definition
annotated target: A process in which genomic fragments or entire chromosomes are eliminated from somatic cells or from micronuclei of ciliates. This process occurs in the developing macronucleus (anlage) of a ciliate, as well as in other species, including vertebrates and is an irreversible mechanism of gene silencing.
database_cross_reference: GOC:mah
database_cross_reference: GOC:ns
database_cross_reference: PMID:18708581
database_cross_reference: PMID:24886889
database_cross_reference: PMID:32986476

nucleocytoplasmic transport complex
type: Class
subclass of: protein-containing complex
definition: Any complex that acts to move proteins or RNAs into or out of the nucleus through nuclear pores.
has_narrow_synonym: nucleocytoplasmic shuttling complex
has_obo_namespace: cellular_component
id: GO:0031074
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: nucleocytoplasmic transport complex
annotated property: definition
annotated target: Any complex that acts to move proteins or RNAs into or out of the nucleus through nuclear pores.
database_cross_reference: GOC:mah

BLOC complex
type: Class
subclass of: protein-containing complex
definition: Any of several protein complexes required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes, platelet dense granules, and other related organelles; acronym for biogenesis of lysosomal-related organelles complex.
has_exact_synonym: BLOC-1 related complex
has_obo_namespace: cellular_component
id: GO:0031082
in_subset: goslim pir

Axiom
annotated source: BLOC complex
annotated property: definition
annotated target: Any of several protein complexes required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes, platelet dense granules, and other related organelles; acronym for biogenesis of lysosomal-related organelles complex.
database_cross_reference: PMID:15102850
database_cross_reference: PMID:15261680

Axiom
annotated source: BLOC complex
annotated property: has_exact_synonym
annotated target: BLOC-1 related complex
database_cross_reference: PMID:25898167

platelet dense tubular network
type: Class
subclass of: intracellular membrane-bounded organelle
definition: A network of membrane-bounded compartments found in blood platelets, where they regulate platelet activation by sequestering or releasing calcium. The dense tubular network exists as thin elongated membranes in resting platelets, and undergoes a major ultrastructural change, to a rounded vesicular form, upon addition of thrombin.
has_obo_namespace: cellular_component
id: GO:0031094
in_subset: goslim pir

Axiom
annotated source: platelet dense tubular network
annotated property: definition
annotated target: A network of membrane-bounded compartments found in blood platelets, where they regulate platelet activation by sequestering or releasing calcium. The dense tubular network exists as thin elongated membranes in resting platelets, and undergoes a major ultrastructural change, to a rounded vesicular form, upon addition of thrombin.
database_cross_reference: PMID:1322202

septin complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
subclass of: Restriction
  on property: part of
  some values from: cytoskeleton
definition: A protein complex containing septins. Typically, these complexes contain multiple septins and are oligomeric.
has_obo_namespace: cellular_component
id: GO:0031105
in_subset: goslim pir

Axiom
annotated source: septin complex
annotated property: definition
annotated target: A protein complex containing septins. Typically, these complexes contain multiple septins and are oligomeric.
database_cross_reference: GOC:mah
database_cross_reference: PMID:15385632

pseudopodium
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.
term tracker item: https://github.com/geneontology/go-ontology/issues/21139
term tracker item: https://github.com/geneontology/go-ontology/issues/21141
database_cross_reference: Wikipedia:Pseudopod
has_exact_synonym: pseudopod
has_exact_synonym: pseudopodial protrusion
has_narrow_synonym: axopodium
has_narrow_synonym: lobopodium
has_narrow_synonym: reticulopodium
has_obo_namespace: cellular_component
id: GO:0031143
in_subset: goslim pir

Axiom
annotated source: pseudopodium
annotated property: definition
annotated target: A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.
database_cross_reference: ISBN:0198506732

endoplasmic reticulum Sec complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: endoplasmic reticulum
subclass of: Restriction
  on property: part of
  some values from: membrane
subclass of: Restriction
  on property: has part
  some values from: translocon complex
definition: An endoplasmic reticulum membrane-associated complex involved in the translocation of proteins that are targeted to the ER. In yeast, this complex consists of two subcomplexes, namely, the Sec61 complex and the Sec62/Sec63 complex.
has_obo_namespace: cellular_component
id: GO:0031205
in_subset: goslim pir

Axiom
annotated source: endoplasmic reticulum Sec complex
annotated property: definition
annotated target: An endoplasmic reticulum membrane-associated complex involved in the translocation of proteins that are targeted to the ER. In yeast, this complex consists of two subcomplexes, namely, the Sec61 complex and the Sec62/Sec63 complex.
database_cross_reference: GOC:mtg_sensu
database_cross_reference: PMID:14617809

protein acetyltransferase complex
type: Class
subclass of: protein-containing complex
definition: A complex that catalyzes the transfer of an acetyl group to a protein acceptor molecule.
has_obo_namespace: cellular_component
id: GO:0031248
in_subset: goslim pir

Axiom
annotated source: protein acetyltransferase complex
annotated property: definition
annotated target: A complex that catalyzes the transfer of an acetyl group to a protein acceptor molecule.
database_cross_reference: GOC:bf

cell leading edge
type: Class
subclass of: cellular anatomical structure
definition: The area of a motile cell closest to the direction of movement.
has_exact_synonym: front of cell
has_exact_synonym: leading edge of cell
has_obo_namespace: cellular_component
id: GO:0031252
in_subset: goslim pir

Axiom
annotated source: cell leading edge
annotated property: definition
annotated target: The area of a motile cell closest to the direction of movement.
database_cross_reference: GOC:pg

cell trailing edge
type: Class
subclass of: cellular anatomical structure
definition: The area of a motile cell opposite to the direction of movement.
has_exact_synonym: back of cell
has_exact_synonym: trailing edge
has_obo_namespace: cellular_component
id: GO:0031254
in_subset: goslim pir

Axiom
annotated source: cell trailing edge
annotated property: definition
annotated target: The area of a motile cell opposite to the direction of movement.
database_cross_reference: GOC:pg

death-inducing signaling complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A protein complex formed by the association of signaling proteins with a death receptor upon ligand binding. The complex includes procaspases and death domain-containing proteins in addition to the ligand-bound receptor, and may control the activation of caspases 8 and 10.
database_cross_reference: Wikipedia:Death-inducing_signaling_complex
has_exact_synonym: DISC
has_exact_synonym: DISC protein complex
has_exact_synonym: death receptor-induced signaling complex
has_exact_synonym: death receptor-induced signalling complex
has_exact_synonym: death-inducing signalling complex
has_obo_namespace: cellular_component
id: GO:0031264
in_subset: goslim pir
comment: Gene products that may be annotated to this term include: 1) ligand-bound receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer); 2) signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10.

Axiom
annotated source: death-inducing signaling complex
annotated property: definition
annotated target: A protein complex formed by the association of signaling proteins with a death receptor upon ligand binding. The complex includes procaspases and death domain-containing proteins in addition to the ligand-bound receptor, and may control the activation of caspases 8 and 10.
database_cross_reference: GOC:mtg_apoptosis
database_cross_reference: PMID:12628743
database_cross_reference: PMID:12655293
database_cross_reference: PMID:8521815

RNAi effector complex
type: Class
subclass of: ribonucleoprotein complex
definition: Any protein complex that mediates the effects of small interfering RNAs on gene expression. Most known examples contain one or more members of the Argonaute family of proteins.
has_obo_namespace: cellular_component
id: GO:0031332
in_subset: goslim pir

Axiom
annotated source: RNAi effector complex
annotated property: definition
annotated target: Any protein complex that mediates the effects of small interfering RNAs on gene expression. Most known examples contain one or more members of the Argonaute family of proteins.
database_cross_reference: GOC:mah
database_cross_reference: PMID:14704433

ubiquitin conjugating enzyme complex
type: Class
subclass of: protein-containing complex
definition: Any complex that possesses ubiquitin conjugating enzyme activity.
has_obo_namespace: cellular_component
has_related_synonym: E2 complex
id: GO:0031371
in_subset: goslim pir

Axiom
annotated source: ubiquitin conjugating enzyme complex
annotated property: definition
annotated target: Any complex that possesses ubiquitin conjugating enzyme activity.
database_cross_reference: GOC:mah

protein tag activity
type: Class
subclass of: molecular_function
definition: A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
has_broad_synonym: covalent modifier
has_exact_synonym: protein tag
has_exact_synonym: ubiquitin-like protein modifier
has_obo_namespace: molecular_function
has_related_synonym: protein tagging activity
has_related_synonym: ubiquitin
id: GO:0031386
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim prokaryote
comment: Use this term to annotate conjugated tags, not for conjugating enzymes. At the time of writing, all known gene products with this activity are ubiquitin-like, either based on overall sequence similarity or the presence of common motifs and structures.

Axiom
annotated source: protein tag activity
annotated property: definition
annotated target: A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
database_cross_reference: GOC:dos
database_cross_reference: PMID:19028679
database_cross_reference: PMID:20054389
database_cross_reference: PMID:6305978

Axiom
annotated source: protein tag activity
annotated property: has_broad_synonym
annotated target: covalent modifier
database_cross_reference: GOC:vw

carboxylic acid binding
type: Class
subclass of: ion binding
definition: Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
has_obo_namespace: molecular_function
id: GO:0031406
in_subset: goslim pir

Axiom
annotated source: carboxylic acid binding
annotated property: definition
annotated target: Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0198506732

pigment binding
type: Class
subclass of: binding
definition: Binding to a pigment, a general or particular coloring matter in living organisms, e.g. melanin.
has_obo_namespace: molecular_function
id: GO:0031409
in_subset: goslim pir

Axiom
annotated source: pigment binding
annotated property: definition
annotated target: Binding to a pigment, a general or particular coloring matter in living organisms, e.g. melanin.
database_cross_reference: GOC:mah

bacterial microcompartment
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy.
term tracker item: https://github.com/geneontology/go-ontology/issues/16852
term tracker item: https://github.com/geneontology/go-ontology/issues/22465
has_broad_synonym: BAC
has_broad_synonym: BMC
has_broad_synonym: MCP
has_obo_namespace: cellular_component
has_related_synonym: polyhedral organelle
id: GO:0031469
in_subset: goslim pir

Axiom
annotated source: bacterial microcompartment
annotated property: definition
annotated target: An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy.
database_cross_reference: GOC:js
database_cross_reference: PMID:10498708
database_cross_reference: PMID:11844753
database_cross_reference: PMID:12923081
database_cross_reference: PMID:34058518
database_cross_reference: PMID:34340100

mannosyltransferase complex
type: Class
subclass of: protein-containing complex
definition: A complex that possesses mannosyltransferase activity.
has_obo_namespace: cellular_component
id: GO:0031501
in_subset: goslim pir

Axiom
annotated source: mannosyltransferase complex
annotated property: definition
annotated target: A complex that possesses mannosyltransferase activity.
database_cross_reference: GOC:mah

PcG protein complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
has_exact_synonym: Polycomb Group protein complex
has_obo_namespace: cellular_component
id: GO:0031519
in_subset: goslim pir

Axiom
annotated source: PcG protein complex
annotated property: definition
annotated target: A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
database_cross_reference: PMID:9372908

killing of cells of another organism
type: Class
subclass of: cell killing
subclass of: biological process involved in interspecies interaction between organisms
definition: Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
has_alternative_id: GO:0001908
has_exact_synonym: killing of cells of other organism
has_obo_namespace: biological_process
id: GO:0031640
in_subset: goslim pir

Axiom
annotated source: killing of cells of another organism
annotated property: definition
annotated target: Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
database_cross_reference: GOC:add

regulation of protein stability
type: Class
subclass of: regulation of biological quality
definition: Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
has_obo_namespace: biological_process
id: GO:0031647
in_subset: goslim pir

Axiom
annotated source: regulation of protein stability
annotated property: definition
annotated target: Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
database_cross_reference: GOC:dph
database_cross_reference: GOC:mah
database_cross_reference: GOC:tb

vesicle
type: Class
subclass of: organelle
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: Any small, fluid-filled, spherical organelle enclosed by membrane.
has_alternative_id: GO:0031988
database_cross_reference: NIF_Subcellular:sao221389602
database_cross_reference: Wikipedia:Vesicle_(biology)
has_obo_namespace: cellular_component
has_related_synonym: membrane-bounded vesicle
has_related_synonym: membrane-enclosed vesicle
id: GO:0031982
in_subset: goslim pir

Axiom
annotated source: vesicle
annotated property: definition
annotated target: Any small, fluid-filled, spherical organelle enclosed by membrane.
database_cross_reference: GOC:mah
database_cross_reference: GOC:pz
database_cross_reference: GOC:vesicles

energy transducer activity
type: Class
subclass of: molecular transducer activity
definition: The biological transducer activity that accepts energy and converts it to another form, often by transfer to another molecule within the cell.
has_obo_namespace: molecular_function
has_related_synonym: light harvesting activity
has_related_synonym: photon capture
id: GO:0031992
in_subset: goslim pir

Axiom
annotated source: energy transducer activity
annotated property: definition
annotated target: The biological transducer activity that accepts energy and converts it to another form, often by transfer to another molecule within the cell.
database_cross_reference: GOC:go_curators

bleb
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
database_cross_reference: Wikipedia:Bleb_(cell_biology)
has_exact_synonym: plasma membrane bleb
has_obo_namespace: cellular_component
id: GO:0032059
in_subset: goslim pir

Axiom
annotated source: bleb
annotated property: definition
annotated target: A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
database_cross_reference: GOC:mtg_apoptosis
database_cross_reference: PMID:12083798
database_cross_reference: PMID:16624291
database_cross_reference: Wikipedia:Bleb_(cell_biology)

Axiom
annotated source: bleb
annotated property: has_exact_synonym
annotated target: plasma membrane bleb
database_cross_reference: GOC:pr

cell division site
type: Class
subclass of: cellular anatomical structure
definition: The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
has_exact_synonym: cell division plane
has_obo_namespace: cellular_component
id: GO:0032153
in_subset: goslim pir
comment: Note that this term refers to the future site of division in a cell that has not yet divided.

Axiom
annotated source: cell division site
annotated property: definition
annotated target: The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
database_cross_reference: GOC:bf
database_cross_reference: GOC:imk
database_cross_reference: GOC:krc
database_cross_reference: GOC:ns
database_cross_reference: PMID:12101122
database_cross_reference: PMID:15380095
database_cross_reference: PMID:16983191
database_cross_reference: PMID:18165305

germ tube
type: Class
subclass of: cellular anatomical structure
definition: The slender tubular outgrowth first produced by most spores in germination.
database_cross_reference: Wikipedia:Germ_tube
has_obo_namespace: cellular_component
id: GO:0032179
in_subset: goslim pir

Axiom
annotated source: germ tube
annotated property: definition
annotated target: The slender tubular outgrowth first produced by most spores in germination.
database_cross_reference: ISBN:0877799148

transposition
type: Class
subclass of: biological_process
definition: Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. For elements that are transcribed as the first step of transposition, the process starts with the transcription of the transposable element, its translation and maturation, and ending with integration into DNA. For elements that are cut out, the process starts with the excision of the donor DNA and integrated into another site.
database_cross_reference: Wikipedia:Transposon
has_obo_namespace: biological_process
id: GO:0032196
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: transposition
annotated property: definition
annotated target: Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. For elements that are transcribed as the first step of transposition, the process starts with the transcription of the transposable element, its translation and maturation, and ending with integration into DNA. For elements that are cut out, the process starts with the excision of the donor DNA and integrated into another site.
database_cross_reference: ISBN:1555812090
database_cross_reference: PMID:14682279
database_cross_reference: PMID:25893143

mismatch repair complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: Any complex formed of proteins that act in mismatch repair.
has_obo_namespace: cellular_component
id: GO:0032300
in_subset: goslim pir

Axiom
annotated source: mismatch repair complex
annotated property: definition
annotated target: Any complex formed of proteins that act in mismatch repair.
database_cross_reference: GOC:mah

DNA geometric change
type: Class
subclass of: chromosome organization
definition: The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.
has_obo_namespace: biological_process
id: GO:0032392
in_subset: goslim pir
comment: Note that DNA geometric change and DNA topological change (GO:0006265) are distinct, but are usually coupled in vivo.

Axiom
annotated source: DNA geometric change
annotated property: definition
annotated target: The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.
database_cross_reference: GOC:mah

stereocilium bundle
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: has part
  some values from: neuron projection
definition: A bundle of cross-linked stereocilia, arranged around a kinocilium on the apical surface of a sensory hair cell (e.g. a neuromast, auditory or vestibular hair cell). Stereocilium bundles act as mechanosensory organelles by responding to fluid motion or fluid pressure changes.
has_exact_synonym: stereocilia bundle
has_obo_namespace: cellular_component
id: GO:0032421
in_subset: goslim pir

Axiom
annotated source: stereocilium bundle
annotated property: definition
annotated target: A bundle of cross-linked stereocilia, arranged around a kinocilium on the apical surface of a sensory hair cell (e.g. a neuromast, auditory or vestibular hair cell). Stereocilium bundles act as mechanosensory organelles by responding to fluid motion or fluid pressure changes.
database_cross_reference: GOC:ecd
database_cross_reference: PMID:15661519
database_cross_reference: PMID:7840137

demethylase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the removal of a methyl group from a substrate.
has_obo_namespace: molecular_function
id: GO:0032451
in_subset: goslim pir

Axiom
annotated source: demethylase activity
annotated property: definition
annotated target: Catalysis of the removal of a methyl group from a substrate.
database_cross_reference: GOC:mah

polyprenyl diphosphate synthase complex
type: Class
subclass of: protein-containing complex
definition: A complex that possesses polyprenyl diphosphate synthase activity involved in the synthesis of the isoprenoid chain of ubiquinone whose length varies between organisms.
term tracker item: https://github.com/geneontology/go-ontology/issues/26833
has_narrow_synonym: decaprenyl diphosphate synthase complex
has_obo_namespace: cellular_component
id: GO:0032476
in_subset: goslim pir

Axiom
annotated source: polyprenyl diphosphate synthase complex
annotated property: definition
annotated target: A complex that possesses polyprenyl diphosphate synthase activity involved in the synthesis of the isoprenoid chain of ubiquinone whose length varies between organisms.
database_cross_reference: GOC:mah
database_cross_reference: PMID:14519123
database_cross_reference: PMID:16262699

multicellular organismal process
type: Class
subclass of: biological_process
definition: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
created by: jl
creation date: 2012-09-19T16:07:47Z
has_alternative_id: GO:0044707
has_alternative_id: GO:0050874
has_exact_synonym: organismal physiological process
has_obo_namespace: biological_process
has_related_synonym: single-multicellular organism process
id: GO:0032501
in_subset: gocheck do not annotate
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: multicellular organismal process
annotated property: definition
annotated target: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
database_cross_reference: GOC:curators
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete
database_cross_reference: GOC:tb

developmental process
type: Class
subclass of: biological_process
definition: A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
created by: jl
creation date: 2012-12-19T12:21:31Z
has_alternative_id: GO:0044767
has_narrow_synonym: development
has_obo_namespace: biological_process
has_related_synonym: single-organism developmental process
id: GO:0032502
in_subset: goslim agr
in_subset: goslim flybase ribbon
in_subset: goslim pir

Axiom
annotated source: developmental process
annotated property: definition
annotated target: A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
database_cross_reference: GOC:isa_complete

cellular anatomical entity morphogenesis
type: Class
subclass of: cellular component organization
definition: The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system.
term tracker item: https://github.com/geneontology/go-ontology/issues/25496
term tracker item: https://github.com/geneontology/go-ontology/issues/26249
has_exact_synonym: cellular component morphogenesis
has_exact_synonym: cellular structure morphogenesis
has_obo_namespace: biological_process
id: GO:0032989
in_subset: goslim pir

Axiom
annotated source: cellular anatomical entity morphogenesis
annotated property: definition
annotated target: The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system.
database_cross_reference: GOC:dph
database_cross_reference: GOC:mah
database_cross_reference: GOC:tb

Axiom
annotated source: cellular anatomical entity morphogenesis
annotated property: has_exact_synonym
annotated target: cellular structure morphogenesis
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

protein-containing complex
type: Class
subclass of: cellular_component
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
has_alternative_id: GO:0043234
has_exact_synonym: macromolecular complex
has_exact_synonym: macromolecule complex
has_exact_synonym: protein containing complex
has_narrow_synonym: protein complex
has_narrow_synonym: protein-protein complex
has_obo_namespace: cellular_component
id: GO:0032991
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.

Axiom
annotated source: protein-containing complex
annotated property: definition
annotated target: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
database_cross_reference: GOC:dos
database_cross_reference: GOC:mah

protein-DNA complex
type: Class
subclass of: protein-containing complex
definition: A macromolecular complex containing both protein and DNA molecules.
has_exact_synonym: DNA-protein complex
has_obo_namespace: cellular_component
id: GO:0032993
in_subset: goslim pir
comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here.

Axiom
annotated source: protein-DNA complex
annotated property: definition
annotated target: A macromolecular complex containing both protein and DNA molecules.
database_cross_reference: GOC:mah

Axiom
annotated source: protein-DNA complex
annotated property: has_exact_synonym
annotated target: DNA-protein complex
database_cross_reference: GOC:mah

Fc receptor complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin.
has_broad_synonym: immunoglobulin receptor complex
has_exact_synonym: Fc-receptor complex
has_exact_synonym: FcR complex
has_obo_namespace: cellular_component
id: GO:0032997
in_subset: goslim pir

Axiom
annotated source: Fc receptor complex
annotated property: definition
annotated target: A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

DNA recombinase mediator complex
type: Class
subclass of: protein-containing complex
definition: A protein complex containing accessory proteins which bind a recombinase (e.g. Rad51) and bind single-stranded DNA (ssDNA), and promote nucleation of the recombinase onto ssDNA through facilitating recombinase-RPA exchange.
has_obo_namespace: cellular_component
id: GO:0033061
in_subset: goslim pir
comment: Many paralogs of Rad51 act as recombinase mediators. These paralogs dimerize (or occasionally form tetramers) amongst themselves to form complexes with ssDNA-binding activity, and which act as mediators of Rad51 presynaptic filament assembly.

Axiom
annotated source: DNA recombinase mediator complex
annotated property: definition
annotated target: A protein complex containing accessory proteins which bind a recombinase (e.g. Rad51) and bind single-stranded DNA (ssDNA), and promote nucleation of the recombinase onto ssDNA through facilitating recombinase-RPA exchange.
database_cross_reference: GOC:elh
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw
database_cross_reference: InterPro:IPR003488
database_cross_reference: PMID:12912992
database_cross_reference: PMID:32414915

attachment organelle
type: Class
subclass of: intracellular membrane-bounded organelle
definition: A membrane-bounded extension of the cell, originally characterized in Mycoplasma species, that contains an electron-dense core that is part of the cytoskeleton and is oriented lengthwise and ends distally in a bulbous knob (terminal button). Required for adherence to host cells and involved in gliding motility and cell division.
has_obo_namespace: cellular_component
id: GO:0033099
in_subset: goslim pir

Axiom
annotated source: attachment organelle
annotated property: definition
annotated target: A membrane-bounded extension of the cell, originally characterized in Mycoplasma species, that contains an electron-dense core that is part of the cytoskeleton and is oriented lengthwise and ends distally in a bulbous knob (terminal button). Required for adherence to host cells and involved in gliding motility and cell division.
database_cross_reference: PMID:11325545
database_cross_reference: PMID:12003948

DNA helicase complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that possesses DNA helicase activity.
has_obo_namespace: cellular_component
id: GO:0033202
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: DNA helicase complex
annotated property: definition
annotated target: A protein complex that possesses DNA helicase activity.
database_cross_reference: GOC:mah

amide binding
type: Class
subclass of: binding
definition: Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
has_obo_namespace: molecular_function
id: GO:0033218
in_subset: goslim pir

Axiom
annotated source: amide binding
annotated property: definition
annotated target: Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
database_cross_reference: GOC:mah

I-kappaB/NF-kappaB complex
type: Class
subclass of: protein-containing complex
definition: A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm.
has_obo_namespace: cellular_component
id: GO:0033256
in_subset: goslim pir

Axiom
annotated source: I-kappaB/NF-kappaB complex
annotated property: definition
annotated target: A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm.
database_cross_reference: GOC:bf
database_cross_reference: GOC:mah
database_cross_reference: PMID:9407099

histone methyltransferase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
definition: A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
has_obo_namespace: cellular_component
id: GO:0035097
in_subset: goslim pir

Axiom
annotated source: histone methyltransferase complex
annotated property: definition
annotated target: A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
database_cross_reference: GOC:bf

cytoneme
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: A long, thin, polarized cell projection that contains actin and can extend for distances many times the diameter of the cell. Cytonemes represent extensions of cell cytoplasm and typically have a diameter of approximately 0.2um.
database_cross_reference: Wikipedia:Membrane_nanotube
has_exact_synonym: membrane nanotube
has_obo_namespace: cellular_component
id: GO:0035230
in_subset: goslim pir

Axiom
annotated source: cytoneme
annotated property: definition
annotated target: A long, thin, polarized cell projection that contains actin and can extend for distances many times the diameter of the cell. Cytonemes represent extensions of cell cytoplasm and typically have a diameter of approximately 0.2um.
database_cross_reference: PMID:10367889
database_cross_reference: PMID:10675901

Axiom
annotated source: cytoneme
annotated property: has_exact_synonym
annotated target: membrane nanotube
database_cross_reference: Wikipedia:Membrane_nanotube

phthalate binding
type: Class
subclass of: carboxylic acid binding
definition: Binding to a phthalate, any ester or salt of phthalic acid.
has_obo_namespace: molecular_function
id: GO:0035273
in_subset: goslim pir

Axiom
annotated source: phthalate binding
annotated property: definition
annotated target: Binding to a phthalate, any ester or salt of phthalic acid.
database_cross_reference: PMID:31116073

protein modification process
type: Class
subclass of: protein metabolic process
subclass of: macromolecule modification
definition: The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
term tracker item: https://github.com/geneontology/go-ontology/issues/23112
created by: bf
creation date: 2012-04-26T01:47:12Z
has_alternative_id: GO:0006464
has_exact_synonym: cellular protein modification process
has_exact_synonym: process resulting in protein modification
has_exact_synonym: protein modification
has_obo_namespace: biological_process
id: GO:0036211
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim prokaryote

Axiom
annotated source: protein modification process
annotated property: definition
annotated target: The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

Axiom
annotated source: protein modification process
annotated property: has_exact_synonym
annotated target: protein modification
database_cross_reference: GOC:bf

signaling receptor activity
type: Class
subclass of: molecular transducer activity
definition: Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
created by: bf
creation date: 2011-08-01T02:45:27Z
has_alternative_id: GO:0004872
has_alternative_id: GO:0019041
has_broad_synonym: receptor activity
has_exact_synonym: receptor activity involved in signal transduction
has_exact_synonym: signalling receptor activity
has_obo_namespace: molecular_function
id: GO:0038023
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: signaling receptor activity
annotated property: definition
annotated target: Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
database_cross_reference: GOC:bf
database_cross_reference: GOC:signaling

Axiom
annotated source: signaling receptor activity
annotated property: has_exact_synonym
annotated target: receptor activity involved in signal transduction
database_cross_reference: GOC:bf

growth
type: Class
subclass of: biological_process
definition: The increase in size or mass of an entire organism, a part of an organism or a cell.
has_alternative_id: GO:0048590
has_obo_namespace: biological_process
has_related_synonym: growth pattern
has_related_synonym: non-developmental growth
id: GO:0040007
in_subset: gocheck do not annotate
in_subset: goslim chembl
in_subset: goslim pir
in_subset: goslim plant
comment: See also the biological process term 'cell growth ; GO:0016049'.

Axiom
annotated source: growth
annotated property: definition
annotated target: The increase in size or mass of an entire organism, a part of an organism or a cell.
database_cross_reference: GOC:bf
database_cross_reference: GOC:ma

Axiom
annotated source: growth
annotated property: has_related_synonym
annotated target: non-developmental growth
database_cross_reference: GOC:mah

locomotion
type: Class
subclass of: biological_process
definition: Self-propelled movement of a cell or organism from one location to another.
has_obo_namespace: biological_process
id: GO:0040011
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: locomotion
annotated property: definition
annotated target: Self-propelled movement of a cell or organism from one location to another.
database_cross_reference: GOC:dgh

fluid transport
type: Class
subclass of: transport
definition: The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
id: GO:0042044
in_subset: goslim pir

Axiom
annotated source: fluid transport
annotated property: definition
annotated target: The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:ai

chemoattractant activity
type: Class
subclass of: protein binding
subclass of: Restriction
  on property: part of
  some values from: cell communication
subclass of: Restriction
  on property: part of
  some values from: locomotion
subclass of: Restriction
  on property: part of
  some values from: regulation of biological process
subclass of: Restriction
  on property: part of
  some values from: response to stimulus
subclass of: Restriction
  on property: has part
  some values from: protein binding
subclass of: Restriction
  on property: regulates
  some values from: signaling receptor activity
subclass of: Restriction
  on property: positively regulates
  some values from: signaling receptor activity
definition: Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
has_broad_synonym: attractant
has_obo_namespace: molecular_function
id: GO:0042056
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: chemoattractant activity
annotated property: definition
annotated target: Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
database_cross_reference: GOC:go_curators
database_cross_reference: ISBN:0198506732

cellular ketone metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
has_exact_synonym: ketone metabolism
has_obo_namespace: biological_process
id: GO:0042180
in_subset: goslim pir

Axiom
annotated source: cellular ketone metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0787650153

ribosome biogenesis
type: Class
subclass of: cellular component biogenesis
definition: A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
has_alternative_id: GO:0007046
has_exact_synonym: ribosome biogenesis and assembly
has_obo_namespace: biological_process
id: GO:0042254
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: ribosome biogenesis
annotated property: definition
annotated target: A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
database_cross_reference: GOC:ma
database_cross_reference: PMID:26404467
database_cross_reference: Wikipedia:Ribosome_biogenesis

peptide binding
type: Class
subclass of: binding
definition: Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds.
has_obo_namespace: molecular_function
id: GO:0042277
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: peptide binding
annotated property: definition
annotated target: Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds.
database_cross_reference: GOC:jl

molting cycle
type: Class
subclass of: multicellular organismal process
definition: The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc.
has_obo_namespace: biological_process
id: GO:0042303
in_subset: goslim drosophila
in_subset: goslim pir

Axiom
annotated source: molting cycle
annotated property: definition
annotated target: The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732

pigment metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms, e.g. melanin.
has_exact_synonym: pigment metabolism
has_obo_namespace: biological_process
id: GO:0042440
in_subset: goslim drosophila
in_subset: goslim pir

Axiom
annotated source: pigment metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms, e.g. melanin.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732

hormone metabolic process
type: Class
subclass of: metabolic process
subclass of: regulation of biological quality
definition: The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
term tracker item: https://github.com/geneontology/go-ontology/issues/23965
has_alternative_id: GO:0034754
has_exact_synonym: hormone metabolism
has_obo_namespace: biological_process
has_related_synonym: cellular hormone metabolic process
id: GO:0042445
in_subset: goslim pir

Axiom
annotated source: hormone metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
database_cross_reference: GOC:jl

hormone binding
type: Class
subclass of: binding
definition: Binding to an hormone, a naturally occurring substance secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor.
has_obo_namespace: molecular_function
id: GO:0042562
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: hormone binding
annotated property: definition
annotated target: Binding to an hormone, a naturally occurring substance secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor.
database_cross_reference: GOC:jl

hydrogenosome
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A spherical, membrane-bounded organelle found in some anaerobic protozoa, which participates in ATP and molecular hydrogen formation.
database_cross_reference: Wikipedia:Hydrogenosome
has_obo_namespace: cellular_component
id: GO:0042566
in_subset: goslim pir

Axiom
annotated source: hydrogenosome
annotated property: definition
annotated target: A spherical, membrane-bounded organelle found in some anaerobic protozoa, which participates in ATP and molecular hydrogen formation.
database_cross_reference: GOC:jl
database_cross_reference: PMID:11197234
database_cross_reference: PMID:11293569

DNA polymerase complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
has_obo_namespace: cellular_component
id: GO:0042575
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: DNA polymerase complex
annotated property: definition
annotated target: A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
database_cross_reference: GOC:jl
database_cross_reference: PMID:12045093

microbody
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2).
database_cross_reference: Wikipedia:Microbody
has_obo_namespace: cellular_component
id: GO:0042579
in_subset: goslim pir

Axiom
annotated source: microbody
annotated property: definition
annotated target: Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2).
database_cross_reference: ISBN:0198506732

periplasmic space
type: Class
subclass of: cellular anatomical structure
definition: The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
has_alternative_id: GO:0005620
has_exact_synonym: periplasm
has_obo_namespace: cellular_component
id: GO:0042597
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: periplasmic space
annotated property: definition
annotated target: The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:md

egg chorion
type: Class
subclass of: external encapsulating structure
definition: A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish.
has_obo_namespace: cellular_component
id: GO:0042600
in_subset: goslim pir
comment: Note that this term does not refer to the extraembryonic membrane surrounding the embryo of amniote vertebrates as this is an anatomical structure and is therefore not covered by GO.

Axiom
annotated source: egg chorion
annotated property: definition
annotated target: A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0721662544

MHC protein complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
has_obo_namespace: cellular_component
id: GO:0042611
in_subset: goslim pir

Axiom
annotated source: MHC protein complex
annotated property: definition
annotated target: A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
database_cross_reference: GOC:add
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0781735149
database_cross_reference: PMID:15928678
database_cross_reference: PMID:16153240

poly(3-hydroxyalkanoate) metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving poly(3-hydroxyalkanoates), polyesters of 3-hydroxyacids produced as intracellular granules by a large variety of bacteria.
has_broad_synonym: PHA metabolic process
has_broad_synonym: PHA metabolism
has_exact_synonym: poly(3-hydroxyalkanoate) metabolism
has_obo_namespace: biological_process
id: GO:0042620
in_subset: goslim pir

Axiom
annotated source: poly(3-hydroxyalkanoate) metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving poly(3-hydroxyalkanoates), polyesters of 3-hydroxyacids produced as intracellular granules by a large variety of bacteria.
database_cross_reference: GOC:jl
database_cross_reference: PMID:9925580

biofilm formation
type: Class
subclass of: biological_process
definition: A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
term tracker item: https://github.com/geneontology/go-ontology/issues/17727
has_obo_namespace: biological_process
id: GO:0042710
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: biofilm formation
annotated property: definition
annotated target: A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
database_cross_reference: GOC:di
database_cross_reference: PMID:11932229

pheromone metabolic process
type: Class
subclass of: secondary metabolic process
subclass of: hormone metabolic process
definition: The chemical reactions and pathways involving pheromones, a substance that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
has_exact_synonym: pheromone metabolism
has_obo_namespace: biological_process
id: GO:0042810
in_subset: goslim pir

Axiom
annotated source: pheromone metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving pheromones, a substance that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
database_cross_reference: ISBN:0198506732

MHC class I peptide loading complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: endoplasmic reticulum
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A large, multisubunit complex which consists of the MHC class I-beta 2 microglobulin dimer, the transporter associated with antigen presentation (TAP), tapasin (an MHC-encoded membrane protein), the chaperone calreticulin and the thiol oxidoreductase ERp57. Functions in the assembly of peptides with newly synthesized MHC class I molecules.
has_exact_synonym: peptide-loading complex
has_obo_namespace: cellular_component
has_related_synonym: PLC
id: GO:0042824
in_subset: goslim pir
comment: Note that although this complex is located in the endoplasmic reticulum, there is some evidence that it may also be found in the Golgi.

Axiom
annotated source: MHC class I peptide loading complex
annotated property: definition
annotated target: A large, multisubunit complex which consists of the MHC class I-beta 2 microglobulin dimer, the transporter associated with antigen presentation (TAP), tapasin (an MHC-encoded membrane protein), the chaperone calreticulin and the thiol oxidoreductase ERp57. Functions in the assembly of peptides with newly synthesized MHC class I molecules.
database_cross_reference: GOC:jl
database_cross_reference: PMID:10631934

Axiom
annotated source: MHC class I peptide loading complex
annotated property: has_exact_synonym
annotated target: peptide-loading complex
database_cross_reference: GOC:bhm

Axiom
annotated source: MHC class I peptide loading complex
annotated property: has_related_synonym
annotated target: PLC
database_cross_reference: GOC:bhm

amide transport
type: Class
subclass of: transport
definition: The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has_obo_namespace: biological_process
id: GO:0042886
in_subset: goslim pir

Axiom
annotated source: amide transport
annotated property: definition
annotated target: The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732

xenobiotic transport
type: Class
subclass of: transport
definition: The directed movement of a xenobiotic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
term tracker item: https://github.com/geneontology/go-ontology/issues/19460
has_alternative_id: GO:0015893
has_obo_namespace: biological_process
has_related_synonym: drug transport
id: GO:0042908
in_subset: goslim pir

Axiom
annotated source: xenobiotic transport
annotated property: definition
annotated target: The directed movement of a xenobiotic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:krc

cell projection
type: Class
subclass of: cellular anatomical structure
definition: A prolongation or process extending from a cell, e.g. a flagellum or axon.
has_broad_synonym: cell process
has_broad_synonym: cellular process
has_exact_synonym: cellular projection
has_obo_namespace: cellular_component
id: GO:0042995
in_subset: goslim agr
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: cell projection
annotated property: definition
annotated target: A prolongation or process extending from a cell, e.g. a flagellum or axon.
database_cross_reference: GOC:jl
database_cross_reference: PMID:16318917

neuron projection
type: Class
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
database_cross_reference: NIF_Subcellular:sao867568886
has_exact_synonym: neuron process
has_exact_synonym: neuron protrusion
has_exact_synonym: neuronal cell projection
has_narrow_synonym: neurite
has_obo_namespace: cellular_component
has_related_synonym: nerve fiber
id: GO:0043005
in_subset: goslim pir

Axiom
annotated source: neuron projection
annotated property: definition
annotated target: A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
database_cross_reference: GOC:jl
database_cross_reference: PMID:3077060

Axiom
annotated source: neuron projection
annotated property: has_exact_synonym
annotated target: neuron protrusion
database_cross_reference: NIF_Subcellular:sao250931889

Axiom
annotated source: neuron projection
annotated property: has_related_synonym
annotated target: nerve fiber
database_cross_reference: GOC:dph

ribonucleoprotein complex binding
type: Class
subclass of: binding
definition: Binding to a complex of RNA and protein.
has_exact_synonym: RNP binding
has_exact_synonym: protein-RNA complex binding
has_exact_synonym: ribonucleoprotein binding
has_obo_namespace: molecular_function
id: GO:0043021
in_subset: goslim pir

Axiom
annotated source: ribonucleoprotein complex binding
annotated property: definition
annotated target: Binding to a complex of RNA and protein.
database_cross_reference: GOC:bf
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:vk

Axiom
annotated source: ribonucleoprotein complex binding
annotated property: has_exact_synonym
annotated target: protein-RNA complex binding
database_cross_reference: GOC:bf
database_cross_reference: GOC:vk

Axiom
annotated source: ribonucleoprotein complex binding
annotated property: has_exact_synonym
annotated target: ribonucleoprotein binding
database_cross_reference: GOC:bf
database_cross_reference: GOC:vk

neuronal cell body
type: Class
subclass of: cellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
database_cross_reference: NIF_Subcellular:sao1044911821
database_cross_reference: Wikipedia:Soma_(biology)
has_exact_synonym: neuron cell body
has_exact_synonym: neuronal cell soma
has_obo_namespace: cellular_component
id: GO:0043025
in_subset: goslim pir
comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections.

Axiom
annotated source: neuronal cell body
annotated property: definition
annotated target: The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
database_cross_reference: GOC:go_curators

isoamylase complex
type: Class
subclass of: protein-containing complex
definition: A protein complex whose composition varies amongst species; in rice it probably exists in a homo-tetramer to homo-hexamer form and in Gram-negative bacteria as a dimer. Functions in the hydrolysis of alpha-(1,6)-D-glucosidic branch linkages.
has_broad_synonym: debranching enzyme complex
has_obo_namespace: cellular_component
id: GO:0043033
in_subset: goslim pir

Axiom
annotated source: isoamylase complex
annotated property: definition
annotated target: A protein complex whose composition varies amongst species; in rice it probably exists in a homo-tetramer to homo-hexamer form and in Gram-negative bacteria as a dimer. Functions in the hydrolysis of alpha-(1,6)-D-glucosidic branch linkages.
database_cross_reference: GOC:jl
database_cross_reference: PMID:10333591

extracellular structure organization
type: Class
subclass of: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite.
has_exact_synonym: extracellular structure organisation
has_exact_synonym: extracellular structure organization and biogenesis
has_obo_namespace: biological_process
id: GO:0043062
in_subset: goslim pir
in_subset: goslim prokaryote

Axiom
annotated source: extracellular structure organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: extracellular structure organization
annotated property: has_exact_synonym
annotated target: extracellular structure organization and biogenesis
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

cellular metabolic compound salvage
type: Class
subclass of: metabolic process
definition: Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.
has_obo_namespace: biological_process
id: GO:0043094
in_subset: goslim pir

Axiom
annotated source: cellular metabolic compound salvage
annotated property: definition
annotated target: Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.
database_cross_reference: GOC:mlg

purine-containing compound salvage
type: Class
subclass of: nucleobase-containing compound metabolic process
subclass of: cellular metabolic compound salvage
definition: Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
has_obo_namespace: biological_process
has_related_synonym: purine salvage
id: GO:0043101
in_subset: goslim pir

Axiom
annotated source: purine-containing compound salvage
annotated property: definition
annotated target: Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
database_cross_reference: GOC:jl

cell envelope organization
type: Class
subclass of: external encapsulating structure organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cell envelope, everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present.
has_exact_synonym: cell envelope organisation
has_obo_namespace: biological_process
has_related_synonym: cell envelope organization and biogenesis
id: GO:0043163
in_subset: goslim pir

Axiom
annotated source: cell envelope organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cell envelope, everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present.
database_cross_reference: GOC:jl

Axiom
annotated source: cell envelope organization
annotated property: has_related_synonym
annotated target: cell envelope organization and biogenesis
database_cross_reference: GOC:mah

ion binding
type: Class
subclass of: binding
definition: Binding to an ion, a charged atoms or groups of atoms.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
has_obo_namespace: molecular_function
has_related_synonym: atom binding
id: GO:0043167
in_subset: gocheck do not annotate
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: ion binding
annotated property: definition
annotated target: Binding to an ion, a charged atoms or groups of atoms.
database_cross_reference: GOC:jl

macromolecule metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
has_alternative_id: GO:0034960
has_alternative_id: GO:0043283
has_alternative_id: GO:0044259
has_exact_synonym: biopolymer metabolic process
has_exact_synonym: macromolecule metabolism
has_exact_synonym: organismal macromolecule metabolism
has_narrow_synonym: multicellular organismal macromolecule metabolic process
has_obo_namespace: biological_process
id: GO:0043170
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: macromolecule metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
database_cross_reference: GOC:mah

Axiom
annotated source: macromolecule metabolic process
annotated property: has_exact_synonym
annotated target: biopolymer metabolic process
database_cross_reference: GOC:mtg_chebi_dec09

amine binding
type: Class
subclass of: binding
definition: Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group.
has_obo_namespace: molecular_function
id: GO:0043176
in_subset: goslim pir

Axiom
annotated source: amine binding
annotated property: definition
annotated target: Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group.
database_cross_reference: GOC:jl

alcohol binding
type: Class
subclass of: binding
definition: Binding to an alcohol, any of a class of alkyl compounds containing a hydroxyl group.
has_obo_namespace: molecular_function
id: GO:0043178
in_subset: goslim pir

Axiom
annotated source: alcohol binding
annotated property: definition
annotated target: Binding to an alcohol, any of a class of alkyl compounds containing a hydroxyl group.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198506732

ATP-binding cassette (ABC) transporter complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
has_alternative_id: GO:0043191
has_alternative_id: GO:0043192
has_narrow_synonym: ABC-type efflux permease complex
has_narrow_synonym: ABC-type efflux porter complex
has_narrow_synonym: ABC-type uptake permease complex
has_narrow_synonym: mating pheromone exporter
has_obo_namespace: cellular_component
id: GO:0043190
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: ATP-binding cassette (ABC) transporter complex
annotated property: definition
annotated target: A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
database_cross_reference: GOC:jl
database_cross_reference: GOC:mtg_sensu
database_cross_reference: PMID:11421269
database_cross_reference: PMID:15111107

organelle
type: Class
subclass of: cellular anatomical structure
definition: Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
database_cross_reference: NIF_Subcellular:sao1539965131
database_cross_reference: Wikipedia:Organelle
has_obo_namespace: cellular_component
id: GO:0043226
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: organelle
annotated property: definition
annotated target: Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
database_cross_reference: GOC:go_curators

intracellular organelle
type: Class
subclass of: organelle
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
term tracker item: https://github.com/geneontology/go-ontology/issues/28153
has_obo_namespace: cellular_component
id: GO:0043229
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: intracellular organelle
annotated property: definition
annotated target: Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
database_cross_reference: GOC:go_curators

extracellular organelle
type: Class
equivalent class: Class
  intersection of: organelle
  intersection of: Restriction
    on property: part of
    some values from: extracellular region
subclass of: organelle
subclass of: Restriction
  on property: part of
  some values from: extracellular region
definition: Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi.
has_obo_namespace: cellular_component
id: GO:0043230
in_subset: goslim pir

Axiom
annotated source: extracellular organelle
annotated property: definition
annotated target: Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi.
database_cross_reference: GOC:jl
database_cross_reference: PMID:9914479

intracellular membrane-bounded organelle
type: Class
subclass of: intracellular organelle
subclass of: Restriction
  on property: has part
  some values from: membrane
definition: Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
has_exact_synonym: intracellular membrane-enclosed organelle
has_obo_namespace: cellular_component
id: GO:0043231
in_subset: goslim pir

Axiom
annotated source: intracellular membrane-bounded organelle
annotated property: definition
annotated target: Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
database_cross_reference: GOC:go_curators

intracellular non-membrane-bounded organelle
type: Class
subclass of: intracellular organelle
definition: Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
has_exact_synonym: intracellular non-membrane-enclosed organelle
has_obo_namespace: cellular_component
id: GO:0043232
in_subset: goslim pir

Axiom
annotated source: intracellular non-membrane-bounded organelle
annotated property: definition
annotated target: Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
database_cross_reference: GOC:go_curators

receptor complex
type: Class
subclass of: protein-containing complex
definition: Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
has_obo_namespace: cellular_component
id: GO:0043235
in_subset: goslim pir

Axiom
annotated source: receptor complex
annotated property: definition
annotated target: Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
database_cross_reference: GOC:go_curators

laminin complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: extracellular matrix
definition: A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes.
has_obo_namespace: cellular_component
id: GO:0043256
in_subset: goslim pir

Axiom
annotated source: laminin complex
annotated property: definition
annotated target: A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes.
database_cross_reference: GOC:jl
database_cross_reference: PMID:10842354

glycyl-radical enzyme activating activity
type: Class
subclass of: oxidoreductase activity
definition: Catalyzes the activation of an enzyme by generating an organic free radical on a glycine residue via a homolytic cleavage of S-adenosyl-L-methionine (SAM).
term tracker item: https://github.com/geneontology/go-ontology/issues/14190
has_broad_synonym: catalysis of free radical formation
database_cross_reference: EC:1.97.1.-
has_obo_namespace: molecular_function
id: GO:0043364
in_subset: goslim pir

Axiom
annotated source: glycyl-radical enzyme activating activity
annotated property: definition
annotated target: Catalyzes the activation of an enzyme by generating an organic free radical on a glycine residue via a homolytic cleavage of S-adenosyl-L-methionine (SAM).
database_cross_reference: GOC:jl
database_cross_reference: PMID:24486374

macromolecule modification
type: Class
subclass of: macromolecule metabolic process
definition: The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
has_obo_namespace: biological_process
id: GO:0043412
in_subset: gocheck obsoletion candidate
in_subset: goslim pir

Axiom
annotated source: macromolecule modification
annotated property: definition
annotated target: The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.
database_cross_reference: GOC:go_curators

cellular alkane metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving an alkane, any acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, as carried out by individual cells.
has_exact_synonym: alkane metabolism
has_obo_namespace: biological_process
id: GO:0043446
in_subset: goslim pir

Axiom
annotated source: cellular alkane metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving an alkane, any acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, as carried out by individual cells.
database_cross_reference: GOC:jl
database_cross_reference: Wikipedia:Alkane

cellular alkene metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving an alkene, any acyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n, as carried out by individual cells.
has_exact_synonym: alkene metabolism
has_obo_namespace: biological_process
id: GO:0043449
in_subset: goslim pir

Axiom
annotated source: cellular alkene metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving an alkene, any acyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n, as carried out by individual cells.
database_cross_reference: GOC:jl
database_cross_reference: Wikipedia:Alkene

cellular alkyne metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving an alkyne, any acyclic branched or unbranched hydrocarbon (compound composed only of carbon and hydrogen) having a carbon-carbon triple bond and the general formula CnH2n-2, as carried out by individual cells.
has_exact_synonym: alkyne metabolism
has_obo_namespace: biological_process
id: GO:0043452
in_subset: goslim pir

Axiom
annotated source: cellular alkyne metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving an alkyne, any acyclic branched or unbranched hydrocarbon (compound composed only of carbon and hydrogen) having a carbon-carbon triple bond and the general formula CnH2n-2, as carried out by individual cells.
database_cross_reference: GOC:jl
database_cross_reference: GOC:krc
database_cross_reference: Wikipedia:Alkyne

pigmentation
type: Class
subclass of: biological_process
definition: The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
has_obo_namespace: biological_process
id: GO:0043473
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: pigmentation
annotated property: definition
annotated target: The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
database_cross_reference: GOC:jl

muscle adaptation
type: Class
subclass of: multicellular organismal process
subclass of: response to stimulus
definition: A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
has_obo_namespace: biological_process
has_related_synonym: muscle plasticity
id: GO:0043500
in_subset: goslim pir

Axiom
annotated source: muscle adaptation
annotated property: definition
annotated target: A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities.
database_cross_reference: GOC:mtg_muscle
database_cross_reference: PMID:11181628
database_cross_reference: PMID:11449884
database_cross_reference: PMID:12605307

inhibin complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: extracellular region
definition: Heterodimeric hormone composed of an inhibin alpha subunit complexed with either an inhibin beta-A subunit, to form inhibin A, or an inhibin beta-B subunit, to form inhibin B.
has_obo_namespace: cellular_component
id: GO:0043511
in_subset: goslim pir
comment: Note that the actions of the inhibin complex are the opposite of those of the activin complex, which is a dimer of an inhibin beta-A and/or inhibin beta-B subunit. See also the cellular component term 'activin complex ; GO:0048180'.

Axiom
annotated source: inhibin complex
annotated property: definition
annotated target: Heterodimeric hormone composed of an inhibin alpha subunit complexed with either an inhibin beta-A subunit, to form inhibin A, or an inhibin beta-B subunit, to form inhibin B.
database_cross_reference: GOC:jl

tRNA methyltransferase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cellular anatomical structure
definition: A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.
term tracker item: https://github.com/geneontology/go-ontology/issues/27929
has_obo_namespace: cellular_component
id: GO:0043527
in_subset: goslim pir

Axiom
annotated source: tRNA methyltransferase complex
annotated property: definition
annotated target: A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.
database_cross_reference: GOC:jl
database_cross_reference: PMID:24904644
database_cross_reference: PMID:9851972

endospore external encapsulating structure
type: Class
subclass of: cell wall
definition: The structures that lie outside the inner membrane and surround the entire endospore; consists of a peptidoglycan-containing inner layer (the endospore cortex) surrounded by a multilayered proteinaceous coat. An exosporium may be present as an extreme outer layer.
has_alternative_id: GO:0055030
has_broad_synonym: spore wall
has_exact_synonym: endospore wall
has_exact_synonym: peptidoglycan-based spore wall
has_obo_namespace: cellular_component
id: GO:0043591
in_subset: goslim pir

Axiom
annotated source: endospore external encapsulating structure
annotated property: definition
annotated target: The structures that lie outside the inner membrane and surround the entire endospore; consists of a peptidoglycan-containing inner layer (the endospore cortex) surrounded by a multilayered proteinaceous coat. An exosporium may be present as an extreme outer layer.
database_cross_reference: GOC:go_curators
database_cross_reference: PMID:15035041

Axiom
annotated source: endospore external encapsulating structure
annotated property: has_broad_synonym
annotated target: spore wall
database_cross_reference: GOC:mtg_sensu

Axiom
annotated source: endospore external encapsulating structure
annotated property: has_exact_synonym
annotated target: endospore wall
database_cross_reference: GOC:mah

Axiom
annotated source: endospore external encapsulating structure
annotated property: has_exact_synonym
annotated target: peptidoglycan-based spore wall
database_cross_reference: GOC:mtg_sensu

amide metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
has_exact_synonym: amide metabolism
has_exact_synonym: cellular amide metabolic process
has_obo_namespace: biological_process
id: GO:0043603
in_subset: gocheck do not annotate
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: amide metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
database_cross_reference: GOC:curators

cellular component biogenesis
type: Class
subclass of: biological_process
definition: A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
term tracker item: https://github.com/geneontology/go-ontology/issues/27194
has_alternative_id: GO:0071843
has_exact_synonym: cellular component biogenesis at cellular level
has_obo_namespace: biological_process
id: GO:0044085
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: cellular component biogenesis
annotated property: definition
annotated target: A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

primary metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
database_cross_reference: Wikipedia:Primary_metabolite
has_exact_synonym: primary metabolism
has_obo_namespace: biological_process
id: GO:0044238
in_subset: gocheck do not annotate
in_subset: goslim euk cellular processes ribbon
in_subset: goslim pir
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: primary metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
database_cross_reference: GOC:go_curators

cellular lipid metabolic process
type: Class
subclass of: lipid metabolic process
definition: The chemical reactions and pathways involving lipids, as carried out by individual cells.
has_exact_synonym: cellular lipid metabolism
has_obo_namespace: biological_process
id: GO:0044255
in_subset: goslim pir

Axiom
annotated source: cellular lipid metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving lipids, as carried out by individual cells.
database_cross_reference: GOC:jl

biological process involved in interspecies interaction between organisms
type: Class
subclass of: biological_process
definition: Any process evolved to enable an interaction with an organism of a different species.
term tracker item: https://github.com/geneontology/go-ontology/issues/20191
has_exact_synonym: interaction with another species
has_exact_synonym: interspecies interaction
has_exact_synonym: interspecies interaction between organisms
has_exact_synonym: interspecies interaction with other organisms
has_obo_namespace: biological_process
id: GO:0044419
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: biological process involved in interspecies interaction between organisms
annotated property: definition
annotated target: Any process evolved to enable an interaction with an organism of a different species.
database_cross_reference: GOC:cc

virion component
type: Class
subclass of: cellular_component
disjoint with: cellular anatomical structure
definition: Any constituent part of a virion, a complete fully infectious extracellular virus particle.
has_alternative_id: GO:0019012
database_cross_reference: Wikipedia:Virus
has_exact_synonym: virion part
has_obo_namespace: cellular_component
has_related_synonym: complete virus particle
has_related_synonym: virion
id: GO:0044423
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: virion component
annotated property: definition
annotated target: Any constituent part of a virion, a complete fully infectious extracellular virus particle.
database_cross_reference: GOC:jl

apical part of cell
type: Class
subclass of: cellular anatomical structure
definition: The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
has_exact_synonym: apical region of cell
has_obo_namespace: cellular_component
id: GO:0045177
in_subset: goslim pir

Axiom
annotated source: apical part of cell
annotated property: definition
annotated target: The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0815316194

Axiom
annotated source: apical part of cell
annotated property: has_exact_synonym
annotated target: apical region of cell
database_cross_reference: GOC:krc

basal part of cell
type: Class
subclass of: cellular anatomical structure
definition: The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
has_obo_namespace: cellular_component
id: GO:0045178
in_subset: goslim pir

Axiom
annotated source: basal part of cell
annotated property: definition
annotated target: The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0815316194

translation regulator activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: part of
  some values from: regulation of biological process
definition: Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
has_exact_synonym: translation factor activity
has_obo_namespace: molecular_function
id: GO:0045182
in_subset: goslim candida
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: translation regulator activity
annotated property: definition
annotated target: Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
database_cross_reference: GOC:ai

synapse
type: Class
subclass of: cellular anatomical structure
definition: The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
database_cross_reference: NIF_Subcellular:sao914572699
database_cross_reference: Wikipedia:Chemical_synapse
has_exact_synonym: synaptic junction
has_narrow_synonym: mixed synapse
has_obo_namespace: cellular_component
has_related_synonym: electrotonic synapse
id: GO:0045202
in_subset: goslim agr
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim synapse

Axiom
annotated source: synapse
annotated property: definition
annotated target: The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
database_cross_reference: GOC:aruk
database_cross_reference: ISBN:0198506732
database_cross_reference: PMID:24619342
database_cross_reference: PMID:29383328
database_cross_reference: PMID:31998110

Axiom
annotated source: synapse
annotated property: has_narrow_synonym
annotated target: mixed synapse
database_cross_reference: NIF_Subcellular:sao1506103497

Axiom
annotated source: synapse
annotated property: has_related_synonym
annotated target: electrotonic synapse
database_cross_reference: NIF_Subcellular:sao1311109124

external encapsulating structure organization
type: Class
subclass of: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell.
has_exact_synonym: external encapsulating structure organisation
has_exact_synonym: external encapsulating structure organization and biogenesis
has_obo_namespace: biological_process
id: GO:0045229
in_subset: goslim pir

Axiom
annotated source: external encapsulating structure organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: external encapsulating structure organization
annotated property: has_exact_synonym
annotated target: external encapsulating structure organization and biogenesis
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

capsule organization
type: Class
subclass of: external encapsulating structure organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the capsule, a protective structure surrounding some species of bacteria and fungi.
has_exact_synonym: capsule organisation
has_obo_namespace: biological_process
has_related_synonym: capsule organization and biogenesis
id: GO:0045230
in_subset: goslim pir

Axiom
annotated source: capsule organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the capsule, a protective structure surrounding some species of bacteria and fungi.
database_cross_reference: GOC:ai

slime layer organization
type: Class
subclass of: external encapsulating structure organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a slime layer. A slime layer is an easily removed, diffuse, unorganized layer of extracellular material that surrounds a cell.
has_exact_synonym: slime layer organisation
has_obo_namespace: biological_process
has_related_synonym: slime layer organization and biogenesis
id: GO:0045231
in_subset: goslim pir

Axiom
annotated source: slime layer organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a slime layer. A slime layer is an easily removed, diffuse, unorganized layer of extracellular material that surrounds a cell.
database_cross_reference: GOC:ai

Axiom
annotated source: slime layer organization
annotated property: has_related_synonym
annotated target: slime layer organization and biogenesis
database_cross_reference: GOC:mah

tricarboxylic acid cycle heteromeric enzyme complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: Any of the heteromeric enzymes that act in the TCA cycle.
has_exact_synonym: TCA cycle enzyme complex
has_obo_namespace: cellular_component
id: GO:0045239
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: tricarboxylic acid cycle heteromeric enzyme complex
annotated property: definition
annotated target: Any of the heteromeric enzymes that act in the TCA cycle.
database_cross_reference: GOC:mah

electron transfer flavoprotein complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A protein complex facilitating the electron transfer from an acyl-CoA molecule to ubiquinone via its flavin adenine dinucleotide (FAD) cofactor. Usually contains an alpha and a beta subunit and the structural cofactor adenosine monophosphate (AMP). Part of a system that oxidizes an acyl-CoA molecule and reduces ubiquinone and other acceptors in the electron transport system.
has_exact_synonym: ETF complex
has_obo_namespace: cellular_component
id: GO:0045251
in_subset: goslim pir

Axiom
annotated source: electron transfer flavoprotein complex
annotated property: definition
annotated target: A protein complex facilitating the electron transfer from an acyl-CoA molecule to ubiquinone via its flavin adenine dinucleotide (FAD) cofactor. Usually contains an alpha and a beta subunit and the structural cofactor adenosine monophosphate (AMP). Part of a system that oxidizes an acyl-CoA molecule and reduces ubiquinone and other acceptors in the electron transport system.
database_cross_reference: GOC:bhm
database_cross_reference: ISBN:0198506732

Axiom
annotated source: electron transfer flavoprotein complex
annotated property: has_exact_synonym
annotated target: ETF complex
database_cross_reference: GOC:bhm

oxoglutarate dehydrogenase complex
type: Class
subclass of: tricarboxylic acid cycle heteromeric enzyme complex
definition: A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.
term tracker item: https://github.com/geneontology/go-ontology/issues/26122
term tracker item: https://github.com/geneontology/go-ontology/issues/26881
database_cross_reference: Wikipedia:Oxoglutarate_dehydrogenase_complex
has_exact_synonym: KGDHC
has_exact_synonym: alpha-ketoglutarate dehydrogenase complex
has_exact_synonym: dihydrolipoamide S-succinyltransferase complex
has_obo_namespace: cellular_component
id: GO:0045252
in_subset: goslim pir
comment: The catalytic activities of the individual components of this complex are represented by the molecular function terms 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591' (E1), 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' (E2), and 'dihydrolipoyl dehydrogenase activity ; GO:0004148' (E3). The overall catalytic activity of the complex is represented by the molecular function term 'oxoglutarate dehydrogenase (NAD+) activity ; GO:0034602'.

Axiom
annotated source: oxoglutarate dehydrogenase complex
annotated property: definition
annotated target: A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.
database_cross_reference: PMID:10672230

pyruvate dehydrogenase (lipoamide) phosphatase complex
type: Class
subclass of: protein serine/threonine phosphatase complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A complex of a regulatory and catalytic subunit that catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
has_obo_namespace: cellular_component
id: GO:0045253
in_subset: goslim pir
comment: See also the cellular component term 'cytosolic pyruvate dehydrogenase complex ; GO:0045250'.

Axiom
annotated source: pyruvate dehydrogenase (lipoamide) phosphatase complex
annotated property: definition
annotated target: A complex of a regulatory and catalytic subunit that catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
database_cross_reference: PMID:9395502

pyruvate dehydrogenase complex
type: Class
subclass of: protein-containing complex
definition: A multi-enzyme complex that catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: pyruvate dehydrogenase (E1, which may be a homodimer or a heterotetramer of two alpha and two beta subunits, depending on species), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.
term tracker item: https://github.com/geneontology/go-ontology/issues/26122
term tracker item: https://github.com/geneontology/go-ontology/issues/26881
has_alternative_id: GO:0009364
database_cross_reference: Wikipedia:Pyruvate_dehydrogenase_complex
has_exact_synonym: pyruvate dehydrogenase complex (lipoamide)
has_obo_namespace: cellular_component
id: GO:0045254
in_subset: goslim pir
comment: The catalytic activities of the individual components of this complex are represented by the molecular function terms 'pyruvate dehydrogenase (acetyl-transferring) activity ; GO:0004739' (E1), 'dihydrolipoyllysine-residue acetyltransferase activity ; GO:0004742' (E2), and 'dihydrolipoyl dehydrogenase activity ; GO:0004148' (E3). The overall catalytic activity of the complex is represented by the molecular function term 'pyruvate dehydrogenase (NAD+) activity ; GO:0034604'.

Axiom
annotated source: pyruvate dehydrogenase complex
annotated property: definition
annotated target: A multi-enzyme complex that catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: pyruvate dehydrogenase (E1, which may be a homodimer or a heterotetramer of two alpha and two beta subunits, depending on species), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.
database_cross_reference: PMID:36863425

respiratory chain complex II (succinate dehydrogenase)
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A part of the respiratory chain, containing the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain.
term tracker item: https://github.com/geneontology/go-ontology/issues/27253
term tracker item: https://github.com/geneontology/go-ontology/issues/28017
has_obo_namespace: cellular_component
has_related_synonym: electron transport complex II
id: GO:0045273
in_subset: goslim pir

Axiom
annotated source: respiratory chain complex II (succinate dehydrogenase)
annotated property: definition
annotated target: A part of the respiratory chain, containing the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain.
database_cross_reference: ISBN:0198547684

respiratory chain complex III
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A protein complex that transfers electrons from ubiquinol to cytochrome c and translocates two protons across a membrane. The complex contains a core structure of three catalytic subunits: cytochrome b, the Rieske iron sulfur protein (ISP), and cytochrome c1, which are arranged in an integral membrane-bound dimeric complex; additional subunits are present, and vary among different species.
has_alternative_id: GO:0032842
has_alternative_id: GO:0045285
database_cross_reference: Wikipedia:Coenzyme_Q_-_cytochrome_c_reductase
has_exact_synonym: complex III
has_exact_synonym: cytochrome bc(1) complex
has_exact_synonym: cytochrome bc1 complex
has_exact_synonym: ubiquinol-cytochrome c oxidoreductase complex
has_exact_synonym: ubiquinol-cytochrome-c reductase complex
has_obo_namespace: cellular_component
has_related_synonym: CoQH2-cytochrome c reductase complex
has_related_synonym: coenzyme Q-cytochrome c oxidoreductase complex
has_related_synonym: coenzyme Q-cytochrome c reductase complex
has_related_synonym: electron transport complex III
id: GO:0045275
in_subset: goslim pir

Axiom
annotated source: respiratory chain complex III
annotated property: definition
annotated target: A protein complex that transfers electrons from ubiquinol to cytochrome c and translocates two protons across a membrane. The complex contains a core structure of three catalytic subunits: cytochrome b, the Rieske iron sulfur protein (ISP), and cytochrome c1, which are arranged in an integral membrane-bound dimeric complex; additional subunits are present, and vary among different species.
database_cross_reference: PMID:16228398
database_cross_reference: PMID:16352458
database_cross_reference: PMID:17200733

respiratory chain complex IV
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A part of the respiratory chain, containing the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2).
term tracker item: https://github.com/geneontology/go-ontology/issues/27727
has_alternative_id: GO:0045287
has_exact_synonym: cytochrome c oxidase complex
has_obo_namespace: cellular_component
has_related_synonym: electron transport complex IV
id: GO:0045277
in_subset: goslim pir

Axiom
annotated source: respiratory chain complex IV
annotated property: definition
annotated target: A part of the respiratory chain, containing the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2).
database_cross_reference: ISBN:0198547684

mRNA editing complex
type: Class
subclass of: protein-containing complex
definition: A protein complex that posttranscriptionally catalyzes insertion, deletion or substitution of nucleotides at multiple sites within nascent mRNA transcripts to produce mature mRNAs in eukaryotes.
has_exact_synonym: editosome
has_obo_namespace: cellular_component
id: GO:0045293
in_subset: goslim pir

Axiom
annotated source: mRNA editing complex
annotated property: definition
annotated target: A protein complex that posttranscriptionally catalyzes insertion, deletion or substitution of nucleotides at multiple sites within nascent mRNA transcripts to produce mature mRNAs in eukaryotes.
database_cross_reference: PMID:11564867
database_cross_reference: PMID:12139607
database_cross_reference: PMID:24316715

cellular respiration
type: Class
subclass of: generation of precursor metabolites and energy
definition: The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
has_broad_synonym: respiration
database_cross_reference: Wikipedia:Cellular_respiration
has_exact_synonym: oxidative metabolic process
has_exact_synonym: oxidative metabolism
has_obo_namespace: biological_process
id: GO:0045333
in_subset: goslim candida
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: cellular respiration
annotated property: definition
annotated target: The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
database_cross_reference: GOC:das
database_cross_reference: ISBN:0140513590
database_cross_reference: ISBN:0198506732

fusome organization
type: Class
subclass of: organelle organization
subclass of: reproductive process
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fusome, a large intracellular spectrin-rich structure found in insect germline cells and mammalian hematopoietic cells.
has_exact_synonym: fusome organisation
has_obo_namespace: biological_process
has_related_synonym: fusome organization and biogenesis
id: GO:0045478
in_subset: goslim pir

Axiom
annotated source: fusome organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fusome, a large intracellular spectrin-rich structure found in insect germline cells and mammalian hematopoietic cells.
database_cross_reference: GOC:dph
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: fusome organization
annotated property: has_related_synonym
annotated target: fusome organization and biogenesis
database_cross_reference: GOC:mah

chemorepellent activity
type: Class
subclass of: protein binding
subclass of: Restriction
  on property: part of
  some values from: cell communication
subclass of: Restriction
  on property: part of
  some values from: locomotion
subclass of: Restriction
  on property: part of
  some values from: regulation of biological process
subclass of: Restriction
  on property: part of
  some values from: response to stimulus
subclass of: Restriction
  on property: has part
  some values from: protein binding
subclass of: Restriction
  on property: regulates
  some values from: signaling receptor activity
subclass of: Restriction
  on property: positively regulates
  some values from: signaling receptor activity
definition: Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal.
has_exact_synonym: chemorepellant activity
has_obo_namespace: molecular_function
id: GO:0045499
in_subset: goslim pir

Axiom
annotated source: chemorepellent activity
annotated property: definition
annotated target: Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal.
database_cross_reference: GOC:ai

nutrient reservoir activity
type: Class
subclass of: molecular_function
definition: Functions in the storage of nutritious substrates.
has_obo_namespace: molecular_function
has_related_synonym: storage protein
has_related_synonym: storage protein of fat body
has_related_synonym: yolk protein
id: GO:0045735
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim prokaryote
comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.

Axiom
annotated source: nutrient reservoir activity
annotated property: definition
annotated target: Functions in the storage of nutritious substrates.
database_cross_reference: GOC:ai

isopentenyl diphosphate metabolic process
type: Class
subclass of: lipid metabolic process
subclass of: phosphorus metabolic process
definition: The chemical reactions and pathways involving isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids.
has_exact_synonym: IPP metabolic process
has_exact_synonym: IPP metabolism
has_exact_synonym: isopentenyl diphosphate metabolism
has_exact_synonym: isopentenyl pyrophosphate metabolic process
has_exact_synonym: isopentenyl pyrophosphate metabolism
has_obo_namespace: biological_process
id: GO:0046490
in_subset: goslim pir

Axiom
annotated source: isopentenyl diphosphate metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids.
database_cross_reference: ISBN:0198506732

dosage compensation complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: nucleus
subclass of: Restriction
  on property: part of
  some values from: chromosome
definition: A protein or protein-RNA complex that localizes to one or more of the sex chromosome(s), where it acts to normalize transcription between different sexes.
has_obo_namespace: cellular_component
id: GO:0046536
in_subset: goslim pir

Axiom
annotated source: dosage compensation complex
annotated property: definition
annotated target: A protein or protein-RNA complex that localizes to one or more of the sex chromosome(s), where it acts to normalize transcription between different sexes.
database_cross_reference: GOC:kmv
database_cross_reference: GOC:mah

transport of virus
type: Class
subclass of: viral process
definition: The directed movement of a virus, or part of a virus, into, out of, or within a host cell.
has_exact_synonym: viral transport
has_narrow_synonym: virion transport
has_obo_namespace: biological_process
id: GO:0046794
in_subset: goslim pir

Axiom
annotated source: transport of virus
annotated property: definition
annotated target: The directed movement of a virus, or part of a virus, into, out of, or within a host cell.
database_cross_reference: GOC:ai

Axiom
annotated source: transport of virus
annotated property: has_exact_synonym
annotated target: viral transport
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

Axiom
annotated source: transport of virus
annotated property: has_narrow_synonym
annotated target: virion transport
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

host cell surface binding
type: Class
subclass of: binding
definition: Binding to the surface of a host cell.
term tracker item: https://github.com/geneontology/go-ontology/issues/21459
has_obo_namespace: molecular_function
id: GO:0046812
in_subset: goslim pir

Axiom
annotated source: host cell surface binding
annotated property: definition
annotated target: Binding to the surface of a host cell.
database_cross_reference: GOC:ai

isoprenoid transport
type: Class
subclass of: lipid transport
definition: The directed movement of isoprenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
has_obo_namespace: biological_process
id: GO:0046864
in_subset: goslim pir

Axiom
annotated source: isoprenoid transport
annotated property: definition
annotated target: The directed movement of isoprenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
database_cross_reference: GOC:ai

secretion
type: Class
subclass of: transport
definition: The controlled release of a substance by a cell or a tissue.
has_obo_namespace: biological_process
id: GO:0046903
in_subset: goslim pir

Axiom
annotated source: secretion
annotated property: definition
annotated target: The controlled release of a substance by a cell or a tissue.
database_cross_reference: GOC:ai

tetrapyrrole binding
type: Class
subclass of: binding
definition: Binding to a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position.
has_narrow_synonym: porphyrin binding
has_obo_namespace: molecular_function
id: GO:0046906
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: tetrapyrrole binding
annotated property: definition
annotated target: Binding to a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position.
database_cross_reference: GOC:curators
database_cross_reference: ISBN:0198506732

cellular ketone body metabolic process
type: Class
subclass of: metabolic process
definition: The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism.
has_exact_synonym: cellular ketone body metabolism
has_obo_namespace: biological_process
id: GO:0046950
in_subset: goslim pir

Axiom
annotated source: cellular ketone body metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism.
database_cross_reference: ISBN:0198506732

activin complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: extracellular region
definition: A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit.
has_obo_namespace: cellular_component
id: GO:0048180
in_subset: goslim pir
comment: Note that the actions of the activin complex are the opposite of those of the inhibin complex, which is a dimer of an inhibin beta-A or inhibin beta-B subunit and a inhibin alpha subunit. See 'inhibin complex ; GO:0043511'.

Axiom
annotated source: activin complex
annotated property: definition
annotated target: A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit.
database_cross_reference: GOC:go_curators

organelle fusion
type: Class
subclass of: organelle organization
definition: The creation of a single organelle from two or more organelles.
has_obo_namespace: biological_process
id: GO:0048284
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: organelle fusion
annotated property: definition
annotated target: The creation of a single organelle from two or more organelles.
database_cross_reference: GOC:jid

organelle fission
type: Class
subclass of: organelle organization
definition: The creation of two or more organelles by division of one organelle.
has_obo_namespace: biological_process
id: GO:0048285
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: organelle fission
annotated property: definition
annotated target: The creation of two or more organelles by division of one organelle.
database_cross_reference: GOC:jid

organelle inheritance
type: Class
subclass of: organelle organization
definition: The partitioning of organelles between daughter cells at cell division.
has_obo_namespace: biological_process
id: GO:0048308
in_subset: goslim pir
in_subset: goslim yeast

Axiom
annotated source: organelle inheritance
annotated property: definition
annotated target: The partitioning of organelles between daughter cells at cell division.
database_cross_reference: GOC:jid

cell maturation
type: Class
subclass of: developmental process
subclass of: Restriction
  on property: part of
  some values from: developmental process
definition: The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state.
term tracker item: https://github.com/geneontology/go-ontology/issues/24390
has_obo_namespace: biological_process
has_related_synonym: functional differentiation
id: GO:0048469
in_subset: goslim pir

Axiom
annotated source: cell maturation
annotated property: definition
annotated target: The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state.
database_cross_reference: GOC:go_curators

Axiom
annotated source: cell maturation
annotated property: has_related_synonym
annotated target: functional differentiation
database_cross_reference: GOC:dph

Holliday junction resolvase complex
type: Class
subclass of: protein-containing complex
definition: An endodeoxyribonuclease complex that resolves the 4-way DNA intermediates of a Holliday junction into two separate duplex DNA molecules. Can be branch-migration associated.
has_exact_synonym: resolvasome
has_narrow_synonym: Mus81-Eme1 complex
has_narrow_synonym: Mus81-Eme1 holliday resolvase complex
has_narrow_synonym: Mus81-Eme2 complex
has_narrow_synonym: Mus81-Eme2 holliday resolvase complex
has_obo_namespace: cellular_component
id: GO:0048476
in_subset: goslim pir

Axiom
annotated source: Holliday junction resolvase complex
annotated property: definition
annotated target: An endodeoxyribonuclease complex that resolves the 4-way DNA intermediates of a Holliday junction into two separate duplex DNA molecules. Can be branch-migration associated.
database_cross_reference: PMID:11207366
database_cross_reference: PMID:12374758

Axiom
annotated source: Holliday junction resolvase complex
annotated property: has_exact_synonym
annotated target: resolvasome
database_cross_reference: PMID:11207366

ribulose bisphosphate carboxylase complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate.
has_exact_synonym: RubisCO complex
has_obo_namespace: cellular_component
id: GO:0048492
in_subset: goslim pir

Axiom
annotated source: ribulose bisphosphate carboxylase complex
annotated property: definition
annotated target: A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate.
database_cross_reference: GOC:mlg

signal recognition particle
type: Class
subclass of: ribonucleoprotein complex
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A complex of protein and RNA which facilitates translocation of proteins across membranes.
database_cross_reference: Wikipedia:Signal_recognition_particle
has_obo_namespace: cellular_component
id: GO:0048500
in_subset: goslim metagenomics
in_subset: goslim pir

Axiom
annotated source: signal recognition particle
annotated property: definition
annotated target: A complex of protein and RNA which facilitates translocation of proteins across membranes.
database_cross_reference: GOC:mlg

rhythmic process
type: Class
subclass of: biological_process
definition: Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
has_obo_namespace: biological_process
has_related_synonym: rhythm
id: GO:0048511
in_subset: goslim pir

Axiom
annotated source: rhythmic process
annotated property: definition
annotated target: Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
database_cross_reference: GOC:jid

pigment granule organization
type: Class
subclass of: vesicle organization
subclass of: Restriction
  on property: part of
  some values from: pigmentation
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule.
has_exact_synonym: pigment granule organisation
has_obo_namespace: biological_process
has_related_synonym: pigment granule organization and biogenesis
id: GO:0048753
in_subset: goslim pir

Axiom
annotated source: pigment granule organization
annotated property: definition
annotated target: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule.
database_cross_reference: GOC:rc

Axiom
annotated source: pigment granule organization
annotated property: has_related_synonym
annotated target: pigment granule organization and biogenesis
database_cross_reference: GOC:mah

tissue remodeling
type: Class
subclass of: multicellular organismal process
definition: The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.
has_exact_synonym: tissue remodelling
has_obo_namespace: biological_process
id: GO:0048771
in_subset: goslim pir

Axiom
annotated source: tissue remodeling
annotated property: definition
annotated target: The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.
database_cross_reference: GOC:ebc

depsipeptide metabolic process
type: Class
subclass of: amide metabolic process
definition: The chemical reactions and pathways involving depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively.
has_exact_synonym: depsipeptide metabolism
has_obo_namespace: biological_process
id: GO:0050761
in_subset: goslim pir

Axiom
annotated source: depsipeptide metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively.
database_cross_reference: GOC:go_curators

regulation of biological process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: biological_process
subclass of: biological regulation
subclass of: Restriction
  on property: regulates
  some values from: biological_process
definition: Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
has_alternative_id: GO:0050791
has_exact_synonym: regulation of physiological process
has_obo_namespace: biological_process
id: GO:0050789
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: regulation of biological process
annotated property: definition
annotated target: Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
database_cross_reference: GOC:ai
database_cross_reference: GOC:go_curators

coagulation
type: Class
subclass of: multicellular organismal process
definition: The process in which a fluid solution, or part of it, changes into a solid or semisolid mass.
has_exact_synonym: clotting
has_obo_namespace: biological_process
id: GO:0050817
in_subset: goslim pir

Axiom
annotated source: coagulation
annotated property: definition
annotated target: The process in which a fluid solution, or part of it, changes into a solid or semisolid mass.
database_cross_reference: ISBN:0198506732

extracellular matrix binding
type: Class
subclass of: binding
definition: Binding to a component of the extracellular matrix.
has_exact_synonym: extracellular matrix constituent binding
has_obo_namespace: molecular_function
has_related_synonym: adhesive extracellular matrix constituent
id: GO:0050840
in_subset: goslim chembl
in_subset: goslim pir

Axiom
annotated source: extracellular matrix binding
annotated property: definition
annotated target: Binding to a component of the extracellular matrix.
database_cross_reference: GOC:ai

nervous system process
type: Class
subclass of: multicellular organismal process
definition: A organ system process carried out by any of the organs or tissues of neurological system.
term tracker item: https://github.com/geneontology/go-ontology/issues/13824
has_exact_synonym: neurological system process
has_exact_synonym: neurophysiological process
has_obo_namespace: biological_process
has_related_synonym: pan-neural process
id: GO:0050877
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim pir

Axiom
annotated source: nervous system process
annotated property: definition
annotated target: A organ system process carried out by any of the organs or tissues of neurological system.
database_cross_reference: GOC:ai
database_cross_reference: GOC:mtg_cardio

regulation of body fluid levels
type: Class
subclass of: regulation of biological quality
definition: Any process that modulates the levels of body fluids.
has_obo_namespace: biological_process
id: GO:0050878
in_subset: goslim pir

Axiom
annotated source: regulation of body fluid levels
annotated property: definition
annotated target: Any process that modulates the levels of body fluids.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

multicellular organismal movement
type: Class
subclass of: multicellular organismal process
definition: Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism.
has_obo_namespace: biological_process
id: GO:0050879
in_subset: goslim pir

Axiom
annotated source: multicellular organismal movement
annotated property: definition
annotated target: Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism.
database_cross_reference: GOC:dph
database_cross_reference: GOC:mtg_muscle
database_cross_reference: GOC:tb

endocrine process
type: Class
subclass of: multicellular organismal process
definition: The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
has_exact_synonym: endocrine physiological process
has_exact_synonym: endocrine physiology
has_obo_namespace: biological_process
id: GO:0050886
in_subset: goslim generic
in_subset: goslim pir

Axiom
annotated source: endocrine process
annotated property: definition
annotated target: The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
database_cross_reference: ISBN:0721662544

response to stimulus
type: Class
subclass of: biological_process
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
has_alternative_id: GO:0051869
has_exact_synonym: physiological response to stimulus
has_obo_namespace: biological_process
id: GO:0050896
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: response to stimulus
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
database_cross_reference: GOC:ai
database_cross_reference: GOC:bf

localization
type: Class
subclass of: biological_process
definition: Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
term tracker item: https://github.com/geneontology/go-ontology/issues/27052
created by: jl
creation date: 2013-12-18T13:51:04Z
has_alternative_id: GO:1902578
has_exact_synonym: establishment and maintenance of localization
has_exact_synonym: establishment and maintenance of position
has_exact_synonym: localisation
has_narrow_synonym: establishment and maintenance of cellular component location
has_narrow_synonym: establishment and maintenance of substance location
has_narrow_synonym: establishment and maintenance of substrate location
has_obo_namespace: biological_process
has_related_synonym: single organism localization
has_related_synonym: single-organism localization
id: GO:0051179
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: localization
annotated property: definition
annotated target: Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dos

Axiom
annotated source: localization
annotated property: has_exact_synonym
annotated target: localisation
database_cross_reference: GOC:mah

Axiom
annotated source: localization
annotated property: has_related_synonym
annotated target: single organism localization
database_cross_reference: GOC:TermGenie

vitamin transport
type: Class
subclass of: transport
definition: The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
has_broad_synonym: vitamin or cofactor transport
has_obo_namespace: biological_process
id: GO:0051180
in_subset: goslim pir

Axiom
annotated source: vitamin transport
annotated property: definition
annotated target: The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
database_cross_reference: GOC:ai

prosthetic group metabolic process
type: Class
subclass of: metabolic process
subclass of: Restriction
  on property: part of
  some values from: protein metabolic process
definition: The chemical reactions and pathways involving a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein.
has_broad_synonym: coenzyme and prosthetic group metabolic process
has_broad_synonym: coenzyme and prosthetic group metabolism
has_exact_synonym: prosthetic group metabolism
has_obo_namespace: biological_process
id: GO:0051189
in_subset: goslim pir

Axiom
annotated source: prosthetic group metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein.
database_cross_reference: GOC:ai

dioxygenase activity
type: Class
subclass of: oxidoreductase activity
definition: Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
database_cross_reference: Reactome:R-HSA-112120
database_cross_reference: Reactome:R-HSA-112121
database_cross_reference: Reactome:R-HSA-112124
database_cross_reference: Reactome:R-HSA-112125
has_obo_namespace: molecular_function
id: GO:0051213
in_subset: goslim pir

Axiom
annotated source: dioxygenase activity
annotated property: definition
annotated target: Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
database_cross_reference: DOI:10.1016/S0040-4020(03)00944-X
database_cross_reference: GOC:bf

Oxidative demethylation of 3-meC damaged DNA by ALKBH2
type: Axiom
annotated source: dioxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-112120

Oxidative dealkylation of 1-etA damaged DNA By ALKBH2
type: Axiom
annotated source: dioxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-112121

Oxidative demethylation of 3-meC damaged DNA By ALKBH3
type: Axiom
annotated source: dioxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-112124

Oxidative dealkylation of 1-EtA damaged DNA by ABH3
type: Axiom
annotated source: dioxygenase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-112125

establishment of localization
type: Class
subclass of: localization
definition: Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
term tracker item: https://github.com/geneontology/go-ontology/issues/24200
has_exact_synonym: establishment of localisation
has_obo_namespace: biological_process
id: GO:0051234
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir

Axiom
annotated source: establishment of localization
annotated property: definition
annotated target: Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dos

Axiom
annotated source: establishment of localization
annotated property: has_exact_synonym
annotated target: establishment of localisation
database_cross_reference: GOC:mah

protein polymerization
type: Class
subclass of: protein-containing complex assembly
definition: The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
has_exact_synonym: protein polymer biosynthesis
has_exact_synonym: protein polymer biosynthetic process
has_exact_synonym: protein polymer formation
has_obo_namespace: biological_process
id: GO:0051258
in_subset: goslim pir

Axiom
annotated source: protein polymerization
annotated property: definition
annotated target: The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
database_cross_reference: GOC:ai

protein depolymerization
type: Class
subclass of: cellular component disassembly
definition: The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein.
has_exact_synonym: protein polymer breakdown
has_exact_synonym: protein polymer catabolic process
has_exact_synonym: protein polymer catabolism
has_exact_synonym: protein polymer degradation
has_obo_namespace: biological_process
id: GO:0051261
in_subset: goslim pir

Axiom
annotated source: protein depolymerization
annotated property: definition
annotated target: The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein.
database_cross_reference: GOC:ai

chromosome organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
term tracker item: https://github.com/geneontology/go-ontology/issues/22811
term tracker item: https://github.com/geneontology/go-ontology/issues/4585
has_alternative_id: GO:0006323
has_alternative_id: GO:0007001
has_alternative_id: GO:0051277
has_exact_synonym: DNA condensation
has_exact_synonym: chromosome organisation
has_narrow_synonym: DNA packaging
has_obo_namespace: biological_process
has_related_synonym: chromosome organization and biogenesis
has_related_synonym: maintenance of genome integrity
has_related_synonym: nuclear genome maintenance
id: GO:0051276
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim pir

Axiom
annotated source: chromosome organization
annotated property: definition
annotated target: A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: chromosome organization
annotated property: has_related_synonym
annotated target: chromosome organization and biogenesis
database_cross_reference: GOC:mah

cell division
type: Class
subclass of: biological_process
definition: The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
database_cross_reference: Wikipedia:Cell_division
has_obo_namespace: biological_process
id: GO:0051301
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim pir
comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.

Axiom
annotated source: cell division
annotated property: definition
annotated target: The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
database_cross_reference: GOC:di
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:pr

metal cluster binding
type: Class
subclass of: binding
definition: Binding to a cluster of atoms including both metal ions and nonmetal atoms, usually sulfur and oxygen. Examples include iron-sulfur clusters and nickel-iron-sulfur clusters.
term tracker item: https://github.com/geneontology/go-ontology/issues/21211
has_obo_namespace: molecular_function
id: GO:0051540
in_subset: goslim pir

Axiom
annotated source: metal cluster binding
annotated property: definition
annotated target: Binding to a cluster of atoms including both metal ions and nonmetal atoms, usually sulfur and oxygen. Examples include iron-sulfur clusters and nickel-iron-sulfur clusters.
database_cross_reference: GOC:jsg

protein maturation
type: Class
subclass of: protein metabolic process
subclass of: Restriction
  on property: part of
  some values from: macromolecule biosynthetic process
definition: Any process leading to the attainment of the full functional capacity of a protein.
has_obo_namespace: biological_process
id: GO:0051604
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: protein maturation
annotated property: definition
annotated target: Any process leading to the attainment of the full functional capacity of a protein.
database_cross_reference: GOC:ai

detection of stimulus
type: Class
subclass of: response to stimulus
definition: The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
has_exact_synonym: stimulus detection
has_obo_namespace: biological_process
has_related_synonym: perception of stimulus
has_related_synonym: stimulus sensing
id: GO:0051606
in_subset: goslim pir

Axiom
annotated source: detection of stimulus
annotated property: definition
annotated target: The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
database_cross_reference: GOC:add
database_cross_reference: GOC:ai
database_cross_reference: GOC:dph
database_cross_reference: GOC:mah

organelle localization
type: Class
subclass of: localization
definition: Any process in which an organelle is transported to, and/or maintained in, a specific location.
term tracker item: https://github.com/geneontology/go-ontology/issues/19809
has_exact_synonym: establishment and maintenance of organelle localization
has_exact_synonym: organelle localisation
has_obo_namespace: biological_process
id: GO:0051640
in_subset: goslim pir

Axiom
annotated source: organelle localization
annotated property: definition
annotated target: Any process in which an organelle is transported to, and/or maintained in, a specific location.
database_cross_reference: GOC:ai

Axiom
annotated source: organelle localization
annotated property: has_exact_synonym
annotated target: organelle localisation
database_cross_reference: GOC:mah

cellular localization
type: Class
subclass of: localization
definition: A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
created by: jl
creation date: 2013-12-18T14:04:32Z
has_alternative_id: GO:1902580
has_exact_synonym: cellular localisation
has_exact_synonym: establishment and maintenance of cellular localization
has_exact_synonym: establishment and maintenance of localization in cell or cell membrane
has_exact_synonym: single organism cellular localization
has_narrow_synonym: intracellular localization
has_narrow_synonym: localization within cell
has_obo_namespace: biological_process
has_related_synonym: single-organism cellular localization
id: GO:0051641
in_subset: gocheck do not annotate
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: cellular localization
annotated property: definition
annotated target: A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
database_cross_reference: GOC:tb
database_cross_reference: GOC:vw

Axiom
annotated source: cellular localization
annotated property: has_exact_synonym
annotated target: cellular localisation
database_cross_reference: GOC:mah

Axiom
annotated source: cellular localization
annotated property: has_exact_synonym
annotated target: single organism cellular localization
database_cross_reference: GOC:TermGenie

biological process involved in intraspecies interaction between organisms
type: Class
subclass of: biological_process
definition: Any process in which an organism has an effect on an organism of the same species.
term tracker item: https://github.com/geneontology/go-ontology/issues/20191
has_exact_synonym: intraspecies interaction between organisms
has_exact_synonym: intraspecies interaction with other organisms
has_obo_namespace: biological_process
id: GO:0051703
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: biological process involved in intraspecies interaction between organisms
annotated property: definition
annotated target: Any process in which an organism has an effect on an organism of the same species.
database_cross_reference: GOC:ai

phytoalexin metabolic process
type: Class
subclass of: toxin metabolic process
definition: The chemical reactions and pathways involving phytoalexins, any of a range of substances produced by plants as part of their defense response.
has_exact_synonym: phytoalexin metabolism
has_obo_namespace: biological_process
id: GO:0052314
in_subset: goslim pir

Axiom
annotated source: phytoalexin metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving phytoalexins, any of a range of substances produced by plants as part of their defense response.
database_cross_reference: Wikipedia:Phytoalexin

symplast
type: Class
subclass of: cellular anatomical structure
definition: The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.
database_cross_reference: Wikipedia:Symplast
has_obo_namespace: cellular_component
id: GO:0055044
in_subset: goslim pir

Axiom
annotated source: symplast
annotated property: definition
annotated target: The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.
database_cross_reference: GOC:mtg_sensu

molecular transducer activity
type: Class
subclass of: molecular_function
definition: A compound molecular function in which an effector function is controlled by one or more regulatory components.
has_obo_namespace: molecular_function
id: GO:0060089
in_subset: gocheck do not annotate
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim prokaryote

Axiom
annotated source: molecular transducer activity
annotated property: definition
annotated target: A compound molecular function in which an effector function is controlled by one or more regulatory components.
database_cross_reference: GOC:dos
database_cross_reference: GOC:pdt

molecular adaptor activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: has part
  some values from: binding
definition: The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
has_alternative_id: GO:0032947
has_broad_synonym: protein complex scaffold activity
has_broad_synonym: protein-containing complex scaffold activity
has_exact_synonym: binding, bridging
has_obo_namespace: molecular_function
id: GO:0060090
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: molecular adaptor activity
annotated property: definition
annotated target: The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
database_cross_reference: GOC:mtg_MIT_16mar07
database_cross_reference: GOC:vw

membrane organization
type: Class
subclass of: cellular component organization
definition: A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
created by: jl
creation date: 2010-02-08T02:43:11Z
has_alternative_id: GO:0016044
has_alternative_id: GO:0044802
has_exact_synonym: cellular membrane organisation
has_exact_synonym: cellular membrane organization
has_exact_synonym: membrane organisation
has_obo_namespace: biological_process
has_related_synonym: membrane organization and biogenesis
has_related_synonym: single-organism membrane organization
id: GO:0061024
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote

Axiom
annotated source: membrane organization
annotated property: definition
annotated target: A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

Axiom
annotated source: membrane organization
annotated property: has_exact_synonym
annotated target: membrane organisation
database_cross_reference: GOC:mah

Axiom
annotated source: membrane organization
annotated property: has_related_synonym
annotated target: membrane organization and biogenesis
database_cross_reference: GOC:mah

protein-containing complex assembly
type: Class
subclass of: cellular component assembly
definition: The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
term tracker item: https://github.com/geneontology/go-ontology/issues/22580
has_alternative_id: GO:0006461
has_alternative_id: GO:0034622
has_alternative_id: GO:0043623
has_exact_synonym: cellular protein complex assembly
has_obo_namespace: biological_process
has_related_synonym: cellular macromolecule complex assembly
has_related_synonym: cellular protein-containing complex assembly
has_related_synonym: chaperone activity
has_related_synonym: macromolecular complex assembly
has_related_synonym: macromolecule complex assembly
has_related_synonym: protein complex assembly
has_related_synonym: protein complex formation
id: GO:0065003
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim pombe
in_subset: goslim prokaryote

Axiom
annotated source: protein-containing complex assembly
annotated property: definition
annotated target: The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
database_cross_reference: GOC:jl

biological regulation
type: Class
subclass of: biological_process
definition: Any process that modulates a measurable attribute of any biological process, quality or function.
has_broad_synonym: regulation
has_obo_namespace: biological_process
id: GO:0065007
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: biological regulation
annotated property: definition
annotated target: Any process that modulates a measurable attribute of any biological process, quality or function.
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete
database_cross_reference: GOC:mah
database_cross_reference: GOC:pr
database_cross_reference: GOC:vw

regulation of biological quality
type: Class
subclass of: biological regulation
definition: Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
has_exact_synonym: regulation of biological attribute
has_exact_synonym: regulation of biological characteristic
has_obo_namespace: biological_process
id: GO:0065008
in_subset: goslim pir

Axiom
annotated source: regulation of biological quality
annotated property: definition
annotated target: Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete
database_cross_reference: GOC:mah
database_cross_reference: GOC:pr
database_cross_reference: GOC:vw

regulation of molecular function
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: molecular_function
subclass of: biological regulation
subclass of: Restriction
  on property: regulates
  some values from: molecular_function
definition: Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
has_exact_synonym: regulation of a molecular function
has_obo_namespace: biological_process
id: GO:0065009
in_subset: gocheck obsoletion candidate
in_subset: goslim pir
in_subset: goslim plant

Axiom
annotated source: regulation of molecular function
annotated property: definition
annotated target: Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
database_cross_reference: GOC:isa_complete

translocon complex
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: endoplasmic reticulum
subclass of: Restriction
  on property: part of
  some values from: membrane
definition: A protein complex that constitutes a specific site of protein translocation across the endoplasmic reticulum, which involves the signal recognition particle receptor. The complex contains a core heterotrimer of alpha, beta and gamma subunits, and may contain additional proteins.
created by: mah
creation date: 2009-12-08T02:08:03Z
has_alternative_id: GO:0031206
has_narrow_synonym: Sec complex-associated translocon complex
has_obo_namespace: cellular_component
id: GO:0071256
in_subset: goslim pir

Axiom
annotated source: translocon complex
annotated property: definition
annotated target: A protein complex that constitutes a specific site of protein translocation across the endoplasmic reticulum, which involves the signal recognition particle receptor. The complex contains a core heterotrimer of alpha, beta and gamma subunits, and may contain additional proteins.
database_cross_reference: GOC:mah
database_cross_reference: PMID:10611978
database_cross_reference: PMID:18166647
database_cross_reference: PMID:8612571

Axiom
annotated source: translocon complex
annotated property: has_narrow_synonym
annotated target: Sec complex-associated translocon complex
database_cross_reference: GOC:mah

cell wall organization
type: Class
subclass of: external encapsulating structure organization
definition: A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
created by: mah
creation date: 2010-01-13T03:33:07Z
has_alternative_id: GO:0007047
has_alternative_id: GO:0044234
has_exact_synonym: cell wall organisation
has_exact_synonym: cell wall organisation in other organism
has_exact_synonym: cell wall organization at cellular level
has_exact_synonym: cell wall organization in other organism
has_exact_synonym: cellular cell wall organisation
has_exact_synonym: cellular cell wall organization
has_obo_namespace: biological_process
has_related_synonym: cell wall organization and biogenesis
id: GO:0071555
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: cell wall organization
annotated property: definition
annotated target: A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
database_cross_reference: GOC:mah

Axiom
annotated source: cell wall organization
annotated property: has_exact_synonym
annotated target: cell wall organisation in other organism
database_cross_reference: GOC:mah

Axiom
annotated source: cell wall organization
annotated property: has_exact_synonym
annotated target: cell wall organization at cellular level
database_cross_reference: GOC:mah

Axiom
annotated source: cell wall organization
annotated property: has_related_synonym
annotated target: cell wall organization and biogenesis
database_cross_reference: GOC:mah

cellular anatomical structure
type: Class
subclass of: cellular_component
definition: A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.
term tracker item: https://github.com/geneontology/go-ontology/issues/24200
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
term tracker item: https://github.com/geneontology/go-ontology/issues/28978
created by: kmv
creation date: 2019-08-12T18:01:37Z
has_exact_synonym: cellular anatomical entity
has_obo_namespace: cellular_component
id: GO:0110165
in_subset: gocheck do not annotate
in_subset: goslim pir

Axiom
annotated source: cellular anatomical structure
annotated property: definition
annotated target: A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.
database_cross_reference: GOC:kmv

proton transmembrane transport
type: Class
subclass of: monoatomic ion transport
definition: The directed movement of a proton across a membrane.
created by: pr
creation date: 2013-12-20T11:08:37Z
has_alternative_id: GO:0006818
has_alternative_id: GO:0015991
has_alternative_id: GO:0015992
has_broad_synonym: hydrogen transport
has_broad_synonym: proton transport
has_exact_synonym: hydrogen ion transmembrane transport
has_exact_synonym: hydrogen transmembrane transport
has_narrow_synonym: ATP hydrolysis coupled proton transport
has_narrow_synonym: passive proton transport, down the electrochemical gradient
has_obo_namespace: biological_process
has_related_synonym: hydrogen ion transport
id: GO:1902600
in_subset: goslim pir

Axiom
annotated source: proton transmembrane transport
annotated property: definition
annotated target: The directed movement of a proton across a membrane.
database_cross_reference: GOC:TermGenie
database_cross_reference: GOC:pr
database_cross_reference: GO_REF:0000069

ribonucleoprotein complex
type: Class
subclass of: protein-containing complex
definition: A macromolecular complex that contains both RNA and protein molecules.
created by: pr
creation date: 2015-11-19T12:26:37Z
has_alternative_id: GO:0030529
has_alternative_id: GO:1990903
database_cross_reference: Wikipedia:Ribonucleoprotein
has_exact_synonym: RNA-protein complex
has_exact_synonym: RNP
has_exact_synonym: protein-RNA complex
has_narrow_synonym: extracellular ribonucleoprotein complex
has_narrow_synonym: intracellular ribonucleoprotein complex
has_obo_namespace: cellular_component
id: GO:1990904
in_subset: goslim pir

Axiom
annotated source: ribonucleoprotein complex
annotated property: definition
annotated target: A macromolecular complex that contains both RNA and protein molecules.
database_cross_reference: GOC:krc
database_cross_reference: GOC:vesicles