Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]
DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)
Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH].
One of paired external openings of the nasal chamber.[AAO]
Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]
in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity
we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure
DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)
The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
the organ that is specialized for smell and is part of the respiratory system
the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
The clusters of hormone-producing cells that are scattered throughout the pancreas.
Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]
Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]
A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)
PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995)
The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]
An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]
It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9]
Terminology note: hypophysis and pituitary gland are often used informally as synonyms, but the hypophysis also includes the small infundibular or pituitary stalk[Neumann 2020]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO].
Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]
In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]
parasympathetic part of autonomic division of nervous system
pars parasympathica divisionis autonomici systematis nervosi
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998)
Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors.
somatic nervous system, somatic division
somatic part of peripheral nervous system
The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)
pars sympathica divisionis autonomici systematis nervosi
sympathetic part of autonomic division of nervous system
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.
create a separate class for distributed pancreas, eg cyclostomes?
The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]
The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys
DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)
The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]
A light sensing organ composed of ommatidia.
The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
A cavitated compound organ that transduces light waves into neural signals.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
camera-type eye plus associated structures
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
An organ that is capable of transducing sensory stimulus to the nervous system.
Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here.
Appendage that is shaped in order to produce lift for flight through the air.
This class is not monophyletic. See also: GO:0007629
we do not consider flying frogs to have wings
Forelimb that is used to produce lift for flight through the air.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
Major subdivision of an organism that protrudes from the body[DOS, CARO].
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
A lamina propria that is part of a respiratory airway.
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82
An ovarian follicle that has one layer of granulosa cells.
A maturing ovarian follicle that has two more more layers of granulosa cells, up to the onset of antrum formation.
A follicle that has reached the most mature stage of folliculogenesis, characterized by the presence of the antrum.
folliculus ovaricus tertiarius (vesiculosus)
folliculus ovaricus tertiarius (vesiculous)
The fluid surrounding the ovum and granulosa cells in the ovarian follicle.
Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441]
The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid.
Region of ovarian follicle filled with follicular fluid.
Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
Dense regular connective tissue that connects muscle to bone[VSAO].
Dense regular connective tissue that connects muscle to bone.[VSAO]
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)
Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP).
Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]
From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]
The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[DOI:10.1093/icb/icn065]
MA and EMAPA introduce distinct classes for what appears to be the same thing
spinal ganglion part of peripheral nervous system
DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)
A biological tissue mass, most commonly a mass of nerve cell bodies.
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures
Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302].
Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
in humans, consists of adventitial, muscular and mucoa layers
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543
The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts.
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
Uberon includes clade-specific subclasses, e.g. nematod larva
It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form
A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
The pupal stage is found only in holometabolous insects, those that undergo a complete metamorphosis, going through four life stages; embryo, larva, pupa and imago
may be better to model pupal development as including the pre-pupal stage
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
proximo-distal subdivision of respiratory tract
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO].
ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
mixed ectoderm/mesoderm/endoderm-derived structure
The organs associated with producing offspring in the gender that produces spermatozoa.
By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.
A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney
By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639
In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO].
A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]
During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis
A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]
An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP].
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159
A mass of cells that develop into the body of the embryo and some extraembryonic tissues.
A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]
A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]
This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]
embryoblastus; massa cellularis interna; pluriblastus senior
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144
The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta.
the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]
The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta
Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast]
Missing definition for term UBERON:0000089. Please replace it using linked reference.
TODO - consider relationship to UBERON:0000091 ! bilaminar disc
this term groups together disparate structures with different relationships.
A primary germ layer that can give rise to both mesoderm and endoderm.[AAO]
The inner of the two layers of the blastoderm that forms during gastrulation and give rise to the definitive mesoderm and endoderm. Kimmel et al, 1995.[TAO]
In mammal and avian, extraembryonic endoderm such as visceral endoderm and hypoblast play essential roles in the embryonic axis formation and germ layer development. These extraembryonic tissues are generally considered to have been created in ancestral amniotes evolved from the Xenopus-type ancestor (reference 1); The endomesoderm secretes as yet unidentified signals that posteriorize the ectoderm, which would otherwise adopt an anterior fate. Our results point to a conserved function at the base of deuterostomes for beta-catenin in germ layer specification and to a causal link in the definition of the posterior part of the embryonic ectoderm by way of activating posteriorizing endomesodermal factors (reference 2).[well established][VHOG]
DOI:10.1016/j.ydbio.2009.05.543 Takeuchi M, Takahashi M, Okabe M, Aizawa S, Germ layer patterning in bichir and lamprey; an insight into its evolution in vertebrates. Developmental Biology (2009) (reference 1), Darras S, Gerhart J, Terasaki M, Kirschner M, Lowe CJ, Beta-catenin specifies the endomesoderm and defines the posterior organizer of the hemichordate Saccoglossus kowalevskii. Development (2011) (reference 2)
A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
Stage succeeding embryo, including mature structure.
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
A depression or fissure in the surface of an organ.
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA].
Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].
A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751].
A lung lobe is one of the rounded projections that compose the lung[GO].
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
A chordate developmental stage defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
The stage of being a sexually mature adult animal.
The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin.
it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]
Primitive gas exchange portion of the lung composed of type I and type II cells[GO].
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
Structure derived from foregut that becomes a lung[GO].
Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium.
Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions.
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
we limit this structure by definition to chordate and vertebrate nervous systems
Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves.
The group of motor neurons residing in the pons that innervate the muscles of facial expression.
FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus.
Prominent oval structure in the medulla oblongata, present in pairs, the lower portion of the brainstem. They contain the olivary nuclei.
Paired fin that is located in the thoracic region of the body.
Paired fin that is located in the thoracic region of the body.[TAO]
Paired fin that is located in the thoracic region of the body.[VSAO]
Paired fin located in the abdominal position of the body.
Paired fin located in the abdominal position of the body.[TAO]
Paired fin located in the abdominal position of the body.[VSAO]
A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures.
The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus.
requires alignment with EHDAA2 and complete developmental relationships
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]
Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]
Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
hindgut endoderm and proctodeal ectoderm.
most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572
Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.
The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females.
The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]
In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]
the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal
ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present).
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
A section dividing a colon along a proximal-distal axis.
The pair of anatomical structures comprised of a left lung and right lung.
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity.
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
A ridge on the cerebral cortex. It is generally surrounded by one or more sulci .
A blood brain barrier that is composed of endothelial cells.
A blood brain barrier composed of glial cells.
Dorsal part (roof region) of the telencephalon[GO].
In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume.
In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus
Ventral part (base region) of the telencephalon.
BTO term refers specifically to the avian structure
A chitinous extracellular secretion of the four underlying cone cells and the pigment cells.
The bone forming the forehead and roof of the eye orbit.
fused in humans, paired in other animals
In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993).
In humans: bone forming side and roof of cranium. Each bone is irregularly quadrilateral in form, and has two surfaces, four borders, and four angles.
The homologization of cranial bones of actinopterygians with those of sarcopterygians based on the bone names established in human anatomy is favored in order to permit the building of phylogenetic relationship schemes beyond the taxonomic boundaries of osteichthyans (including tetrapods). (...) In actinopterygians, the terms parietal and postparietal bones have to replace the commonly used terms 'frontal' and 'parietal' bones for the two paired bones on the skull roof.[well established][VHOG]
The frontal bone in teleost fish is the homolog of the parietal bone in tetrapods[various]. In many non-mammalian tetrapods, they are bordered to the rear by a pair of postparietal bones that may be solely in the roof of the skull, or slope downwards to contribute to the back of the skull, depending on the species. In the living tuatara, and many fossil species, a small opening, the parietal foramen, lies between the two parietal bones. This opening is the location of a third eye in the midline of the skull, which is much smaller than the two main eyes
ISBN:978-3899370805 Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.
Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496].
Portion of connective tissue that connects bone or cartilage.[TAO]
Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]
this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament
PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)
A neural arch that is part of a vertebral bone 2.
vertebral foramen of cervical vertebra 2
The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital.
A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath.
TODO - add layer relations. 'tendon sheath' GAT in FMA.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity.
defined generically to encompass both vertebrates and invertebrates
The upper ventral region of the torso of an organism.
The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia
A mucosa that is part of a cecum [Automatically generated definition].
intestinum crassum caecum mucosa of organ
intestinum crassum caecum mucous membrane
mucosa of organ of intestinum crassum caecum
mucous membrane of intestinum crassum caecum
organ mucosa of intestinum crassum caecum
The space between the arachnoid and pia mater.
subarachnoid space of central nervous system
A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells.
A mucosa that is part of a duodenum [Automatically generated definition].
An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.
Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919].
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach.
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
We model the digestive tract as consisting of two parts: the wall and the lumen.
Bone marrow in which the fat cells predominate in the meshes of the reticular network.
A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
Note that some sources treat 'intestinal gland' as synonymous with crypts
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP].
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead.
Sensory medial ramus of the trigeminal nerve.[AAO]
The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG]
ophthalmic division of fifth cranial nerve
ophthalmic division of trigeminal nerve (V1)
ophthalmic division of trigeminal nerve (Va)
Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html]
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177
A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex].
obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.
includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]
A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae.
In humans it is a tendon-like structure that has developed independently in humans and other animals well adapted for running. In some four legged animals, particularly ungulates, the nuchal ligament serves to sustain the weight of the head
As it is required for running, not all animals have a nuchal ligament
Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin
the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated
A mucosa that is part of a pharynx [Automatically generated definition].
The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)
The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream.
The inner portion of the kidney consisting of the renal pyramids.
The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water
Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different.
An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.
The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP].
Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]
The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2]
* According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum
DOI:10.1146/annurev.ne.04.030181.001505, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.487 Figure 14-10
The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini.
mandibular division of fifth cranial nerve
mandibular division of trigeminal nerve [Vc; V3]
The part of the hindlimb between pelvis and the knee, corresponding to the femur.
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
Naming conventions for pod terms under discussion within phenoscape group.
ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
Medial ramus (sensory) of the trigeminal nerve.[AAO]
relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]
maxillary division of fifth cranial nerve
maxillary division of trigeminal nerve (Vb; V2)
The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]
DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)
Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP].
In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region.
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
The core of the crystalline lens, surrounded by the cortex.
in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular
The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus.
in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems
cochlear part of vestibulocochlear ganglion
vestibulocochlear VIII ganglion cochlear component
vestibulocochlear ganglion cochlear component
An epithelium that is part of a colon [Automatically generated definition].
Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]
Any portion of cartilage tissue that is part of the sternum.
Examples: cartilage of manubrium, cartilage of xiphoid process
The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted].
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A mucosa that is part of a bronchus [Automatically generated definition].
A gland in which the principal secretory cells are mucus secreting cells.
In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
An anatomical wall that is part of an artery [Automatically generated definition].
A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies.
The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges.
A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP].
A vein that drains the left pampiniform plexus and empties into the left renal vein.
A vein that drains the right pampiniform plexus and empties into the inferior vena cava.
introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle'
The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain.
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses.
cavernous branch of cavernous part of internal carotid artery
ramus sinus cavernosi (pars cavernosa) (arteria carotis interna)
The region of the opening of the uterine cervix into the uterine cavity.
An anatomical wall that is part of a uterus [Automatically generated definition].
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
this relationship may be too strong and may be weakened in future
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
Multi-tissue structure that is part of a compound organ.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
A gonad of a male animal. A gonad produces and releases sperm.
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
The organs and associated structures associated with bearing offspring in a female animal.
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group whose component anatomical structures lie in close proximity to each other.
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
see also conceptus extraembryonic component in EHDAA2.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59
Unilaminar epithelium that consists of a single layer of cuboidal cells.
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA].
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA].
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Epithelium that consists of epithelial cells not arranged in one ore more layers.
Compound organ that contains one or more macroscopic anatomical spaces.
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
One of the repeated divisions of the whole organism.
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish [GO].
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
A double row of cells which are located at the midline from the end of gastrulations. The morphology of these cells is distinct from adjacent ectodermal cells - they are elongated such that one end remains exposed to the outside of the embryo at the mideline while the other end bissects the internalised mesoderm.
Split term? The part of the mesenchyme derived from ectoderm, especially from the embryonic neural crest from which the pigment cells, meninges, and most of the branchial cartilages develop.[TFD]
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.
removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
A muscle that acts on the pharynx[WP, vetted].
A pharyngeal muscle is any muscle that forms part of the pharynx[GO].
Innervation notes: They are innervated by the pharyngeal branch of the Vagus nerve (CN X) with the exception of the stylopharyngeus muscle which is innervated by the glossopharyngeal nerve (CN IX).[WP]
does not quite work for some muscles such as stylopharyngeus
The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO].
A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath.
The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral ('belly', as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects.
A bundle of myelinated nerve fibers passing transversely through the lamina terminalis and connecting symmetrical parts of the two cerebral hemispheres; it consists of a smaller anterior part (pars anterior commissurae anterioris) and a larger posterior part (pars posterior commissurae anterioris).
In all vertebrates the thin structure that connects the two halves of the telencephalon shows a ridge-like thickening at the basal side known as the anterior commissure.[well established][VHOG]
Rounded band of white fibers crossing the middle line on the dorsal aspect of the upper end of the cerebral aqueduct. It is important in the bilateral pupillary light reflex. Its fibers acquire their medullary sheaths early, but their connections have not been definitely determined. Most of them have their origin in a nucleus, the nucleus of the posterior commissure (nucleus of Darkschewitsch), which lies in the central gray substance of the upper end of the cerebral aqueduct, in front of the nucleus of the oculomotor nerve. Some are probably derived from the posterior part of the thalamus and from the superior colliculus, whereas others are believed to be continued downward into the medial longitudinal fasciculus. The posterior commissure interconnects the pretectal nuclei, mediating the consensual pupillary light reflex[WP]. Diencephalic tract which is located in the vicinity of the dorsal diencephalon and mesencephalon and connects the pretectal nuclei. From Neuroanatomy of the Zebrafish Brain[ZFA].
add connects relationships and check these outside mammalia
part_of brainstem in MA; midbrain tectum in NIF
One of the parts of a holometabolous insect larva that will become a portion of the outside of the adult insect during the pupal transformation.
Though inaginal discs are sometimes described as “epithelial sacs”, we do not classify them as such, because an “epithelial sac” is defined in Uberon as being a single epithelium, whereas imaginal discs are made of several epithelia with distinct properties.
Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].
Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]
A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]
(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
A membranous fold of the heart that prevents reflux of fluid.
One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG]
Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]
Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve
DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.
The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)
Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column.
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus).
The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex].
Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]
hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743]
DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969)
Middle part of an organ, surrounded by the cortex.
this class is used in a very general sense
A decussation of the diencephalon where the fibers of the optic nerve cross.
The point at which fibers of the optic nerves cross.[AAO]
The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]
DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005)
The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted].
Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP]
this term should be ceded to the arthropod anatomy ontology
The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina.
This class excludes compound eye corneal lenses.
The lens is avascular and nourished by diffusion from the aqueous and vitreous humors.
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.
The paired, usually multiple jointed, sensory organs articulating on the procephalic region of the head capsule; its highly versatile sensory structures are capable to detect the various environmental stimuli. In the context of Drosophila refers to they are the most anterior segmented sensory appendage of the head.
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad].
in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum
Single element that constitutes the postzonal area of the pectoral girdle.[AAO]
relationship loss: part_of postzonal element (AAO:0000938)[AAO]
Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG]
It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life
in birds, either ratite (no keel or carina) or carinate (keel and carina present)
While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad].
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294
Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah].
Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]
proximal metapterygial mesomere of pectoral appendage
proximal metapterygial mesomere of pectoral fin
The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86
The portion of the hindlimb that contains both the stylopod and zeugopod.
The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot
The major preaxial endochondral bone in the posterior zeugopod[Phenoscape].
One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]
Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]
proximal metapterygial mesomere of pelvic appendage
proximal metapterygial mesomere of pelvic fin
Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
A metapodium region that is part of a pes.
mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
A flight organ of the adult external thorax that is derived from a dorsal mesothoracic disc.
TODO - review. hymenoptera thorax = fusion of thorax and mesosoma/metasoma
In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery
The capitate stalk on both sides of the thorax having developed from the dorsal metathoracic wing-buds, it is freely movable and capable of vibration, representing the hind wing of Diptera; used for flight balance.
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.
The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474
An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination.
Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
The gonad of a female organism which contains germ cells.
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
A tube or collection of tubes in an animal from the ovaries to the outside of the body.
sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus
A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]
The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]
in birds divided into infundibulum, magnum, isthmus, uterus, and vagina
tubular parts of female reproductive system
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688
An organ of the female reproductive tract that functions to receive and store sperm from the male, and can sometimes be the site of fertilization when the oocytes are ready.
Some species have multiple spermathecae, as seen in earthworms, where four pairs of spermathecae are present. One pair in 6,7,8 and 9 segments. They receive and store the spermatozoa of another earthworm during copulation
The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688
External genital organs of the female mammal[WP].
The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct.
Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]
(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]
The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556
The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted].
A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct.
The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]
Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670
A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP].
EDITOR_NOTE TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO
Tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP].
EDITOR_NOTE TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part
Rieger - Evolution of the Cuticle in the Lower Eumetazoa
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406
Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
WBbt coelomocyte currently classified as circulating cell
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)
WP says this is the analog of peripheral nerves in CNS.
A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed).
EDITOR_NOTE note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle'
Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt].
White matter fiber bundle that crosses the midline of the brain or spinal cord, that connects similar structures on both sides. (CUMBO; Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
A portion of tissue which is a fasiculated group of axons.[TAO]
A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
The sensory system for the sense of taste.
The sensory system for the sense of taste[NLXANAT:090803].
The sensory system used for the sense of taste.[AAO]
in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
A filament, mostly protein, that grows from follicles found in the dermis[WP].
TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)
A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]
the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells
Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
Consider generalizing to deuterostome pharynx
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)
Saliva-secreting exocrine glands of the oral cavity[GO].
currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.
A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]
The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
in FMA this represents an embryonic region.
The caudalmost subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class
the caudal portion of the primitive digestive tube of the embryo
in FMA this class has no children. In MA it has a single child hindgut epithelium
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
The terminal portion of the intestinal tube, terminating with the anus.
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified].
It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]
EDITOR_NOTE this will be ceded to the Arthropod Anatomy Ontology
Prominent lobed neuropils found in annelids and all arthropods except crustaceans. They are thought to be involved in olfactory associative learning and memory[MESH] Mushroom body neuropils are divided into calyces, pedunculus, and its subsequent lobes. In Drosophila these are the alpha, beta, and gamma lobes.
Also in annelids. 'Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times'
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.
These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]
Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.
EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue
DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)
A zone of skin that is part of a back [Automatically generated definition].
EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
superficial branch of transverse cervical artery
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455
A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice.
A potential space between the visceral and parietal layers of the pericardium.
Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206
An extension of a neural arches dorsal to the neural canal[TAO,modified].
Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]
Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO]
Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]
relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]
The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback. [Wikipedia:Spinous_process]
The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted].
Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae.
Endocardium that is part of the cardiac ventricle.
An epicardial layer that lines a cardiac ventricle.
The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
A zone of skin that is part of a head [Automatically generated definition].
A zone of skin that is part of a trunk [Automatically generated definition].
Transudate contained in the pleural cavity.
Excretion that is the output of a kidney.
kidney excreta from some taxa (e.g. in aves) may not be liquid
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food.
The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]
absent in living platypus, present in toothed Miocene platypus Obduron dicksoni
EDITOR_NOTE we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures
PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)
The first vertebral bone in the vertebral column.
First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]
Vertebra that is posteriorly adjacent to the neurocranium.[TAO]
The second vertebral bone in the vertebral column.
Vertebra that is posteriorly adjacent to vertebra 1.[TAO]
Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx).
Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]
we deliberately merge the MA classes as we believe them equivalent
Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae
An anatomical wall that is part of a esophagus [Automatically generated definition].
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].
The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]
The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]
The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)
barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus
originate from the cervical somites, likely C3-C5[PMID:23586979]
ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278
A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad].
Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]
relationship loss: part_of zonal element (AAO:0000936)[AAO]
In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG]
The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X].
In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal.
FMA and MA differ in whether they consider this part of the shoulder
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18
The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted].
In humans it inserts along a roughened line deep in the groove. In other mammals (most, I believe) it is an actual projection, the latissimus dorsi process [FEED:rd] [https://github.com/obophenotype/uberon/issues/1192]
spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula
floor of intertubercular groove of the humerus
Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe.
some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts
The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]
The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted].
Portion of the liver which develops on the fish's left side.[TAO]
A lobe of tissue that is part of a thyroid gland.
Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]
The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids
A lobe of thyroid gland that is in the right side of a thyroid gland.
A lobe of thyroid gland that is in the left side of a thyroid gland.
The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted].
fleshy slips from the outer surface of upper 8 or 9 ribs
costal aspect of medial margin of the scapula
Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton
Anatomical cluster that consists of all the vertebra in the body.[VSAO]
The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]
Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53
The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism.
Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]
Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]
The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]
Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP]
In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch
table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity.
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
Muscle tissue that consists primarily of skeletal muscle fibers.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
textus muscularis levis; textus muscularis nonstriatus
DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
A vein that drains the pelvis and lower limbs into the inferior vena cava.
In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries.
Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava.
The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein].
in EHDAA2, the renal vein is part of the kidney
A renal vein that drains the right kidney.
A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus].
A renal vein that drains the left kidney.
A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus].
Vein that carries blood away from the liver[ZFA].
todo - add developmental relationships for other taxa
A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis.
TODO - check testicular vs spermatic vein (MA:0002218)
In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel
A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries.
gonad of female reproductive system vein
gonada of female reproductive system vein
vein of female reproductive system gonad
vein of female reproductive system gonada
vein of gonad of female reproductive system
vein of gonada of female reproductive system
The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct.
Duct that connects the gall bladder and the common bile duct.[TAO]
The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong]
A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
Some references do not consider the caecum to be part of the colon.
TODO - abstract this such that it legitimately covers all vertebrates
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified].
The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified].
The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
we include this as zone of stomach even though it is not distinguished by gland type
The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells.
The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum.
We follow Kardong in defining stomach regions by glands
The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between.
An anatomical wall that is part of a small intestine [Automatically generated definition].
An anatomical wall that is part of a large intestine [Automatically generated definition].
The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP].
The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids.
A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.
Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]
The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP]
The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct.
Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO]
The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]
Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP].
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part
The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct.
The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]
The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct.
The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]
The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space.
Anatomical cavity bounded by visceral and parietal peritoneum.
The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted].
One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates.
renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability.
Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO]
The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia]
Renal artery that supplies the right kidney.
The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP]
Renal artery that supplies the left kidney.
The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP]
One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad.
A testicular artery that supplies a right testicle.
A testicular artery that supplies a left testicle.
In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP].
The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted].
Artery that supplies blood to the liver.[TAO]
The mucosal layer that lines the stomach.
The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa].
The fibrous connective tissue layer beneath the stomach mucosa.
The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum.
anatomical wall of stomach serous membrane
anatomical wall of ventriculus serous membrane
serosa of anatomical wall of ventriculus
serous membrane of anatomical wall of stomach
serous membrane of anatomical wall of ventriculus
serous membrane of stomach anatomical wall
serous membrane of ventriculus anatomical wall
ventriculus anatomical wall serous membrane
A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP].
(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]
A mucosa that is part of a small intestine [Automatically generated definition].
Submucosal tissue in the small intestines.
A serous membrane that is part of a small intestine [Automatically generated definition].
duodenum, 1st part serosa, 2nd - 4th adventitia
A mucosa that is part of a large intestine [Automatically generated definition].
A submucosa that is part of a large intestine [Automatically generated definition].
A serous membrane that is part of a large intestine [Automatically generated definition].
The protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles.
Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas).
FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]
Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs
aggregated lymphoid follicle of intestine
A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP].
currently defined as equivalent to any submucosal gland in the duodenum.
Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds
The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold.
in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine
The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]
the BTO class refers to a generic villous
A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted].
An ureter that is part of a right side of organism [Automatically generated definition].
An ureter that is part of a left side of organism [Automatically generated definition].
A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP].
In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter
Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]
The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron.
A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]
A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]
The part of the nephron that filters blood.[TAO]
Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron
A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus.
Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]
Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP].
One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]
An epithelial tube that is part of the nephron, the functional part of the kidney.
note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA
The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient.
Renal duct that collects the output from renal tubules.[TAO]
in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron
An adrenal gland that is in the right side of the abdomen.
In humans, the right adrenal gland is triangular shaped
An adrenal gland that is in the left side of the abdomen.
In humans, the left adrenal gland is semilunar shaped
The thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone.
All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
The inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine.
Lamina propria that is part_of the small intestine.
lamina propria mucosa of small intestine
lamina propria mucosae of small intestine
lamina propria of mucosa of small intestine
A serous membrane that is part of a wall of intestine [Automatically generated definition].
anatomical wall of bowel serous membrane
anatomical wall of intestine serous membrane
intestine anatomical wall serous membrane
serous membrane of anatomical wall of bowel
serous membrane of anatomical wall of intestine
serous membrane of bowel anatomical wall
serous membrane of intestine anatomical wall
Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.
opening of terminal part of digestive tract
The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad.
A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP].
in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament
The area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur.
A lamina propria that is part of a ureter [Automatically generated definition].
The luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP].
MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium
Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78
An anatomical wall that lines the insider of a urinary bladder.
The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP].
The mucous membrane lining the urinary bladder.
A serous membrane that is part of a urinary bladder [Automatically generated definition].
A lamina propria that is part of a urinary bladder [Automatically generated definition].
Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue
lamina propria mucosa of urinary bladder
lamina propria mucosae of urinary bladder
An anatomical wall that is part of a intestine [Automatically generated definition].
we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different
The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct.
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
Transudate contained in the peritoneal cavity.
The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions.
this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]
A fused bone consisting of the ilium, ischium and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified].
currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage
The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column
in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra.
in FMA this is classified as simple columnar, MA divides this into squamous and glandular
Epithelial layer that lines the intestine.
Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]
An epithelium that is part of a large intestine [Automatically generated definition].
A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver.
The functional units of the liver including the lobules.
the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG]
DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)
Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers.
(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]
DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)
The tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule.
Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct)
An intercellular channel that takes up bile from hepatocytes, transporting it to the bile ducts.
conducts the flow of bile countercurrent to the direction of portal blood flow and connects with the canal of Hering[DOI:10.1002/cphy.c120027]
The bile canaliculi merge and form bile ductules, which eventually become common hepatic duct. Hepatocytes are polyhedral in shape, therefore having no set shape or design. They have surfaces facing the sinusoids, (called sinusoidal faces) and surfaces which contact other hepatocytes, (called lateral faces). Bile canaliculi are formed by grooves on some of the lateral faces of these hepatocytes. Microvilli are present in the canaliculi but are sparse. [WP]
The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP].
kidney terms require review for cross-vertebrate compatibility and developmental relationships.
Functional unit of the kidney that filters waste.[TAO]
In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)
The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule.
Renal tubule that connects to the renal corpuscle.[TAO]
The section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine.
the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review.
A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]
The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva .
The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids.
The portion of the renal tubule that constitutes the proximal part of the loop of Henle, has low permeability to ions and urea, and is highly permeable to water; it consists of an initial short thick segment lined by low simple cuboidal epithelium and a long thin segment lined by simple squamous epithelium; however, this distinction is not as important physiologically as in the ascending limb, so often the two are treated as one structure.
The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule.
TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)
Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]
thick descending limb of proximal tubule
The distal sub-portion of the ascending loop of Henle which is lined by simple cuboidal epithelium and enters the renal cortex to empty a hypotonic filtrate into the distal convoluted tubule.
TODO - thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions
loop of Henle ascending limb thick segment
straight portion of distal convoluted renal tubule
straight portion of distal convoluted tubule
The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa.
a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule].
in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter.
The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO].
Innermost region of the mammalian kidney.
The glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy.
The mucous membrane lining the uterus. [TFD][VHOG]
The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]
Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead
in FMA this is subdivided into basal and outer
TODO - check for parallel structure with peritoneum
The conic expansion of the corpus spongiosum that forms the head of the penis.
The elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens.
A similar, but probably non-homologous, structure is found in cartilaginous fishes
Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
A fallopian tube that is part of a right side of organism [Automatically generated definition].
non-functional in monotremes[ISBN:978-0226870137]
A fallopian tube that is part of a left side of organism [Automatically generated definition].
Layer of simple cuboidal cells covering surface of ovary[WP].
Controversial - see article. Requires expert input. Also check BTO placement
A spherical aggregation of cells in the ovary that contains a single oocyte[WP,modified].
TODO - align subtypes based on staging, which is taxon-specific
Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[TAO]
These structures are periodically initiated to grow and develop, culminating in ovulation of usually a single competent oocyte in humans. These eggs/ova are only developed once every menstrual cycle (e.g. once a month in humans)
The somatic cell component of the follicle produces hormones important for oocyte development and proper endocrine function
follicle of ovary viewed macroscopically
A cluster of cells that project into the cavity of the mature ovarian follicle. It is released with the embedded oocyte during ovulation. In order for fertilization to occur this layer must be penetrated by the spermatocyte. [WP,modified].
A capsule that surrounds a female gonad.
The external iliac artery is a large artery in the pelvic region that carries blood to the lower limb. The external iliac artery is a paired artery, meaning there is one on each side of the body: a right external iliac artery and left external iliac artery. The external iliac artery is accompanied by the external iliac vein, which is located posterior to the artery. [WP,unvetted].
The internal iliac artery (formerly known as the hypogastric artery) is the main artery of the pelvis. [WP,unvetted].
The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted].
todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships
An artery that supplies blood to the upper urinary bladder.
The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP]
A large vein that connects the femoral vein to the common iliac vein. Their origin is at the inferior margin of the inguinal ligaments and they terminate when they join the internal iliac veins (to form the common iliac veins). Both external iliac veins are accompanied along their course by external iliac arteries. [WP,modified].
A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted].
One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified].
Muscle (organ) which is a part of the pelvis. Examples: levator ani,.
A portion of a prostate that forms a lobe.
Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue
The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted].
venous plexus of fascia of prostate gland
A zone of skin that is part of a penis [Automatically generated definition].
A urethra that is part of a male reproductive system.
A urethra that is part of a female reproductive system.
Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine.
NCIT:C12339 paraurethral gland belongs here
The tubules in the testes where spermatogenesis occurs.
Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO]
One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG]
Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28
FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)
Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified].
Adipose tissue, cells of which contain a single large lipid droplet.
A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified].
Adipose tissue, cells of which contain multiple small lipid droplets.[FMA]
especially abundant in newborns and in hibernating mammals
A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter.
consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct.
tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469]
The anus and surrounding regions. Encompasses both internal and external regions, where present.
The profunda femoris artery (also known as the deep femoral artery, or the deep artery of the thigh) is a branch of the femoral artery that, as its name suggests, travels more deeply (posteriorly) than the rest of the femoral artery. [WP,unvetted].
The medial circumflex femoral artery (internal circumflex artery, medial femoral circumflex artery) is an artery in the upper thigh that helps supply blood to the neck of the femur. [WP,unvetted].
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]
Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]
EHDAA2 models this as developing from CP, which is wrong
the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)
In the human body, the femoral vein is a blood vessel that accompanies the femoral artery in the femoral sheath. It begins at the adductor canal (also known as Hunter's canal) and is a continuation of the popliteal vein. It ends at the inferior margin of the inguinal ligament, where it becomes the external iliac vein. [WP,unvetted].
Either of the primary veins in the hindlimbs which collect blood from the hindlimb region.[AAO]
The great saphenous vein (GSV), also greater saphenous vein, is the large (subcutaneous) superficial vein of the leg and thigh. The terms 'safaina' (Greek) and 'el safin' (Arabic) have both been claimed as the origin for the word 'saphenous'. [WP,unvetted].
The outer layer of peritoneum that is attached to the abdominal and pelvic walls.
Peritoneum attached to the abdominal wall.[AAO]
A muscle that is part of the region of the hindlimb between the pelvis and ankle.
see notes on UBERON:0000978 for possible confusion over the term 'leg'.
muscle of upper or lower hindlimb segment
In human anatomy, the axillary artery is a large blood vessel that conveys oxygenated blood to the lateral aspect of the thorax, the axilla (armpit) and the upper limb. Its origin is at the lateral margin of the first rib, before which it is called the subclavian artery. After passing the lower margin of teres major it becomes the brachial artery.
axillary part of trunk of subclavian artery
The subscapular artery, the largest branch of the axillary artery, arises at the lower border of the Subscapularis, which it follows to the inferior angle of the scapula, where it anastomoses with the lateral thoracic and intercostal arteries and with the descending branch of the transverse cervical, and ends in the neighboring muscles. About 4 cm. from its origin it gives off two branches, first the scapular circumflex artery and then the thoracodorsal artery. [WP,unvetted].
A zone of skin that is part of a pelvis [Automatically generated definition].
A zone of skin that is part of an abdomen [Automatically generated definition].
A zone of skin that is part of a neck [Automatically generated definition].
A zone of skin that is part of a thorax [Automatically generated definition].
A zone of skin that is part of a limb [Automatically generated definition].
An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]
Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]
A lymphatic vessel that is part of a face [Automatically generated definition].
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)
A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm].
In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist.
A phalanx that is part of a forelimb autopod[Automatically generated definition].
Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO]
The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified].
Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO]
Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur.
Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA].
todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA.
Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]
The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle.
TODO - find a home for: FMA:24139 ! skeleton of upper limb
Skeletal structure of the paired, anterior appendages.[AAO]
Subdivision of skeleton consisting of all skeletal elements in an hindlimb region.
Skeletal structure of the paired, posterior appendages.[AAO]
Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape].
here 'manus' includes both the wrist region, metatarsal region and acropodial region
Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA].
FMA:24216 present in FMA1, but gone in subsequent versions
Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape].
here 'pes' includes both the ankle region, metatarsals and acropodial region
The major postaxial endochondral bone in the posterior zeugopod[Phenoscape].
One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO]
A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia.
In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment
The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted].
A phalanx that is part of a hindlimb autopod[Automatically generated definition].
Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO]
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
A zone of skin that is part of a eyelid [Automatically generated definition].
A zone of skin that is part of a lip [Automatically generated definition].
A zone of skin that is part of a external ear [Automatically generated definition].
zone of skin of auricular region of head
The part of the forelimb extending from the shoulder to the autopod[cjm].
currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand
this class refers to the combination of the stylopod and zeugopod of a forelimb. Sometimes (cf FMA), 'arm' denotes the stylopod only; sometimes (cf MA), 'arm' denotes the part of the forelimb covering both (i.e. shoulder to hand). Also note distinction between arm and forelimb: hand is part of forelimb, but not part of arm
The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific].
The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified].
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333
A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.
pedal digit (phalangeal portion) plus soft tissue
A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).
(...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]
In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332
The sternoclavicular articulation is a double arthrodial joint composed of two portions separated by an articular disc. The parts entering into its formation are the sternal end of the clavicle, the upper and lateral part of the manubrium sterni, and the cartilage of the first rib, visible from the outside as the suprasternal notch. The articular surface of the clavicle is much larger than that of the sternum, and is invested with a layer of cartilage, which is considerably thicker than that on the latter bone. The ligaments of this joint are: Articular capsule Anterior sternoclavicular ligament Posterior sternoclavicular ligament Interclavicular ligament Costoclavicular ligament Articular disk [WP,unvetted].
The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted].
note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship
in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle
The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted].
A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO].
A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]
A vessel that contains or conveys lymph.[AAO]
Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)
A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized].
Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO]
We use a generic definition that includes the deltoideus as represented in AAO: 'Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus'. Kardong: Dorsal group
the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula
A sesamoid element that is composed of bone tissue.
Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage.[VSAO]
A carpal bone that proximally_connected_to a forelimb zeugopod skeleton.
Any muscle organ that is part of a shoulder [Automatically generated definition].
A zone of skin that is part of a shoulder region.
in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted].
A skeletal joint that is part of a pes [Automatically generated definition].
TODO check FMA - use the set class for now
joint of terminal segment of free lower limb
A joint that connects the hindlimb autopod and zeugopod skeletons.
todo - accurately represent different types of ankle joint
A skeletal joint that is part of a manus (hand) [Automatically generated definition].
joint of terminal segment of free upper limb
A joint that connects the forelimb zeugopod and stylopod skeletons[Obol].
In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis
A joint connecting the forelimb zeugopod skeleton with the carpal skeleton.
in FMA this includes radio-carpal and radio-ulnar *ligaments*
The axillary nerve is a nerve of the human body, that comes off the posterior cord of the brachial plexus at the level of the axilla (armpit) and carries nerve fibers from C5 and C6. The axillary nerve travels through the quadrangular space with the posterior circumflex humeral artery and vein. [WP,unvetted].
The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia].
Any muscle organ that is part of a pelvic girdle [Automatically generated definition].
Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle.
Any muscle organ that is part of a pes [Automatically generated definition].
A muscle organ that is part of an arm [Automatically generated definition].
See notes on UBERON:0001460 for possible terminological confusion over term 'arm'. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand)
Any muscle organ that is part of a manus [Automatically generated definition].
The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery.
The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG]
The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG]
birds have right aortic arch, mammals left.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20
A zone of skin that is part of a knee [Automatically generated definition].
A zone of skin that is part of a leg [Automatically generated definition].
A zone of skin that is part of an ankle [Automatically generated definition].
A zone of skin that is part of a pes [Automatically generated definition].
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].
results from fusion of left and right dorsal aortae
The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
A zone of skin that is part of a elbow [Automatically generated definition].
A zone of skin that is part of a wrist [Automatically generated definition].
A zone of skin that is part of a manus [Automatically generated definition].
The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery.
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'
This class represents the adult and developing structures'
in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk.
placement of the MA class here is not strictly correct, as the MA class does not include the branches
right common carotid artery plus branches
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP].
Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG]
One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO]
One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta.
Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)
Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]
In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]
The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]
The subclavian artery that supplies the right pectoral appendage.
in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery
proximal part arises from right 4th aortic arch in humans
The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax.
left common carotid artery plus branches
The lymph nodes which drain the legs; contained in the popliteal fossa.
In the popliteal fossa between biceps femoris m. and semitendinosus m..
The popliteal vein course runs alongside the popliteal artery but carries the blood from the knee joint and muscles in the thigh and calf back to the heart. Its origin is defined by the junction of the posterior tibial vein and anterior tibial vein. It drains the peroneal vein before reaching the knee joint and turns into the femoral vein when leaving the adductor canal (also known as Hunter's canal). The popliteal artery extends from the femoral artery behind the popliteal fossa which is the space behind the knee. [WP,unvetted].
A vein of the lower limb that carries blood from the anterior compartment of the leg to the popliteal vein which is forms when it joins with the posterior tibial vein. Like most deep veins, the anterior tibial vein is accompanied by an artery of the same name, the anterior tibial artery, along its course. [WP,unvetted].
The small saphenous vein (also lesser saphenous vein), is a relatively large vein of the superficial posterior leg. [WP,unvetted].
The dorsal metatarsal veins are veins which drain the metatarsus of the foot. [WP,unvetted].
A continuation of the Dorsal venous arch of the foot and is the origin of the long saphenous vein.
One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries.
A zone of skin that is part of a hip region.
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
Subdivision of urinary system which consists of the urinary bladder and the urethra.
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP]
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue.
Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG]
Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO]
relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]
Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.
A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII.
Makes up part of the tongue in frogs and salamanders.[AAO]
The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED]
A muscle organ that attaches the tongue to some other structure.
main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement
All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus.
The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII.
The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED]
The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone
Nerve that carries information from the olfactory epithelium to the olfactory bulb[Butler and Hodos].
Nerve that carries information from the olfactory epithelium through the olfactory bulb to the olfactory cortex of the telencephalon.[AAO]
Segment of neural tree organ which is continuous with the olfactory epithelium and an olfactory bulb[FMA:46787].
The 1st cranial nerve. The olfactory nerve conveys the sense of smell. It is formed by the axons of OLFACTORY RECEPTOR NEURONS which project from the olfactory epithelium (in the nasal epithelium) to the OLFACTORY BULB[MESH:A08.800.800.120.640].
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]
connects to main OB (in taxa where main/accessory distinction is important)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625
The subclavian artery that supplies the left pectoral appendage.
in humans, branches off the arch of aorta
arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans
A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart.
The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green).
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
The subclavian vein is a paired large vein, one on either side of the body. Their diameter is approximately that of the smallest finger.
Vein which collects blood from the forelimb via the brachial veins and from the muscles and skin of the trunk via the anterior epigastric and lateral veins.[AAO]
A vein that drains blood from the thymus.
thymic tributary of brachiocephalic vein
The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted].
Skeletal muscle derived from cranial mesoderm and controls eye movements.
todo - resolve discrepancies in which muscles are considered extra-ocular
Any of the six small muscles that control movement of the eyeball within the socket. [TFD][VHOG]
Muscles surrounding the eye (bulbus oculi) and having an effect on eye movements.[AAO]
The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these (extrinsic ocular) muscles tend to be conservative. They change little during the course of evolution.[well established][VHOG]
Mammals have 7 extra-ocular muscles, but humans lack the M. retractor bulbi.
Myofibers in extraocular muscles are derived from mesoderm, whereas muscle connective tissue cells arise from neural crest.[PMID:16638982]
BTO and MA consider this part of the eye; we follow them here (inferred from skeletal muscle). Not clear if omission from FMA is deliberate.
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.331
The medial rectus muscle is a muscle in the orbit. As with most of the muscles of the orbit, it is innervated by the inferior division of the oculomotor nerve (Cranial Nerve III). This muscle shares an origin with several other extrinsic eye muscles, the anulus tendineus, or common tendon. It is the largest of the extraocular muscles and its only action is adduction of the eyeball. [WP,unvetted].
The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution.[well established][VHOG]
Taxon notes (from VHOG): "The ability to rotate the eyeball is common to all vertebrates with well-developed eyes, regardless of the habitat in which they live, so these [extrinsic ocular] muscles tend to be conservative. They change little during the course of evolution." Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.331 [VHOG:0001127]
inferior division of the oculomotor nerve
The lateral rectus muscle is a muscle in the orbit. It is one of six extraocular muscles that control the movements of the eye (abduction in this case) and the only muscle innervated by the abducens nerve, cranial nerve VI. [WP,unvetted].
Cranial nerve VI innervated; lateral in the rectus group.[AAO]
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
A sphincter muscle that is part of the iris.
In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]
WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure
A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted].
It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina
The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP].
Part of the external carotid which supplies blood to the tongue.[AAO]
relationship loss: part_of external carotid (AAO:0010218)[AAO]
lingual branch of external carotid artery
A branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries
The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified].
Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO]
relationship loss: part_of internal carotid (AAO:0010219)[AAO]
The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted].
One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery.
An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO]
todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery
posterior communicating segment of the basilar artery
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system.
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
A portal vein that transports nutrients from the digestive tract to the liver[Kardong].
Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG]
In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted]
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.265
The first major branch of the abdominal aorta.
Cranial nerve which connects the midbrain to the extra-ocular and intra-ocular muscles.
Somatic efferent fibers which innervate four eye muscles.[AAO]
A cranial nerve that runs to the eye muscles.
Somatic efferent nerve which supplies a single eye muscle, the m. obliquus superior.[AAO]
Homologous trochlear nerves are found in all jawed vertebrates
The human trochlear nerve is derived from the basal plate of the embryonic midbrain.
Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw).
Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]
the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls
Cranial nerve that runs to the eye muscles.
Somatic motor nerve which bifurcates innervating m. rectus lateralis and m. retractor bulbi (eye muscles).[AAO]
Homologous abducens nerves are found in all vertebrates except lampreys and hagfishes.[WP] It controls the movement of a single muscle, the lateral rectus muscle of the eye, in humans. In most other mammals it also innervates the musculus retractor bulbi, which can retract the eye for protection
found in all vertebrates except lampreys and hagfishes
Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches).
Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO]
Cranial nerve that transmits sound and equilibrium (balance) information from the inner ear to the brain.
Nerve primarily composed of special somatic afferent fibers innervating the inner ear, and is involved in balance, position, and hearing.[AAO]
Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult).
Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO]
Cranial nerve that innervates the muscles of the tongue.
Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis
Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO]
Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]
we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves
The pulmonary artery that supplies the right lung.
TODO - add class 'pulmonary artery tree organ'
The pulmonary artery that supplies the left lung.
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
MA and NCITA also has 'anterior facial vein'
The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted].
The cranial ganglion that is associated with and extends fibers into the trigeminal nerve.
consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)
A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]
In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.
The bone at the lower, posterior part of the skull.
formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII
fusion of basi-, exo- and supra-occipitals (and maybe tabular)
basi paired exo and supra occipital bones
An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended.
part of viscerocranium (facial skeleton) in FMA
The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous.
In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process
fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic)
The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP].
Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA
A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP].
A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG]
The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG]
todo - homology e.g. mesethmoid of teleost
Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259
One of two small oblong bones, varying in size and form in different individuals; they are placed side by side at the middle and upper part of the face, and form, by their junction, 'the bridge' of the nose[WP]. Paired dermal bones, likened to a bone tube, positioned lateral to the supraethmoid. Nasal bones are transversed by the anterior most part of the supraorbital canals and bear one neuromast foramen in zebrafish[ZFA].
Paired bone of intramembranous origin that roofs the olfactory capsule.[AAO]
Paired dermal bones, likened to a bone tube, positioned lateral to the supraethmoid. Nasal bones are transversed by the anterior most part of the supraorbital canals and bear one neuromast foramen in zebrafish Cubbage and Mabee, 1996.[TAO]
relationship loss: overlaps mesethmoid-nasal joint (TAO:0001677)[TAO]
relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]
Synonym adnasal used in Weitzman 1960, and synonym discussed in Vari 1995.[TAO]
In primitive bony fish and tetrapods, the nasal bones are the most anterior of a set of four paired bones forming the roof of the skull, being followed in sequence by the frontals, the parietals, and the postparietals. Their form in living species is highly variable, depending on the shape of the head, but they generally form the roof of the snout or beak, running from the nostrils to a position short of the orbits. In most animals, they are generally therefore proportionally larger than in humans or great apes, because of the shortened faces of the latter. Turtles, unusually, lack nasal bones, with the prefrontal bones of the orbit reaching all the way to the nostrils (ISBN 0-03-910284-X)
A paired dermal bone situated in the mid-palate that helps form the hard palate [Palaeos].
Dermal bone that forms the antero-lateral region of the palate and is located ventral to the autopalatine. The dermopalatine is bilaterally paired and usually bears teeth.[TAO]
Dermopalatine: same as palatine. The prefix is used by fish people because the palatine is a dermal replacement bone for a section of the autopalatine section of the palatoquadrate. In that context, palatine is potentially ambiguous.[Palaeos]
In ostariophysans, the dermopalatine is absent.[TAO]
A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified].
Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]
relationship loss: part_of hyoid plate (AAO:0000664)[AAO]
The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia.
One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted].
This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5.
The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG]
Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG]
Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry.
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.695
Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
The organ of hearing and of equilibrium. [TFD][VHOG]
Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)
Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO].
The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG]
in XAO this includes and is only the tympanum
DOI:10.1007/s00359-008-0327-1 Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008)
The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted].
The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG]
Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball.
Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO]
in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit
The group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve).
resolve facial VII vs geniculate (see EHDAA2)
These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
The group of neuron cell bodies associated with the ninth cranial nerve.
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]
It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].
It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].
Use this class for both the nails of primates and the homologous claws of mammals such as mouse.
A primate's nail consists of the unguis alone; the subunguis has disappeared
The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]
An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.
Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO]
a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity].
Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG]
in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures
DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006)
Subdivision of skeleton which includes upper and lower jaw skeletons.
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO]
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
See notes for jaw w.r.t skeletal element vs subdivision of head.
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
A movable or semi-movable ocular covering that protects the eye and contributes to surface maintenance; structure and composition vary widely among vertebrate species.
In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva.
FMA divides this into skin, fascia, conjunctiva
The groups of nerve cell bodies associated with the twelve cranial nerves.
Ganglion which is located in the head.[TAO]
cranial ganglion part of peripheral nervous system
Nuclear complex containing subnuclei that give rise to the axons of the occulomotor nerve, both motor and parasympathetic fibers, situated at the midline at the level of the superior colliculus in the midbrain tegmentum (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 533-534).
The nucleus of the oculomotor nerve (cranial nerve III)[XAO:0004389].
The part of the palate formed from the fusion of the two palatine shelves, extensions of the maxillary prominences.
present in mammals and some reptiles. A similar structure is found in crocodilians, but, in most other tetrapods, the oral and nasal cavities are not truly separate. The secondary palate is formed by bilateral medial extensions of maxillary processes. The extensions (palatine processes) meet at the midline, merging dorsally with nasal septum and rostrally with primary palate. The secondary palate (hard palate) separates nasal and oral cavities. Caudal extension of the secondary palate into the pharynx, forms a soft palate which divides the rostral pharynx into dorsal (nasopharynx) and ventral (oropharynx) chamber.
Nucleus extending from the upper spinal cord through the pontine tegmentum that receives sensory inputs from the trigeminal nerve. It is continuous caudally with the dorsal gray matter of the spinal cord.
Elongated nucleus located in the midbrain tegmentum that receives proprioceptive input from both teh extraocular and the masticatory muscles. Contrary to the general rule, the cell bodies that give rise to these sensory fibers are located within the mesencephalic nucleus rather than in a peripheral ganglion. Some of the sensory fibers in the mesencephalic root give off collaterals to the trigeminal motor nucleus, thereby providing the anatomic basis for the monosynaptic jaw reflex. (Heimer, L. The Human Brain and Spinal Cord, 2nd ed. 1996, page 248).
develops from NC in some species[https://github.com/obophenotype/uberon/wiki/The-neural-crest] Not of NC origin[DOI:10.1002/dvdy.1197].
part of midbrain tegmentum in NIF and MA. the neurons of the mesencephalic trigeminal nucleus are the only centrally located primary sensory neurons in amniotes; all others are extramedullary
mesencephalic nuclei of trigeminal nerves
mesencephalic nucleus of the trigeminal nerve
nucleus mesencephalicus nervi trigeminalis
nucleus tractus mesencephalici nervi trigemini
nucleus tractus mesencephalicus nervi trigemini
mesencephalic nucleus of trigeminal nerve
A region of histologically disparate cells located just dorsal to the inferior olivary nucleus in the lateral portion of the upper medulla. It receives upper motor neuron innervation directly via the corticobulbar tract This nucleus gives rise to the efferent motor fibers of the vagus nerve terminating in the laryngeal and pharyngeal muscles, as well as to the efferent motor fibers of the glossopharyngeal nerve (CN IX) terminating in the stylopharyngeus. [WP,unvetted].
Any of the nuclei of the cochlear nuclear complex.
cochlear nucleus of eighth cranial nerve
A muscular organ in the floor of the mouth.
in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence.
A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG]
Muscular organ in the floor of the mouth.[FEED]
The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586].
Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]
Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods
The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions
DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)
The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis.
A specialized receptor organ that is a collection of cells spanning the gustatory epithelium.
One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG]
Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG]
In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish.
arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL)
The section of the pharynx that lies above the soft palate.
The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG]
In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane
An anatomical space that is enclosed by a pharynx.
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
The muscular, non-bony arch-shaped posterior portion of the palate extending from the posterior edge of the hard palate.
A muscular arch-shaped structure that is composed of the musculus uvuli and parts of tensor veli palatini, levator veli palatini, palatoglossus and palatopharyngeus and attaches to the hard palate and modulates the connections between the oral cavity and pharynx soft tissue arch .[FEED]
Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible.
Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG]
The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG]
In humans, they account for 70% of the salivary volume and weigh about 15 grams. [WP,unvetted]
In mouse, multilobed and lobulated, on the ventral midline of the neck
in mice, submandibular gland development initiates as a thickening of the oral epithelium; around E12 an initial (single) epithelial bud on a stalk grows into a condensing neural crest-derived mesenchyme; clefts in the epithelium result in 3-5 epithelial buds at E13.5, and branching morphogenesis occurs with continued proliferation, successive rounds of cleft formation, duct elongation, and duct lumen formation, so that by E14 the gland is highly branched (multi-lobed); functional differentiation, with the appearance of proacinar cells and secretory products begins after E15 and continues to birth; acinar differentiation continues postnatally with final differentiation of the granular convoluted tubules at puberty[MGI:anna]
The submandibular is the first major salivary gland to develop in the embryo, followed by the neighbouring sublingual and then the parotid.[PMID:17336109]
The term submandibular as used in humans, is incorrect due the difference in topography of these structures[http://www.avdc.org]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.525
A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration.
An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED]
Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO]
(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241
The cartilaginous structures that support the larynx.
A ligament that is part of a larynx and connexts the cartilages of the larynx.
Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP].
A lymphoid follicle that contains a germinal center.
A parenchyma that is part of a thyroid follicle [Automatically generated definition].
The dense and irregular connective tissue capsule surrounding a parathyroid gland.
A parenchyma that is part of a parathyroid gland [Automatically generated definition].
A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta.
TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal
this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye
Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular.
Mineralized collagen containing substance that forms the tooth structure.[TAO]
Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG]
Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]
DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)
A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP].
current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)
Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO]
The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO].
The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417
The part of the ear that projects from the head, connecting to the external acoustic meatus.
The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG]
In various species, the pinna can also signal mood and radiate heat
The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch).
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420
The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO].
FMA treats periodontium and periodontal ligament as the same
Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart).
Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO]
A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ.
Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO]
Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO]
Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG]
In humans, the dental papilla appears after 8-10 weeks intra uteral life
DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)
Epithelial tube that transports milk[GO].
The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens.
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye.
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]
The smooth stratified squamous epithelium that covers the outer surface of the cornea.
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709].
Disease notes: implicated in rheumatoid arthritis.
A skeletal muscle organ that is part of the trunk region.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes.
Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
MP treats posterior uvea and optic choroid as distinct
The lamellated connective tissue of the cornea between the Bowman and Descemet membranes.
Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]
relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]
A double layer covering the ciliary body that produces aqueous humor.
The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae.
The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified].
Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]
Any of the layers that make up the retina[MP].
MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP].
A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]
The monolayer of pigmented epithelium covering the neural retina.[AAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.
Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]
See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
The layer within the retina where the photoreceptor cell receptor segments reside.
we follow MA and ZFA in subdividing this into inner and outer segments
stratum segmentorum externorum et internorum (retina)
stratum segmentorum externorum et internorum retinae
The row of jucntional complexes between the plasma membranes of rod segments and the Muller glia cells; this barrier separates the layer of inner and outer segments of the rods and cones from the outer nuclear layer and forms a blood-retina barrier[MP].
The layer within the retina where the photoreceptor cell bodies reside.
The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO].
The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]
Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia).
The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176].
AO notes NLXANAT:1005031 appears to be retired
Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer.
a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer].
NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]
Layer of the retina formed by expansion of the fibers of the optic nerve.
The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP].
Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3].
Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia).
The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842].
The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]
http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.
Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified].
distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body
The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified].
The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells.
Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive).
Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive).
A layer of epithelial cells that is part of the eye.
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
The elastic, clear, membrane-like structure, that is outer most layer of the lens.
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia.
ganglion of sympathetic part of autonomic division of nervous system
sympathetic part of autonomic division of nervous system ganglion
Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands.
Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA].
Made to be a subtype of junction rather than tissue to be consistent with FMA
The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball.
An intermingling of fiber fascicles from adjacent spinal nerves to form a network.
To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436
An arrangement of nerve fibers, running from the spine where it proceeds through the neck then the axilla and into the arm where it innervates skin and muscle. [WP,modified].
check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus'
A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG]
A nerve plexus that is part of an autonomic nervous system [Automatically generated definition].
The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP].
Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands.
The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland].
In humans, they are situated in the upper, outer portion of each orbit
Innervation is highly complex and species-specific
A modified lobulated sebaceous gland at the rim of an eyelid, responsible for the supply of meibum.
in mice, meibomian gland development is initiated around E18.5 with the formation of an epithelial placode and mesenchymal condensation, similar to that observed in hair follicle development; invagination of the epithelium into the developing mesenchyme then continues from birth to about P3 with initial branching of the epithelial cord detected at P5; by P8 the developing meibomian gland shows extensive ductal branching and the formation of distinct acini with mature meibomian glands present by P15 or eyelid opening[PMID:20664693]
Any of the coil glands of the skin that secrete sweat.
TODO - check if all sweat glands are epidermal - see EMAPA:29743
A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG]
Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG]
In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101
A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP].
sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass.
Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG]
Sebaceous glands are also limited to mammals.[well established][VHOG]
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102
One of the cartilage structures in the nose that provide form and support[WP].
The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx.
The mucous membrane that lines the nasal cavity[MP].
TODO - check lining vs part of. split olfactory and nasal mucosa?
Aqueous substance secreted by the lacrimal gland.
The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001].
FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton.
One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands.
There are 3 pairs of major salivary glands in human and mouse
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
Lip that covers the upper portion of the mouth.[TAO].
Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG]
Lip that covers the lower portion of the mouth.[TAO].
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin
A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted].
Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved.
One of three half-circular, interconnected tubes located inside each ear[WP].
Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]
In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG]
MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.414
One of three fluid-filled toroidal spaces, arranged orthogonally to each other in each ear, that detect angular acceleration. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]
relationship loss: develops_from anterior semicircular canal primordium (TAO:0000469)[TAO]
The posterior semicircular canal is a part of the vestibular system and detects rotations of the head in the sagittal plane.
relationship loss: develops_from posterior semicircular canal primordium (TAO:0000412)[TAO]
relationship loss: develops_from lateral semicircular canal primordium (TAO:0000232)[TAO]
The spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified].
A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG]
Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG]
The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)'
the cochlea is coiled in most mammals, monotremes being the exceptions.
sources vary in connection to bony labyrinth
DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998)
Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation.
The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366
Cartilage of the pinna and much of the external ear canal.
Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP].
A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG]
inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now
this class is used more generically than in FMA, and includes e.g. cortex of hair
The part of the membranous labyrinth that includes the utricle and saccule lodged within the vestibule and the semicircular ducts lodged eccentrically in the corresponding canals.
Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP].
The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans.
A cartilage that is part of a external ear [Automatically generated definition].
A zone of skin that is part of a chest [Automatically generated definition].
anterolateral part of thorax zone of skin
zone of skin of anterior thoracic region
zone of skin of anterolateral part of thorax
One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA].
Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO]
The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]
DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)
Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified].
Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally.
Lower lateral part of the cerebral hemisphere. (MSH).
Boundary notes: It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe. [Wikipedia:Temporal_lobe]
Upper central part of the cerebral hemisphere. (MSH).
Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species.
Nucleus of brain which is an elongated crescent-shaped mass lying parallel and adjacent to the lateral ventricle throughout its extent[FMA:61833].
Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion.
check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)
Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease[Wikipedia:Putamen].
All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]
DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)
Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle.
Nucleus of brain which is located medially to the putamen and laterally to the internal capsule[FMA][FMA:61835].
BTO and MA are inconsistent w.r.t striatum and pallidum being non-overlapping as in ABA. Note that we have pallidum as part_of basal gangion, so we can make the direct link to basal ganglion. ISBN:1588900649 says: ... a derivative of the diencephalon, seperates as a result of growing fibers of theinternal capsule and is finally displaced into telencephalon. only a small medial remnannt remains, the entopeduncular nucleus. The globus pallidus should be regarded as part of the subthalamus
Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM).
Subdivision of basal ganglion of telencephalon which is an almond-shaped gray mass in the dorsomedial part of the temporal lobe[FMA:61841]
One part of the striatum is called the archistriatum. (...) The archistriatum of fishes consists of several indistinctly segregated nuclei called the amygdaloid (...) complex. Tetrapods retain the structure, and in mammals the corresponding amygdala is a globular mass that tends to be ventral to the other basal nuclei.[well established][VHOG]
MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.342
A region of the brain consisting of a collection of neurons located in the forebrain ventral to the caudate and putamen. (caudoputamen in rodent) and continuous with these structures. There is no distinct boundary between the nucleus accumbens and the caudate/putamen, but in rodents, it can be identified by its lack of traversing fiber bundles in comparison to the dorsal striatum. Its principle neuron is the medium spiny neuron. Together with the neostriatum (caudate nucleus and putamen), the nucleus accumbens forms the striatum.
a collection of pleomorphic cells in the caudal part of the anterior horn of the lateral ventricle, in the region of the olfactory tubercle, lying between the head of the caudate nucleus and the anterior perforated substance. It is part of the ventral striatum, a composite structure considered part of the basal ganglia[GO][GO:0021768].
The ventral striatopallidal complex in birds corresponds closely to its counterpart in mammals, with a nucleus accumbes present in the rostral telenceaphalon. Note that in birds, a region previously called the nucleus accumbens is now recognized as the lateral part of the bed nucleus of stria terminalis.[ISBN:0471888893]
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium.
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG]
Part of the hippocampal formation forming a 'V' or 'U' shaped structure with the opening bounded by hippocampal area CA3. It consists of 3 layers from superficial to deep: molecular, granule cell and polymorphic or hilar layer.
The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO][GO:0021542].
BTO says dentate gyrus = fascia dentata + hilus. Note that GO classifies dentate gyrus development under hippocampus development
A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces.
TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere
A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO]
Fringe of the tela choroidea of the brain ventricles[MP]
White matter regional part of brain which is flanked by nuclear masses, consisting of both afferent and efferent fibers projecting between the cerebral cortex and the brainstem and spinal cord. It consists of three distinct parts: an anterior limb, posterior limb, and genu. (Adapted from MSH by Maryann Martone).
White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone).
In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells.
The most anterior region of the brain including both the telencephalon and diencephalon.
Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]
The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]
In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]
PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.
Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000].
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]
The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]
relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]
From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]
In mammals the cortex covers almost the whole of the cerebral hemispheres.
In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209]
In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles.
In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum.
In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb.
The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure.
dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight.
DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)
The division of the forebrain that develops from the foremost primary cerebral vesicle.
The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]
Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]
not well differentiated from the cerebrum. (Ariens, p. 868)
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965].
The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)
Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87).
One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG]
Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO]
(...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484
A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia].
A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO]
Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO]
For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG]
Lancelets possess a region similar to the hypothalamus (Murakami, 2005)
Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346.
Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO]
The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG]
DOI:10.1046/j.1469-7580.2001.19910063.x Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001)
Anterior part of the diencephalon that lies between the dorsal thalamus, hypothalamus, and tegmentum of the mesencephalon, including subthalamic nucleus, zona incerta, the fields of Forel, and the nucleus of ansa lenticularis[GO, modified].
Some sources treat the subthalamus as distinct from the thalamus, separated by the zona limitans intrathalamica. In MA, the ventral thalamus is part of the thalamus. Butler Hodos who identify a dorsal to ventral sequence consisting of epithalamus, dorsal thalamus, ventral thalamus and hypothalamus. We solve this by considering dorsal and ventral thalamus distinct, and the label thalamus as being ambiguous w.r.t thalamus proper (dorsal thalamus) or wider thalamus (dorsal plus ventral)
The epithelial lining of the trachea which contains numerous ciliated cells.
An epithelium that is part of a small intestine [Automatically generated definition].
Intestinal epithelium which lines the lumen of the mid intestine.[TAO]
A segment of the epithalamus that has as its parts the habenular nuclei and the habenular commissure[FMA,modified].
The habenula relays impulses from limbic areas of the telencephalon to an unpaired midbrain nucleus, the interpeduncular nucleus.[TAO]
A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399).
A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO]
Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO]
relationship loss: part_of pineal complex (TAO:0001359)[TAO]
The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG]
lobulated in humans, homogeneous in mouse. Calcifies with age in humans.
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.516
The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO].
Lens shaped nucleus lying in the subthalamu[NLXANAT:1010002]s
Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF].
relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'
A brain commissure that is situated in front of the pineal gland and connects the habenular nucleus on one side of the diencephalon with that on the other side.
A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.
Originally this was classified as a female reproductive structure, as it was in the MP in 2011
Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]
The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts
The male Dayak fruit bat has lactating mammary glands
The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges.
The BTO class represents the combination of nipple plus lobe
The FMA class represents an individule lobe. The nipple is not a part
The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224
Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA].
TODO - ensure correct terminology for lobes/lobules. In mouse there are no distinct lobes (ISBN:0123813611), here lobule appears to be synonymous with acinus
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular.
ncit:Milk refers specifically to cow milk
An endothelium that is part of a capillary [Automatically generated definition].
An endothelium that is part of an arteriole [Automatically generated definition].
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
An endothelium that is part of a venule [Automatically generated definition].
An endothelium that is part of a vein [Automatically generated definition].
The group of neurons that serve as the primary processor of visual information received from the retina via the optic tract and send processed information to the visual cortex of the occipital lobe.
BTO has distinct classes for body and nucleus, but other sources treat as identical
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)
Nuclear complex between dorsal thalamus and optic tectum whose nuclei receive afferents primarily from the retina and the optic tectum and are involved in modulating motor behavior in response to visual input.
A narrow, transversely oriented rostral zone of the mesencephalic tectum, bounded caudally by the superior colliculus, rostrally by the habenular trigone, and laterally by the pulvinar thalami; the pretectal area contains several nuclei that receive fibers from the optic tract; it has bilateral efferent connections with the Edinger-Westphal nucleus of the oculomotor nuclear complex by way of which it mediates the pupillary light refle[MP:0009637]x
Region of brain lying between the midbrain tectum and the thalamus (Sefton and Dreher, in Paxinos, G The rat central nervous system, 1995, pg 859), Situated at the level of poterior commissure and just rostral to the superior colliculus (Brodal, Neurological Anatomy, 3rd ed, 1981, pg 542)
in monotremes, undifferentiated and possesses only a single nucleus[ISBN:0471888893]
teleost fishes exhibit hypertrophy of the pretectum[ISBN:0471888893]
within the amniotes, this region is smaller in mammals[ISBN:0471888893]
It receives binocular sensory input from retinal ganglion cells of the eyes, and is the region responsible for maintaining the pupillary light reflex
part of diencephalon in ZFA - modify to adjacent here, supported by pub. Note there is some inconsistency in resources between the region vs nuclei - sometimes they are treated equivalent, sometimes separate (e.g. MP)
Part of the midbrain tecturm consisting of paired bodies that sit caudal to the thalamus and surround the pineal gland in the mesencephalon of vertebrate brains. It comprises the rostral aspect of the midbrain, posterior to the periaqueductal gray and adjacent superior the inferior colliculus. The inferior and superior colliculi are known collectively as the corpora quadrigemina (Latin, quadruplet bodies). It consists of several identified cellular layers and also comprises the brachium of the superior colliculus and commissure of supeior colliculus from Wikipedia.org and Neuronames (MM).
The brain structure where the two separate inputs from the two eyes are combined into a single, integrated map.[AAO]
The roof of the midbrain, morphologically visible by the end of the segmentation period. Kimmel et al, 1995.[TAO]
The tectum is a layered structure, with a number of layers that vary by species. The superficial layers are sensory-related, and receive input from the eyes as well as other sensory systems.[1] The optic tectum is one of the fundamental components of the vertebrate brain, existing across the full range of species from hagfish to human.[4] (See the brain article for background.) Some aspects of the structure are very consistent, including a structure composed of a number of layers, with a dense input from the optic nerve to the superficial layers and another strong input conveying somatosensory input to deeper layers. Other aspects are highly variable, such as the total number of layers (from 3 in the African lungfish to 15 in the goldfish[5]), and the number of different types of cells (from 2 in the lungfish to 27 in the house sparrow[5]
The term SC is used when discussing mammals, and OT for other vertebrates[WP]
strata (grisea et alba) colliculi cranialis
strata (grisea et alba) colliculi superioris
). In hagfish, lamprey, and shark it is a relatively small structure, but in teleost fish it is greatly expanded, in some cases becoming the largest structure in the brain. (See the adjoining drawing of a codfish brain.) In amphibians, reptiles, and especially birds it is also a very significant component, but in mammals it is dwarfed by the massive expansion of the cerebral cortex.
Part of the midbrain tectum, consisting of paired predominantly gray matter elevations on the dorsal aspect of the midbrain, located caudal to the superior colliculus, dorsal to the periaqueductal gray of the cerebral aqueduct and rostral to the cerebellum. According to Neuronames, the inferior colliculus comprises the central, pericentral and external nucleus and two predominantly white matter structures, the brachium of the inferior colliculus and the commissure of the inferior colliculus (MM).
A multi-tissue structure that is part of a spinal cord.
A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO].
In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva
An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN).
The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils
An epithelium that is part of a nasopharynx [Automatically generated definition].
epithelial tissue of nasal part of pharynx
A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum.
Non-mammalian species do not have a brain structure that looks like the mammalian hippocampus, but they have one that is considered homologous to it. The hippocampus, as pointed out above, is essentially the medial edge of the cortex. Only mammals have a fully developed cortex, but the structure it evolved from, called the pallium, is present in all vertebrates, even the most primitive ones such as the lamprey or hagfish. The pallium is usually divided into three zones: medial, lateral, and dorsal. The medial pallium forms the precursor of the hippocampus. It does not resemble the hippocampus visually, because the layers are not warped into an S shape or enwrapped by the dentate gyrus, but the homology is indicated by strong chemical and functional affinities. There is now evidence that these hippocampal-like structures are involved in spatial cognition in birds, reptiles, and fish. In birds, the correspondence is sufficiently well established that most anatomists refer to the medial pallial zone as the 'avian hippocampus'. The story for fish is more complex. In teleost fish (which make up the great majority of existing species), the forebrain is distorted in comparison to other types of vertebrates: most neuroanatomists believe that the teleost forebrain is essentially everted, like a sock turned inside-out, so that structures that lie in the interior, next to the ventricles, for most vertebrates, are found on the outside in teleost fish, and vice versa. One of the consequences of this is that the medial pallium ('hippocampal' zone) of a typical vertebrate is thought to correspond to the lateral pallium of a typical fish. Several types of fish (particularly goldfish) have been shown experimentally to have strong spatial memory abilities, even forming 'cognitive maps' of the areas they inhabit.[WP]
An epithelium that is part of a respiratory bronchiole [Automatically generated definition].
bronchiolus respiratorius epithelial tissue
epithelial tissue of bronchiolus respiratorius
epithelial tissue of respiratory bronchiole
respiratory bronchiole epithelial tissue
The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP].
A submucosa that is part of a bronchus [Automatically generated definition].
An epithelium that lines a terminal bronchiole.
bronchiolus terminalis epithelial tissue
epithelial tissue of bronchiolus terminalis
epithelial tissue of terminal bronchiole
The parenchymatous tissue of the spleen that surrounds splenic blood vessels, consists of compact masses of lymphatic cells and is where foreign material removed from the blood is used to initiate an immune reaction that results in the production of antibodies.
The white pulp contains T cells, B cells and accessory cells. The function of the white pulp is to mount an immunological response to antigens within the blood. The white pulp is present in the form of a periarteriolar lymphoid sheath. This sheath contains B cell follicles and T cells. At the edge of the T zone is a region known as the marginal zone where larger lymphocytes and antigen presenting dendritic cells are located. [Wikipedia:White_pulp]
Diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO].
todo - add part relationships to specific layers
Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO].
guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002).
A diffuse collection of lymphpoid cells that participate in airway immune responses.
Lymphoid tissue associated with airways in mice has functional similarities to human BALT[ISBN:0123813611] Notes: FMA classifies this as organized, not diffuse
Organism substance that is composed of sperm cells suspended in seminal fluid.
Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530).
The liquid component of blood, in which erythrocytes are suspended.
Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
aids the process of digestion of lipids in the small intestine
bile salts function to emulsify dietary fats and facilitate their intestinal absorption
major excretory route for potentially harmful exogenous lipophilic substances
many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
A submucosa that is part of a esophagus [Automatically generated definition].
A lamina propria that is part of a esophagus [Automatically generated definition].
A serous membrane that is part of a esophagus [Automatically generated definition].
The epithelial layer that lines the luminal space of the esophagus.
TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar
Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins.
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA].
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011
Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities.
DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001)
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Excretion in semisolid state processed by the intestine.[FMA]
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783].
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO]
Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.
A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784].
Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO]
The white fibrocartilages admit of arrangement into four groups-interarticular, connecting, circumferential, and stratiform -- WP. EDITOR NOTE: TODO add mineralized
Cartilage tissue that is flexible and contains abundant elastic fibers.
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785].
Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO]
A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP].
Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO]
relationship loss: part_of principal cavity (AAO:0000992)[AAO]
pseudostratified main olfactory epithelium
Any joint that connects a rib to another structure (or another rib). Examples: costochondral, costovertebral, interchondral, sternocostal joints.
The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO].
most sources classify this as autonomic, but in FMA it is placed directly under nervous system.
Peripheral portion of the lymph node, underneath the capsule[WP].
The medullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells.
A plexus of nerves situated at the base of the heart that innervate the heart.
The thoracodorsal artery is a branch of the subscapular artery. It travels inferiorly with the thoracodorsal nerve and supplies the latissimus dorsi. [WP,unvetted].
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Major artery which supplies blood to the lungs.[AAO]
One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]
The tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage.
provides some protection from trauma and damage.
The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule]
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]
One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]
the veins that return oxygenated blood from the lungs to the left atrium of the heart
A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO].
A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord.
A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris.
Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO]
In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve
FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2]
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
The simple columnar epithelial lining of the gall bladder.
Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip.
a male mouse has no nipples - mammary tissue regresses during embryonic development
FMA makes this part of the breast, whereas in MA it is part of the mammary gland -
Nipple being part_of mammary gland is due to a practical modelling in uberon that treats mammary gland as including adnexa. A GCI asserts that nipple is part of the breast in humans. For discussion of this, please refer to https://github.com/obophenotype/uberon/issues/1873.
An epithelium that is part of a bronchus [Automatically generated definition].
A tiny smooth muscle that connects the hair follicle with the dermis.
When contracted the arrector pili causes the raising of the hair
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]
Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]
However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]
The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full]
almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem
Predominantly gray matter midbrain structure lying dorsal to the crus cerebri and ventral to the midbrain tegmentum. It is divided into a dorsal, cellularly compact region known as the pars compacta and a more ventrally located, containing more loosely packed cells, the pars reticulata. The most lateral region of the reticulata is identified as the pars lateralis (MM).
TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA
Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA][FMA:67947].
(...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG]
nucleus pigmentosus subthalamo-peduncularis
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.336
A systemic artery that supplies the lung with with oxygenated blood.
rami bronchiales partis thoracicae aortae
Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung.
An endothelium that is part of a lymphatic vessel [Automatically generated definition].
The vascular endothelium that lines the lymph vessels.[TAO]
A large raphe nucleus extending from the anterior part of the pons through the mesencephalon; its neurons are serotoninergic[NIF]. The dorsal raphe nucleus is a part of the raphe nucleus and consists of rostral and caudal subdivisions. The rostral aspect of the dorsal raphe is further divided into interfascicular, ventral, ventrolateral and dorsal subnuclei. The projections of the dorsal raphe have been found to vary topographically, and thus the subnuclei differ in their projections. An increased number of cells in the lateral aspects of the dorsal raphe is characteristic of humans and other primates. [WP,unvetted].
TODO check dorsal vs inferior. ZF has no pons.
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].
Respiration organ that develops as an outpocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
An epithelium that is part of a bronchiole [Automatically generated definition].
The thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex.
Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted].
In humans this includes the superior and inferior phrenic arteries
The ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands.
The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted].
Artery which supplies blood via branches to the hindlimbs.[AAO]
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA].
Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]
relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]
(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]
GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form
DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3
The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart.
Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]
Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]
In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu
In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO].
The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG]
Development notes:Formation largely takes place during fetal and perinatal skin development. However, after skin wounding de novo hair follicle formation may also occur in adult mouse and rabbit skin[DOI:10.1016/j.cub.2008.12.005].
ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3
The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla.
TODO - add distinct subclasses for coat hair vs vibrissa hair
TODO - check definition of trichocyte in CL
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
Smooth and glossy outer protective cell layer of hair shaft.
A cortex that is part of a hair [Automatically generated definition].
A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]
The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]
A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve.
Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]
The chamber of the heart that receives blood from the lungs[XAO:EJS].
A cardiac ventricle that is in the right side of the heart.
The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]
In mammals continuous with the pulmonary arteries
Cardiac chamber in which blood enters the heart.
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
A cardiac ventricle that is in the left side of the heart.
Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]
DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)
A cardiac septum that divides the left and right atria of the heart.
The partition separating the right and left atria of the heart. [TFD][VHOG]
A valve at the opening of the sinus venosus into the primordial atrium[TFD,modified].
in humans and mouse this is the opening from SV into right atrium. This class represents the valve connecting the SV to any atrium and is applicable to animals with a single atrium
The part of the heart connecting the atrium to the cardiac ventricle[ZFA]. In the developing heart, the constriction between the atrium and ventricle constitutes the atrial canal, and indicates the site of the future atrioventricular valves[WP].
The canal connecting the primitive atrium and ventricle in fishes and amniotes embryo. [TFD][VHOG]
The heart is the first organ to form and function in a vertebrate. (...) Septation of the AV canal is initiated with the formation of inferior and superior endocardial cushions in response to signaling from the overlying myocardium. (...) Analysis of zebrafish mutants with cardiovascular defects uncovered a previously unexpected level of conservation between zebrafish and human cardiovascular physiology.[uncertain][VHOG]
In the embryo, the atrioventricular canal delays the impulse from atrium to ventricle[PMID:22984480]
The right side of the AVC becomes the tricuspid valve whereas the left side of the AVC will become the bicuspid valve
DOI:10.1016/j.ddmec.2004.08.004 Haramis APG, Clevers HC, Holehearted: genetic approaches to congenital cardiac valve malformations. Drug Discovery Today: Disease Mechanisms (2004)
Companion vein of the thoracodorsal artery, draining the apical part of the latissimus dorsi and merging with the circumflex scapular vein to form a subscapular vein.
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer.
The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]
In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639
A dura mater that is part of a spinal cord [Automatically generated definition].
Cardiac septum which separates the right ventricle from the left ventricle.[FMA].
The partition separating the right and left ventricles of the heart. [TFD][VHOG]
The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]
involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430
Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon.
in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery.
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
The thin membranous structure between parts of the heart, including the atria, ventricles, and outflow tract.
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]
A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts.
Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm
Upper limb, which connects the manus with the pectoral girdle.[AAO]
note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb
A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts.
Lower limb, which connects the pes with the pelvic girdle.[AAO]
note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton
The sensory system subserving the sense of vision.
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
The organ that functions to filter blood and to store red corpuscles and platelets.
An organ involved in red blood cell filtration and immune response.[AAO]
With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]
In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron
Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)
It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells
multiple sources - true spleen appear in jawed vertebrates
ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
this is a 'set of anatomical planes' in FMA
An organ that aids digestion and stores bile produced by the liver[WP].
Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]
The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]
Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988)
DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997)
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition].
A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
An ovary that is part of a right side of organism [Automatically generated definition].
An ovary that is part of a left side of organism [Automatically generated definition].
In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].
A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]
Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]
The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]
In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637
The fibrous connective tissue surrounding the thymus.
The outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes.
Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP]
Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size.
A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified].
in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP]
Lymphocytes, reticular cells and macrophages are found in the lobules
The solitary tract and nucleus are structures in the brainstem that carry and receive visceral sensation and taste from the facial (VII), glossopharyngeal (IX) and vagus (X) cranial nerves. [WP,unvetted].
Largest nucleus situated in the olivary body, part of the medulla oblongata. It is closely associated with the cerebellum, but its specific function is voluntary body movements.
The inferior olive appears to be present in all vertebrate classes and is particularly well developed in species with a well-developed cerebellum.[well established][VHOG]
complexus olivaris inferior; nuclei olivares inferiores
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.256
A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system.
In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]
The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.
superior olivary nucleus (Barr & Kiernan)
The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer.
The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695].
The circuits in the cerebellar cortex look similar across all classes of vertebrates, including fish, reptiles, birds, and mammals (e.g., Fig. 2). This has been taken as evidence that the cerebellum performs functions important to all vertebrate species. (Wikipedia)
The gray matter nuclei located in the center of the cerebellum, embedded in the white matter, which receive inhibitory (GABAergic) inputs from Purkinje cells in the cerebellar cortex and excitatory (glutamatergic) inputs from mossy fiber pathways; all output fibers of the cerebellum originate from the these nuclei[MP].
The largest and most lateral of the deep cerebellum nuclei; it receives axons of Purkinje cells in the lateral cerebellar hemisphere (neocerebellum) and receives its afferents from the premotor cortex and the supplementary motor cortex through the pontocerebellar system, and its efferents project through the superior cerebellar peduncle and is a major source of its fibers.
One or more deep cerebellar nuclei appear in agnathans, sharks, ropefishes, lungfishes, Latimeria, and amphibians. Reptiles have two nuclei (a medial and a lateral), and birds and mammals have three nuclei (a medial, a lateral, and an interposed nucleus). The medial nucleus of mammals is known as the fastigial nucleus, and the lateral nucleus is known as the dentate nucleus.[well established][VHOG]
ISBN:978-0471210054 Butler AB, Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.260-261
A cardial valve in the atrioventricular region that separates the atrium from the ventricle and prevent backflow from the ventricles into the atria during systole.
The atrioventricular valve has four distinct leaflets oriented anterior, posterior, left, and right of the atrioventricular orifice. Hu et al. 2001.[TAO]
Valve in the heart through which blood flows from the atria to the ventricles. [TFD][VHOG]
The conus arteriosus is the most distal part of the primitive fish heart and forms the connection between the ventricle and the ventral aorta. At the sinoatrial, the atrioventricular, and the ventriculoconal junctions, valves developed to prevent backflow of blood during relaxation of the preceding compartment.[uncertain][VHOG]
in ZFA this is part of both atrium and ventricle, but we use a connecting relationship here; see also notes for left and right.
An atrioventricular valve that is part of the outflow part of the right atrium.
The three-segmented valve of the heart that keeps blood in the right ventricle from flowing back into the right atrium. [TFD][VHOG]
The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG]
An atrioventricular valve that is part of the outflow part of the left atrium.
A valve of the heart, composed of two triangular flaps, that is located between the left atrium and left ventricle and regulates blood flow between these chambers. [TFD][VHOG]
Cardiac valve which has as its parts the anterior, right posterior and left posterior cusps, attached to the fibrous ring of aortic valve.[FMA].
The valve between the left ventricle of the heart and the ascending aorta, consisting of three semilunar cusps. [TFD][VHOG]
Human variation: It is normally tricuspid (with three leaflets), although in 1% of the population it is found to be congenitally bicuspid (two leaflets)
The pedunculopontine nucleus (PPN) (or pedunculopontine tegmental nucleus, PPTN) is located in the brainstem, caudal to the substantia nigra and adjacent to the superior cerebellar peduncle. It is composed by a wide variety of neurochemical cell types, including cholinergic, glutamatergic and GABAergic cells. In the classical sense, the PPN is considered to be one of the main components of the reticular activating system. [WP,unvetted].
The semilunar valve of the heart that lies between the right ventricle and the pulmonary artery.
The valve with semilunar cusps at the entrance to the pulmonary trunk from the right ventricle of the heart. [TFD][VHOG]
The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].
TODO - check ZFA/pons. also GO says part of dorsorostral pons
Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).
The most medial of the cerebellar nuclei; it receives its afferent input from Purkinje cells of the flocculonodular lobe and the vermis, and most of its efferent connections travel via the inferior cerebellar peduncle to the vestibular nuclei and to the medullary reticular formation.
A nucleus of the lateral medullary nuclear complex.
in ABA this is disjoint from MDR, but we relax this here to accomodate FMA
nucleus reticularis lateralis medullae oblongatae
A long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the optic tectum towards target cells in the premotor reticulospinal system in the hindbrain.
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA].
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210
Lung which consists of the left upper lobe and left lower lobe.[FMA].
The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters.
The respiratory conducting tubes distal to the respiratory bronchiole that lead to the alveolar sacs and the alveoli.
In human anatomy, respiratory bronchioles exists proximal to the alveolar ducts. The epithelial lining consists of smooth muscle knobs covered by nonciliated, simple cuboidal cells. The smooth muscle constricts under parasympathetic innervation and relax under sympathetic innervation
The lobar bronchus is the major airway within the respiratory tree that starts by division of the principal bronchi on both sides and ends at the point of its own subdivision into tertiary or segmental bronchi[GO].
They have relatively large lumens that are lined by respiratory epithelium. There is a smooth muscle layer below the epithelium arranged as two ribbons of muscle that spiral in opposite directions. This smooth muscle layer contains seromucous glands. Irregularly arranged plates of hyaline cartilage surround the smooth muscle. These plates give structural support to the bronchus and maintain the patency of the lumen.
The tertiary bronchi (also known as the segmental bronchi) arise from the secondary bronchi. The respiratory epithelium lining their lumen is surrounded by a layer of smooth muscle. This layer is composed of two ribbons of smooth muscle that spiral in opposite directions. The smooth muscle layer is surrounded by irregular plates of hyaline cartilage which help maintain the patency of the airway. Each of the tertiary bronchi serves a specific bronchopulmonary segment. There are 10 tertiary bronchi in the right lung, and eight in the left. The tertiary bronchi get smaller and divide into primary bronchioles. [WP,unvetted].
The upper conducting airways of the lung; these airways arise from the terminus of the trachea.
Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue
The conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching.
lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer
In FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however, there are two distinct terms for the corresponding epithelium.
In some texts/references/ontologies, bronchiole has been used as an exact synonym of 'lobular bronchiole'. However, a 'lobular bronchiole' is a segment of a bronchiole.
A bronchiole that is part of a secondary pulmonary lobule and the last conducting structure of a non-respiratory bronchiole; after this point, the airways have alveoli in their walls.
A bronchiole that is the first segment of the respiratory zone.
mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
Part of the hippocampal formation that is bounded by the entorhinal cortex and area CA1. It is characterized on the CA1 border by an abrupt widening of the pyramidal cell layer. A molecular layer is present that is continuous with that of CA1, although the stratum radiatum is no longer present. The stratum oriens is also not present. adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 468).
The pyramidal neurons in the subiculum exhibit transitions between two modes of action potential output: bursting and single spiking. The transitions between these two modes is thought to be important for routing information out of the hippocampus. It is the site responsible for ictal activity in some cases of human epilepsy. It has also been implicated in working memory and drug addiction.[Wikipedia:Subiculum]
In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region
in DHBA subicular cortex is divided into subiculum, prosubiculum and supracallosal subiculum
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers.
from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP]
Membranous process coming from capsule of lymph node[WP].
The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA].
Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO]
The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO]
It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish
While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175].
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5
The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon.
request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon'
The infundibular part of the pituitary gland consisting of two regions.[AAO]
todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19)
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
Vasculature that is part of a head [Automatically generated definition].
A vasculature that is part of a trunk [Automatically generated definition].
Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)
One of two hemispherical bulges on the base of the posterior hypothalamus (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 455).
Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA].
A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO]
Fibrous joint in which the articulating bones or cartilages of the vertebral column and the limbs as well as articulating ossicles, are connected by skeletal ligaments or membranes. Examples: Intervertebral syndesmosis, inferior tibiofibular joint.[FMA].
A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system.
We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots.
The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, https://orcid.org/0000-0002-7073-9172].
FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA].
Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA].
WP considers epiphyseal plates as subtypes of this
consider adding link to hyaline cartilage
Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA].
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA].
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
Fibrous connective tissue that surrounds cartilage.
Portion of connective tissue which surrounds cartilage.[TAO]
perichondral region of cartilage element
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses.
Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO]
Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO]
In most vertebrates, ribs surround the chest. In some species, especially snakes, ribs may provide support and protection for the entire body
They protect and support internal organs and enable lungs to expand by expanding the chest.
A proximal phalanx that is part of a finger [Automatically generated definition].
A rib that is ventrally connected to the sternum.
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO).
TODO - add superclass to unify with VNC?
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]
covers the brain dorsally in chondrichthyans
One of the bones of the upper jaw situated between and in front of the maxillae[VHOG].
requires checking embryonic vs adult; isa fetal organ part in FMA; adult bone of upper jaw in AAO and ZFA; split. Note that we have loops if we add develops_from UBERON:0005620 primary palate
Dermal bone that forms the anteriormost element of the upper jaw. It articulates with the maxilla posterodorsally and its antimere medially. The premaxilla is paired.[TAO]
One of the bones of the upper jaw situated between and in front of the maxillae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Paired, intramembranous bones located at the anterior end of the skull; they form the anterior-most segment of the maxillary arch.[AAO]
relationship loss: overlaps inter-premaxillary joint (TAO:0001950)[TAO]
relationship loss: overlaps mesethmoid-premaxillary joint (TAO:0001676)[TAO]
relationship loss: overlaps premaxillary-maxillary joint (TAO:0002260)[TAO]
(...) in all higher vertebrates a premaxilla is present (...) (reference 1); Although the presence of a tooth-bearing outer buccal arcade (premaxilla, maxilla, dentary) is cited as a common character of Osteichthyes, dipnoans lack all three bones (...) (reference 2).[well established][VHOG]
DOI:10.1017/S0022215100025585 O'Malley JF, Evolution of the nasal cavities and sinuses in relation to function. The Journal of Laryngology and Otology (1924), ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.105
The pronounced, dorsolaterally oriented ridge of grey matter in each lateral half of the spinal cord[MP]. the dorsal (more towards the back) grey matter of the spinal cord. It receives several types of sensory information from the body, including light touch, proprioception, and vibration. This information is sent from receptors of the skin, bones, and joints through sensory neurons whose cell bodies lie in the dorsal root ganglion[WP]. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input[GO].
columna grisea posterior medullae spinalis
The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO].
The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord].
columna grisea anterior medullae spinalis
The white substance of the spinal cord lying on either side between the posterior median sulcus and the dorsal root.
ZFA class is undefined. We currently do not place this as part of the DCML pathway as this would lead to taxon constraint violations.
Either of the two pairs of colliculi on the dorsal surface of the midbrain composed of white matter externally and gray matter within, the superior pair containing correlation centers for optic reflexes and the inferior pair containing correlation centers for auditory reflexes[BTO].
this section needs worked on for pan-vertebrate consistency. for now we include a mammal specific definition, even though the child terms are applicable across vertebrates
The dorsal roots contain afferent sensory axons. The dorsal roots of each side continue outwards, along the way forming a dorsal root ganglion (also called a spinal ganglion).
In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted][Wikipedia:Posterior_root_of_spinal_nerve].
The lentiform nucleus or lenticular nucleus comprises the putamen and the globus pallidus within the basal ganglia. It is a large, cone-shaped mass of gray matter just lateral to the internal capsule. [WP,unvetted].
A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO].
Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts
Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO]
Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624].
The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb
Note that in uberon 'main olfactory bulb' is a separate class, but some ontologies may treat this as partially synonymous. The distinction may only make sense in tetrapods with a vomeronasal organ (olfactory nerves terminate in OB in fishes and in main OB in tetrapods - Butler and Hodos)
the olfactory bulbs develop as bilateral evaginations from a region of the prosencephalic neural plate intercalated between the septal and the cortical anlagen (Cobos et al. 2001b, Rubenstein et al. 1998). Comparing the structure of the olfactory bulb among vertebrate species, such as the leopard frog and the lab mouse, reveals that they all share the same fundamental layout(WP).
White matter tract that contains projections from the olfactory bulb to other parts of the brain.
A nervelike, white band composed primarily of nerve fibres originating from the mitral cells and tufted cells of the olfactory bulb but also containing the scattered cells of the anterior olfactory nucleus[BTO:0003647].
The olfactory tract is a bundle of axons connecting the mitral and tufted cells of the olfactory bulb to several target regions in the brain, including piriform cortex, amygdala, and entorhinal cortex. It is a narrow white band, triangular on coronal section, the apex being directed upward. It lies in the olfactory sulcus on the inferior surface of the frontal lobe, and divides posteriorly into two striæ, a medial olfactory stria and a lateral olfactory stria.[Wikipedia].
Tract of brain which is continuous with olfactory bulb and the cerebral cortex.[FMA]
in animals with a long snout, the olfactory tract is long, whereas it is short in short-snouted animals such as primates. In some birds the tract per se does not exist as the bulb is connected directly to the cerebral hemisphere.[ISBN:0471888893]
The definition was adapted from the NIFSTD class which has been retired. It has been generalized so it is applicable to various different kinds of olfactory tracts found in different taxa.
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
hypothalamic medial zone behavioral control column
A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ).
this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.
FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure
Acellular structure composed of calcium carbonate located in the otolith organ.
Currently represented as part of the otolith membrane, but they may also be considered to be embedded in this membrane
Portion of organism substance composed of calcium carbonate located in the otolith organ.[TAO]
relationship loss: develops_from immature otolith (TAO:0000139)[TAO]
Mammals have many tiny otoconia and fish have three large otoliths[ZFIN:df]
A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere.
The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP].
The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO].
Part of the ventricular system of the brain, forming a single large cavity in the midline of the diencephalon; it is continuous with the lateral ventricles through the interventricular foramen and the fourth ventricle through the cerebral aqueduct. (Maryann Martone).
consider adding class for secondary vesicle precursor
Fluid-filled brain cavity. Kimmel et al, 1995.[TAO]
relationship loss: develops_from forebrain ventricle (TAO:0001259)[TAO]
Part of choroid plexus contained in the third ventricle.
chorioid plexus of cerebral hemisphere of third ventricle
third ventricle chorioid plexus of cerebral hemisphere
chorioid plexus of cerebral hemisphere of fourth ventricle
fourth ventricle chorioid plexus of cerebral hemisphere
Spinal cord structure that is part of the ventricular system and is filled with cerebral-spinal fluid and runs the length of the spinal cord.
previously mapped to FMA:75364. Note some ontologies (NIF, SNOMED) subdivide this into lumbar, thoracic, etc. Note we follow FMA in distinguishing between the canal and the lumen
Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree).
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
Spherical outcropping of the respiratory bronchioles and primary site of gas exchange with the blood. Alveoli are particular to mammalian lungs. Different structures are involved in gas exchange in other vertebrates[WP].
One of the layers of the neocortex. These layers are defined by distinctive populations of cells based on somata size, shape, or density, that are aligned into sheets.
The atrial part of middle layer of the heart, comprised of involuntary muscle.
An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP].
One of the three layers of the dentate gyrus of the hippocampal formation.
the basic trilaminar structure of the dentate gyrus is common across all species studied, with relatively minimal phylogenetic variation[PMC2492885]
The layers of the laminar structure of the hippocampus.
cytoarchitectural fields of hippocampal formation
Part of choroid plexus contained in the lateral ventricle.
chorioid plexus of cerebral hemisphere of lateral ventricle
lateral ventricle chorioid plexus of cerebral hemisphere
A neural nucleus that is part of the brain.
Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM).
The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates.[well established][VHOG]
In adult humans it is present only in the mesencephalon as the inferior and the superior colliculi
DOI:10.1371/journal.pone.0003582 Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS ONE (2008)
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.
Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929].
Multi-tissue structure comprised largely of myelinated axons.[TAO]
The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]
nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex
DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)
The regions of the spinal cord that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.
The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries.
WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here.
A thin membrane which helps to support the capillary loops in a renal glomerulus. It is connective tissue composed of mesangial cells - myofibroblasts phenotypically related to vascular smooth muscle cells (muscle, smooth, vascular), phagocytes and the mesangial extracellular matrix.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct
Any muscle organ that is part of a back [Automatically generated definition].
The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes..
A lamina propria that is part of a urethra [Automatically generated definition].
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
The connecting cord from the developing embryo to the placenta.
The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP].
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]
As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]
The duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue.
FMA also has 'main submandibular duct' (FMA:59899)
The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO].
not part of a nephron or distal tubule in MA and FMA
White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres. It is subdivided into a genu, a rostrum, a body, and a splenium. (MM).
The largest commissure of the brain connecting the cerebral hemispheres. [TFD][VHOG]
In addition to the anterior commissure, placental mammals have a phylogenetically new forebrain commissure, the corpus callosum, which primarily interconnects the neocortex of the cerebral hemispheres.[well established][VHOG]
The corpus callosum is found only in placental mammals. other groups do have other brain structures that allow for communication between the two hemispheres, such as the anterior commissure, which serves as the primary mode of interhemispheric communication in marsupials.
DOI:10.1111/j.1749-6632.1969.tb20447.x Ebner FF, A comparison of primitive forebrain organization in metatherian and eutherian mammals. Annals of the New York Academy of Sciences (1969)
The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle.
A lamina propria that is part of a bronchus [Automatically generated definition].
lamina propria mucosa of bronchial trunk
lamina propria mucosae of bronchial trunk
The tissue made up of epithelial cells that lines the inside of the lobar bronchus.
An epithelium that is part of a segmental bronchus [Automatically generated definition].
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest
distinction between abdomen muscle and abdomen musculature
The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
we prefer neuroectoderm to neural ectoderm since placodal ectoderm is not classified here
epithelium tubi neuralis; neuroectoderma
A thoracic vertebra endochondral element that is composed primarily of a bone tissue.
Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs
A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]
The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]
EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
The middle layer of the heart, comprised mainly of striated cardiac muscle fibers.
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The middle layer of the heart, consisting of cardiac muscle.[AAO]
EDITOR_NOTE TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO].
EHDAA2 divides the system from the tissue
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)
The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA].
WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node.
An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles.
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]
A part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers[GO].
The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
Serous membrane which is divided into parietal and visceral serous pericardium.
A serous membrane that lines the peritoneal cavity[VHOG,modified].
An epithelium that lines the peritoneal cavity.[TAO]
Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA].
most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]
Membrane organ that surrounds the brain and the spinal cord.
Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG]
Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx).
Not consider part of the CNS/neuraxis in FMA
The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals.
consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system
delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater].
A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space.
Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections.
the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater].
capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288
some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261]
A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted].
The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG]
The tympanic membrane (TM) has three layers, two epithelia provided by the external acoustic meatus (EAM) and the MEC, derived respectively from the first pharyngeal cleft and pouch, and a mesenchymally derived fibrous stratum
most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint.
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas.
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.
check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland.
Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO]
A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG]
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558
The soft tissue that fills the cavities of bones.
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
consider placement of NCIT:C53466 medullary bone
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
A bone that is part of the metacarpal skeleton.
Any skeletal muscle that is part of the head region.
defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
Any muscle that is part of the cervical (neck) region.
Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.
A large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted].
The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG]
external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12
posterior border of the lateral third of the clavicle acromion process and spine of scapula
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants.
The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG]
Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
middle limb segment of proximal segment of free upper limb
zeugopod of proximal segment of free upper limb
Distal portion of the hind limb, including tarsal region, metatarsal region and digits.
manual digit (phalangeal portion) plus soft tissue
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine.
A duct that carries bile from the liver to the intestine.
Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG]
we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA
The triangular flat bone of the nasal septum.
Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO]
Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO]
relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO]
relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO]
In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP]
The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO]
The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods.
Dermal bone that forms part of the upper jaw, located antero-ventral to the premaxilla. The maxilla is a paired bone.[TAO]
Paired, intramembranous bone located on the lateral sides of the skull, posterior to the premaxillae.[AAO]
relationship loss: overlaps autopalatine-maxillary joint (TAO:0001942)[TAO]
In some teleosts, the maxilla is located postero-ventral to the supramaxilla. Commonly, the articular process of the maxilla articulates with the autopalatine and ethmoidal region antero-medially. The maxilla is usually the largest bone in the upper jaw assemblage.[TAO]
Distal segment of the fore limb, including carpal region, metacarpal region and digits.
like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton
The outer serous membrane of the pulmonary pleural.
the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax
The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs.
Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura].
The fluid-filled cavity that lies between the visceral and parietal pleurae.
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning
the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)
A double-walled sac containing the heart and the roots of the great vessels.
The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.
Peritoneum that surrounds the heart.[AAO]
In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity
this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)
we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium
Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac.
Transudate contained in the pericardial cavity.[FMA].
The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].
Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]
FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib
autonomic division of peripheral nervous system
autonomic part of peripheral nervous system
divisio autonomica systematis nervosi peripherici
pars autonomica systematis nervosi peripherici
The small, erectile body located at the anterior end of the vulva.
The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
Consider changing name to make distinction from inferred superclass 'vertebral element' clear
we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones
Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO]
Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO]
A vertebra that is located in the cervical region of the vertebral column.
In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery.
An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail.
Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)
A gland that is part of a skin of body [Automatically generated definition].
check FMA, use plural for now as general class not there
An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified].
it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment].
The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum
BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says 'hippocampus' it means 'hippocampal formation'. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures.
Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO]
The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592].
The part of the digestive system that contains the liver and the biliary system.
System responsible for the production and movement of bile[ZFIN:curator].
The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues.
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA].
Any muscle organ that is part of a chest [Automatically generated definition].
anterolateral part of thorax muscle organ
muscle organ of anterior thoracic region
muscle organ of anterolateral part of thorax
A zone of skin that is part of an arm [Automatically generated definition].
A bone that is part of a limb [Automatically generated definition].
the formal definition is very inclusive, and includes sesamoids
NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle
Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted].
A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO].
FMA divides 'striatum of neuraxis' into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see Wikipedia:Striatum#History. Check caudoputamen
White matter that is part of a cerebral hemisphere.
sometimes the term 'cerebral white matter' may be used generically but here is refers specifically to the white matter in a hemisphere
The BTO class is inconsistent as it is part of the brain and spinal cord.
white matter structure of cerebral hemisphere
A blood vessel that is part of a choroid [Automatically generated definition].
cannot find singular in FMA, using Set class
A region of the lens consisting of packed elongated enucleate cells packed with crystallin.
Fibres resembling a ribbon and arranged in very thin plates in the lens. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
(...) the line, or Y, or star sutures common to mammalian lenses, including those of primates. In the case of line or Y sutures, the overlapping of lens fibers in each successive shell is coincident and results in the formation of four or six three-dimensional suture planes that extend from the lens nucleus to the periphery.[well established][VHOG]
DOI:10.1167/iovs.03-0466 Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004)
A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad].
The patella, also known as the knee cap or kneepan, is the largest sesamoid bone in the human body. The primary functional role of the patella is knee extension. The patella has convergently evolved in placental mammals and birds; marsupials have only rudimentary, non-ossified patellae. In more primitive tetrapods, including living amphibians and reptiles, the muscle tendons from the upper leg are attached directly to the tibia, and the patella is not present. See also: fabella.
Any of the mushroom-shaped papillae, which have a single taste bud at the tip, located mostly on the dorsal anterior portion of the tongue.
The fungiform papillae are mushroom shaped e (projections) on the tongue. They are located on the top (dorsal) surface of the tongue, scattered throughout the filiform papilla but mainly at the tip and lateral margins of the tongue. They have taste buds on their superior (upper) surface which can distinguish the five tastes: sweet, sour, bitter, salty, and umami. They have a core of connective tissue. They are innervated by the seventh cranial nerve, more specifically via the submandibular ganglion, chorda tympani, and geniculate ganglion ascending to the solitary nucleus (the sensory component of the Vagus nerve in the brainstem). [WP,unvetted][Wikipedia:Fungiform_papilla].
In the mouse, Fungiform and palatal taste buds are innervated by the geniculate ganglion cells of the facial nerve[DOI:10.1523/JNEUROSCI.5142-05.2006]
The maternal uterine-derived portion of the placenta.
formed under the influence of progesterone and forms highly-characteristic cells. [Wikipedia:Decidua]
The mucous secreting gland associated with the mucuous membrane lining the uterus.
An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted].
The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries.
Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061].
Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612
A tributary of the iliac vein that drains the urinary bladder.
The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]
The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013]
The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013]
We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.
Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine.
A mucosa that is part of a esophagus [Automatically generated definition].
Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot.
Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus).
There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators]
The proximal free limb segment. Includes as parts the stylopod skeleton.
A commissure that connects the two cerebral hemispheres. Examples: anterior commissure, corpus callosum.
The bone that is situated in the orbit on either side of the presphenoid; it generally forms a part of the sphenoid in the adult, and may be independent in the young.
Endochondral ossification of the lateral sides of the braincase.[AAO]
Large median unpaired cartilage bone consisting of two diverging plates. Positioned medial to the eye. The orbitosphenoid develops from the Trabeculae communis and forms the anterior and anterolateral boundary of the orbital foramen and constitutes a significant part of the sidewalls and floor of the cranial cavity. Bordered by the lateral ethmoid anteriorly, and the pterosphenoid posteriorly, The orbitosphenoid may extend ventrally to meet the parasphenoid. In the adult, the orbitosphenoid is fused ventrally to the parasphenoid via a thin sheet of bone.[TAO]
relationship loss: develops_from taenia marginalis anterior (TAO:0001505)[TAO]
relationship loss: overlaps orbitosphenoid-lateral ethmoid joint (TAO:0001941)[TAO]
relationship loss: overlaps orbitosphenoid-prootic joint (TAO:0001794)[TAO]
relationship loss: overlaps pterosphenoid-orbitosphenoid joint (TAO:0001831)[TAO]
relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]
relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
Bone tissue that has a regular parallel alignment of collagen into sheets (lamellae) and is mechanically strong.
histological classification, lamellar vs woven. Note that only FMA has woven
Bone tissue that has a lattice-like or spongy structure; it is highly vascular and contains intercommunicating spaces filled with bone marrow.
one of the two types of osseous tissue that form bones. Compared to compact bone, which is the other type of osseous tissue, it has a higher surface area but is less dense, softer, weaker, and less stiff. It typically occurs at the ends of long bones, proximal to joints and within the interior of vertebrae. Cancellous bone is highly vascular and frequently contains red bone marrow where hematopoiesis, which is the production of blood cells, occurs. The primary anatomical and functional unit of cancellous bone is the trabecula.
The minute canals that pass the prostatic secretions to the urethra.
The dense, fibrous connective tissue joint between the tetrapod parietal bones and the frontal bone.
A suture that connects the two frontal bones of the skull.
in humans, the frontal suture is a dense connective tissue structure that divides the two halves of the frontal bone of the skull in infants and children. It usually disappears by the age of six, with the two halves of the frontal bone being fused together. If it does not disappear it may be called a 'metopic suture' or 'sutura frontalis persistens. ' If the suture is not present at birth (craniosynostosis) it will cause a keel-shaped deformity of the skull called 'trigonocephaly. ' It is present in a fetal skull so that the skull can bend and is very elastic at the time of birth. The baby's head literally bends when coming out of the mother's womb. The space is filled as the child grows older. [WP,unvetted]
The dense, fibrous connective tissue joint between the parietal bones and the occipital bone.
The dense, fibrous connective tissue joint between the tetrapod parietal bones.
A long bone is a bone that has a shaft and 2 ends and is longer than it is wide. Long bones have a thick outside layer of compact bone and an inner medullary cavity containing bone marrow. The ends of a long bone contain spongy bone and an epiphyseal plate or line depending on the stage of development. The epiphyseal plate is a hyaline cartilage, where new bone growth takes place, lengthening the bone prior to adulthood. Bone lengthening ceases when this cartilage is lost, leaving a remnant referred to as an epiphyseal line.
Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251]
Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa.
Anterior rounded projection of the pars acromialis of the scapula.[AAO]
relationship loss: part_of pars acromialis (AAO:0000752)[AAO]
A rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches.
In basal Tetrapodomorph lineages often the deltoid process and the pectoral processes are separate and thus should not be made exact synonyms to the deltopectoral crest.[PHENOSCAPE:ad]
An epithelium that is part of a iris [Automatically generated definition].
A lymph node that is part of an abdomen [Automatically generated definition].
The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group.
The supporting bundles of muscular fibers lining the walls of the ventricles of the heart.
The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented
Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea.
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof.
The skull base is formed from a series of cartilages either side of, and rostral to, the notochord, whose tip lies just caudal to the pituitary gland. It is closely associated with the sensory capsules, which partially or completely sur- round the olfactory epithelium, the eye, and the inner ear[PMID:11523816]
The crystalline particles composed of calcium carbonate and a protein which adhere to the gelatinous membrane of the maculae of the utricle and saccule (otolithic membrane).
Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia
In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith (reference 1); (...)considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals (reference 2).[well established][VHOG]
PMID:11581521 Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001), DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)
The layer of the statoconial membrane that is composed of otoliths.
Connective tissue composed of elastic fibers.
The middle layer of an artery or vein. [WP,unvetted].
May be composed of smooth muscle and elastic tissue
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
A lymph node that is part of a pancreas [Automatically generated definition].
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition
FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
An organ that functions as a secretory or excretory organ.
An outgrowth on the lateral trunk of the embryo that develops into a paired fin. The fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Embryonic surface structure that develops into a paired fin.[ZFA]
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)
The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node.
See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest
Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG]
Fin that is one of a pair located ventrally on the organism.
Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt].
A gonad with both testicular and ovarian aspects[WP].
The cells of the hatching gland contain enzymes responsible for solubilization of the egg chorion, facilitating the hatching process[GO]. A transversely oriented set of cells located deep to the EVL on the pericardial membrane, especially prominent during pharyngula period because of the brightly refractile cytoplasmic granules (containing hatching enzymes) of the principal cells of the gland.
A transversely oriented set of cells located deep to the EVL on the pericardial membrane, especially prominent during pharyngula period because of the brightly refractile cytoplasmic granules (containing hatching enzymes) of the principal cells of the gland. Kimmel et al, 1995.[TAO]
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
A line of sensory organs and associated structures along the sides of fish and amphibia that detect vibrations and pressure changes.
we model this as being potentially inclusive of lateral line scales, and thus overlapping with the skeletal system. This is to accomodate TAO
A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]
Sensory system which develops from a specialized series of dorsolateral ectodermal placodes named lateral line placodes.[AAO]
relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO]
The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians.[well established][VHOG]
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.195
The thickend rim of the blastoderm evident during late blastula and gastrula stages[FishBase]. Embryonic structure which is a uniform thickened annulus at the blastoderm margin, consisting of two layers in addition to the EVL, the epiblast and the hypoblast. The germ ring is formed by the involution of the blastoderm back upon itself[ZFA].
TODO - check timing of appearance and disappearance - check relationship with primitive streak. he blastopore lips in amphibians appear to have the equivalent function of the germ ring in zebrafish (ES)
Embryonic structure that forms as a thickened annulus at the blastoderm rim. The germ ring is thickened because it is the involuting margin of the blastoderm[ZFIN:ZDB-PUB-961014-576].
A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion
Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
digit (phalangeal portion) plus soft tissue
DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008)
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass
A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
TODO discriminate between stages and organisms
Whole organism that is premetamorphic or a very immature individual.[TAO]
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
The reticular formation is a series of brain nuclei located in the medulla oblongata.
ZFA:0000421 is part of the the medulla oblongata, so it is placed here, rather than with the generic term
reticular formation of medulla oblongata
reticular formation of medulla oblonmgata
The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube.
cavity of ventricular system of neuraxis
A commissure that is part of a superior colliculus [Automatically generated definition].
anterior corpus quadrigeminum commissure
commissure of anterior corpus quadrigeminum
The principal sensory nucleus (or chief sensory nucleus of V) is a group of second order neurons which have cell bodies in the dorsal Pons. It receives information about discriminative sensation and light touch of the face as well as conscious proprioception of the jaw via first order neurons of CN V. Most of the sensory information crosses the midline and travels to the contralateral ventral posteriomedial (VPM) of the thalamus via the Ventral Trigeminothalamic Tract, but information of the oral cavity travels to the ipsilateral Ventral Posteriomedial (VPM) of the thalamus via the Dorsal Trigeminothalamic Tract. [WP,unvetted].
principal sensory nucleus of trigeminal nerve
trigeminal nerve superior sensory nucleus
nucleus sensibilis superior nervi trigemini
nucleus sensorius principalis nervi trigemini
nucleus sensorius superior nervi trigemini
principal sensory nucleus of the trigeminal
principal sensory nucleus of the trigeminal nerve
GO has pontine nucleus as a child of trigeminal sensory nucleus, WP says this is a synonym, but we have a separate class for this - UBERON:0002151
Part of cerebral hemisphere located on the medial surface, forming a ring around the brain stem.
The small wedge shaped nucleus interposed between the dentate and fastigial nuclei; it receives axons from Purkinje cells of the intermediate area of the cerebral hemispheres and most of its efferent connections travel via the superior cerebellar peduncle.
lateral interpositus (emboliform) nucleus
The cochlear nuclei consist of: (a) the dorsal cochlear nucleus, corresponding to the tuberculum acusticum on the dorso-lateral surface of the inferior peduncle; and (b) the ventral or accessory cochlear nucleus, placed between the two divisions of the nerve, on the ventral aspect of the inferior peduncle. [WP,unvetted].
WP says 'The CN is located at the dorso-lateral side of the brainstem, spanning the junction of the pons and medulla.'. MA places this in pons, other sources the medulla
The two or three small masses of gray matter that is located medial to the emboliform nucleus and lateral to the fastigial nucleus; it receives axons from the intermediate area of the cerebellar hemispheres and its afferents exit through the superior cerebellar peduncle.
One of two nuclei comprising the interpositus cerebellar nuclear complex of the deep cerebellar nuclei.
The globose nucleus is one of the deep cerebellar nuclei. It is located medial to the emboliform nucleus and lateral to the fastigial nucleus. This nucleus contains primarily large and small multipolar neurons. The globose nucleus and emboliform nucleus are occasionally referred to collectively as the interposed nucleus. [WP,unvetted][Wikipedia:Globose_nucleus].
It is recognized in human cerebellum but is not distinguishable in all mammalian species
it is recognized in human cerebellum but is not distinguishable in all mammalian species[MP]
nucleus interpositus posterior cerebelli
inferior decussation (Forel's decussation)
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
Synonym for macrodissected adult human tegmentum (Vicq d'Azyr, 1784; Swanson, 2000); pp. 555-556. Later used thus by for example His (1893b, p. 178), Herrick (1915, p. 160), Strong & Elwyn (1943, p. 17), Carpenter (1976, p. 367), Williams & Warwick (1980, p. 935).
Neuronames includes the substantia nigra, crus cerebri and midbrain tegmentum as substructures of the cerebral peduncle; the mouse atlases only include the crus cerebri as the cerebral peduncle (MM)
Nucleus located in the pontine tegmentum containing cells that give rise to motor innervation of the jaw through the trigeminal nerve. It receives both crossed and uncrossed fibers from the cerebral cortex (Heimer, L. The Human Brain and Spinal Cord, 2nd ed., 1996, pg 248).
this in ZFA this is part of the medulla; pons is a dubious structure for zebrafish
Part of the reticular formation located in the midbrain tegmentum.
formatio reticularis tegmenti mesencephali
Part of cuneate fasciculus found in the medulla.
TODO - change definition to be the *whole* of the CF in the MO. isa parentage to fasciculus of brain should be inferred
nucleus pulvinaris oromedialis (Hassler)
Part of gracile fasiculus located in the medulla.
fasciculus dorsolateralis gracilis (Golli)
Initial segment of the occulomotor nerve as it leaves the midbrain.
todo - determine pattern for central part of nerve vs fibers vs root
Nuclear complex containing the vestibular nuclei.
In TA they are grouped in both the pons and medulla; DHBA has 'vestibular nuclei of pons', with LVN and SVN underneath; WP+MA says the SVN is in the pons, and GO includes VNC development under pons development, but this is not supported by ABA. Todo - check with NIF.
nuclei vestibulares in medulla oblongata
Nucleus located beneath the floor of the 4th ventricle in the pontine tegmentum, containing motor neurons innervating the lateral rectus muscle of the eye (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 533).
Hindbrain motor nucleus which is the origin of motor axons of cranial nerve VI. From Neuroanatomy of the Zebrafish Brain.[TAO]
part of medulla oblongata in ABA and ZFA; part of pons in MA and pontine tegmentum in NIF; note that pons/medulla are spatially disjoint in ABA.
Unpaired midbrain region situated in the ventromedial portion of the reticular formation. The VTA is medial to the substantia nigra and ventral to the red nucleus, and extends caudally from the posterior hypothalamus in the diencephalon. The VTA contains dopamine neurons that project to various limbic and cortical areas and is a critical component of the brain's reward circuitry.
Region of the mesencephalon that arises from a small area of the neural plate, spanning the midline immediately adjacent, and being slightly posterior to the dorsal tegmentum area[XAO:0004226, PMID:2351962].
The metathalamus is a composite structure of the thalamus, consisting of the medial geniculate nucleus and the lateral geniculate nucleus. [WP,unvetted].
we follow FMA in making this a subtype of nucleus, but in fact it is a group containing two nuclei
geniculate thalamic nuclear group (metathalamus)
The corticospinal fibers that arise from the pyramidal cells within the cerebral cortex layer V of the precentral motor area, the premotor area and the postcentral gyrus, then descend into and through the medulla to form the lateral corticospinal tract and the anterior corticospinal tract.
In NIFSTD this is a tract of brain but this leads to issues due to its overlap with the spinal cord
White matter tract arising in red nucleus and projecting to spinal cord ventral horn.
Nucleus in the midbrain at the level of the inferior colliculus near the midline, containing the motor neurons giving rise to the trochlear nerve, innervating the contralateral superior oblique extraocular muscle of the eye (Brodal, Neurological Anatomy, 3rd ed, 1981, pg. 533).
A spinal cord segment that adjacent_to a cervical region.
segmenta cervicalia medullae spinalis [1-8
Either of the two roots that come of the vestibulocochlear nerve.
A region of the brain consisting of ventral and rostral subcortical regions of the telencephalon, including among others, the basal ganglia, septal nuclei, amygdala, ventral pallidum, substantia innominata, and basal nucleus of Meynert.
A regional part of brain that is part of a cerebellar cortex [Automatically generated definition].
A long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the vestibular nucleus of the pons towards target cells in the spinal cord[GO].
Component of the temporal lobe, lateral aspect. The rostral boundary is the rostral extent of the ssuperior temporal sulcus. The caudal boundary is the cauday portion of the superior temporal gyrus (posterior to becoming continuous with the supramarginal gyrus). The medial boundary is the lateral fissure (and when present the supramarginal gyrus), and the lateral boundary is the superior temporal suclus (Christine Fennema-Notestine).
The part of the hypothalamus posterior to the middle region consisting of several nuclei including the medial mamillary nucleus, lateral mamillary nucleus, and posterior hypothalamic nucleus (posterior hypothalamic area). The posterior hypothalamic area is concerned with control of sympathetic responses and is sensitive to conditions of decreasing temperature and controls the mechanisms for the conservation and increased production of heat.
Nuclei in the ventral part of the thalamus, involved in modulating activity of dorsal thalamic nuclei.
The ventral nuclear group is a collection of nuclei on the ventral side of the thalamus. According to MeSH, it consists of the following: ventral anterior nucleus ventral lateral nucleus ventral posterior nucleus [WP,unvetted][Wikipedia:Ventral_nuclear_group].
consider splitting nucleus from nuclear group (FMA has 'nucleus of subthalamus') - but note this is also treated as a nucleus (singular) in FMA. ZFA:0005576 represents an individual nucleus within the group
Nerve fibers arising from motor neurons in the abducens nucleus that are contained within the pontine tegmentum.
The crossing of the two trochlear nerves at their exit through the velum medullare anterius.
decussatio fibrarum nervorum trochlearium
Parietal lobe of the left hemisphere of the brain.
Parietal lobe of the right hemisphere of the brain.
A limbic lobe that is part of a left cerebral hemisphere.
A limbic lobe that is part of a right cerebral hemisphere.
A temporal lobe that is part of a left cerebral hemisphere.
A temporal lobe that is part of a right cerebral hemisphere.
A frontal cortex that is part of a right cerebral hemisphere.
A frontal cortex that is part of a left cerebral hemisphere.
A cerebral hemisphere that is in the left side of a brain.
A cerebral hemisphere that is in the right side of a brain.
The ganglion of the vestibular nerve. It contains the cell bodies of the bipolar primary afferent neurons whose peripheral processes form synaptic contact with hair cells of the vestibular sensory end organs[WP,unvetted]. Distributed to the maculae of the utricle and saccule and to the ampullary crests of the semicircular ducts. The vestibular fibers arise in bipolar cells in the vestibular ganglion in the internal acoustic meatus.
vestibular part of vestibulocochlear ganglion
vestibulocochlear VIII ganglion vestibular component
nucleus nervi oculomotorii, pars medialis
vestibulocochlear ganglion vestibular component
The group of neuron cell bodies associated with the eighth cranial nerve during embryogenesis; splits in later development to form the cochlear and vestibular ganglia.
The sensory ganglion of the ear. (See Anatomical Atlas entry for statoacoustic ganglion by T. Whitfield.)[TAO]
(During the development of the inner ear in a vertebrate embryo) As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII.[well established][VHOG]
The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms 'cochlear nerve fiber' and 'spiral ganglion cell' are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus
nucleus nervi oculomotorii ventrolateralis
nucleus nervi oculomotorii, pars ventralis
PMID:21452441 Park BY, Saint-Jeannet JP, Induction and Segregation of the Vertebrate Cranial Placodes. Developmental Biology (2010)
The ventral cochlear nucleus (or anterior, or accessory), placed between the two divisions of the cochlear nerve, is on the ventral aspect of the inferior peduncle. Composed of several regions of distinct cell types, this nucleus serves primarily as a relay station for ascending auditory information. Bushy cells in the anterior ventral cochlear nucleus (AVCN), which receive end bulbs of held from auditory nerve fibers, project to the superior olivary complex through the trapezoid body and intermediate acoustic stria. Other cell types project to the lateral lemniscus and the inferior colliculus directly. [WP,unvetted].
The dorsal cochlear nucleus (DCN, also known as the 'tuberculum acousticum'), is a cortex-like structure on the dorso-lateral surface of the brainstem. Along with the ventral cochlear nucleus, it forms the cochlear nucleus, where all auditory nerve fibers from the cochlea form their first synapses. [WP,unvetted].
A dorsal root ganglion that is part of a thorax [Automatically generated definition].
A cranial nerve nucleus for the vagus nerve in the medulla that lies under the floor of the fourth ventricle. It mostly serves parasympathetic vagal functions in the gastrointestinal tract, lungs, and other thoracic and abdominal vagal innervations. The cell bodies for the preganglionic parasympathetic vagal neurons that innervate the heart reside in the nucleus ambiguus.[WP,unvetted].
The FMA includes a separate sensoryt nucleus
dorsal motor nucleus of the vagus (vagal nucleus)
Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453).
In the brain, the inferior salivatory nucleus is a cluster of neurons controlling the parasympathetic input to the parotid gland. It is one of the components of the glossopharyngeal nerve. [WP,unvetted].
nucleus salivatorius inferior nervi glossopharyngei
nucleus of the lateral olfactory tract (ganser)
nucleus of tractus olfactorius lateralis
part of amygdala in FMA but this leads to inconsistency when combined with ABA partitions
Aggregate brain region defined as those areas of cerebral cortex receiving direct synaptic input from the olfactory bulb (Price, 1973). It usually includes the piriform cortex and sometimes other areas.
consider relationship: receives_input_from UBERON:0002264 olfactory bulb
That portion of the cerebral cortex that, with the palaeocortex, develops in association with the olfactory system, and which is phylogenetically older than the neocortex and lacks its layered structure. The embryonic archaeocortex corresponds to the cortex of the dentate gyrus and hippocampus in mature mammals[BTO:0001446].
The olfactory cortex is involved in the perception of smell. It receives input from the olfactory bulb and is responsible for the identification of odors[GO][GO:0021989].
(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]
DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)
The central sulcus is a fold in the cerebral cortex of brains in vertebrates. Also called the central fissure, it was originally called the fissure of Rolando or the Rolandic fissure, after Luigi Rolando. The central sulcus is a prominent landmark of the brain, separating the parietal lobe from the frontal lobe and the primary motor cortex from the primary somatosensory cortex. [WP,unvetted].
The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted].
A nucleus of brain that is part of a trigeminal nuclear complex.
massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA.
nucleus tractus mesencephali nervi trigeminalis
A sensory epithelium that is part of a gustatory system.
A cellular layer of the dentate gyrus enclosed by the granule cell layer. A number of cell types are located in the polymorphic layer but the most prominent is the mossy cell.
Part of spinothalamic tract that is in the medulla.
A long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the superior colliculus of the midbrain towards target cells in the ventral spinal cord[GO].
NIF and FMA differ in placement (spinal cord vs medulla)
The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer.
One of the convolutions on the medial surface of the cerebral hemisphere. It surrounds the rostral part of the brain and interhemispheric commissure and forms part of the limbic system. (MSH) One of three essential structures comprising the limbic lobe, the other two being the hippocampus and parahippocampal gyrus. (CSP).
Component of the temporal lobe on the mesial surface, posterior to the entorhinal cortex. The rostral and caudal boundaries are the posterior end of the netorhinal cortex and the caudal portion of the hippocampus, respectively. The medial boudnary is designated as the medial aspect off the temporal lobe and the lateral boundary is the collateral sulcus (Christine Fennema-Notestine).
The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells.
revisit logical definition after using brain layer patterns
Compare with ZFA:0000636 - cerebellar crest, which is also composed of parallel fibers but located in a more restricted nucleus within the cerebellum
The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells.
Purkinje cell layer of cerebellar cortex
Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133).
involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]
A commissure that is part of a inferior colliculus [Automatically generated definition].
commissure of posterior corpus quadrigeminum
posterior corpus quadrigeminum commissure
A wall, dividing a cavity or structure into smaller ones[WP].
The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted].
segmenta thoracica medullae spinalis [1-12]
The horseshoe-shaped tract that connects the two olfactory bulbs.
A nerve fiber that is part of a trigeminal nerve.
The major forebrain commissure that connects the two temporal lobes of the cortex.
A type of cuticle composed of highly cross-linked collagens and specialised insoluble proteins known as cuticlins, together with glycoproteins and lipids[WP].
currently restricted to nematodes, but this may be too strict
A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity.
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]
Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic
An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP].
Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG]
The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG]
MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
Proliferative region that is part of the ventricular system.
Proliferative zone in the region of the neural tube adjacent to the lumen.
There are two primary regions that are thought to give rise to neurons that make up the cerebellum. The first region is the ventricular zone (the roof of the fourth ventricle). This area produces Purkinje cells and deep cerebellar nuclear neurons[BTO:0003654].
in BTO this is restricted to the 4th ventricle - however this class also represents the early ventricular zone as well as its post-natal remnants. The MA class is named 'ventricular zone of brain' and is presumably restricted to the post-natal zone; DHBA class is forebrain; PBA class is neocortex; TAO/ZFA is neocortex
A single row of glia at the dorsal midline of the developing neural tube along the entire anterior-posterior axis. This region provides inductive signals for the specification of neuronal cell types and of the specification of neural crest cells. The cells comprising the roof plate are the precursors to radial glial cells.
TODO - Note that although this is classically defined as being located on the neural tube, in many AOs the roof plate continues post-embryonically after the neural tube has ceased to exist. Consider 'roof plate of neural tube'. TODO - alar plate vs roof plate
Multi-tissue structure that is the dorsal-most aspect of the devleloping neural tube.[TAO]
The outermost layer (or layers, depending on the species) of embryonic skin, essential for the development of the epidermis and establishment of the barrier functions. The periderm derives from the outer layer of the ectoderm.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In humans, the periderm is a monolayer and is shed prenatally.
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In mice, the periderm is bilayered. It consists of the outer layer, which possesses numerous microvilli, and the inner layer that develops specific periderm granules. Both layers can be well recognized as early as at E14.5 and they are shed at different time points: the outer layer is shed in utero, in conjunction with barrier acquisition (E16-18), while the inner layer is retained postnatally.
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
The hypochord is a transient rod-like structure in the embryos of fish, lampreys and amphibians that is located immediately ventral to the notochord. The hypochord may play a role in positioning the dorsal aorta[GO].
A transient rod-like structure which is endodermally derived and located immediately ventral to the notochord. The hypochord is thought to play a role in positioning the dorsal aorta. Eriksson and Lofberg, 2000.[TAO]
Unsegmented ventral structure in the caudal region of anuran larvae; near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle.[AAO]
In other words, we identified variations in gene expression patterns that may contribute to a molecular basis of evolutionary variation of axial structures between Teleostei and Mammalia in the determination of body axis. As already mentioned, one such difference is illustrated by the hypochord present in lower vertebrates but absent in higher animals. Perhaps, Tbx-b and Tbx-c are involved in the mechanisms underlying the formation of this organ that were lost during later evolution leading to the disappearance of the hypochord itself, similarly to other organs, such as the lateral line.[uncertain][VHOG]
Unlike in frogs and axolotl, the hypochord does not appear to be endodermally derived[ZFA]. near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle[AAO]
PMID:11548409 Korzh VP, T-box genes and developmental decisions that cells make. Russian Journal of Developmental Biology (2001)
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)
In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].
Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]
The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]
The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)
Organizer for gastrulation in vertebrates. The primitive knot starts as a regional knot of cells that forms on the blastodisc immediately anterior to where the outer layer of cells will begin to migrate inwards - an area known as the primitive streak. Posterior to the node is the primitive pit, where the cells of the epiblast (the upper layer of embryonic cells) initially begin to invaginate. This invagination expands posteriorly into the primitive groove as the cells layers continue to move into the space between the embryonic cells and the yolk. This differentiates the embryo into the germ layers - endoderm, mesoderm, and ectoderm. The primitive knot migrates posteriorly as gastrulation proceeds, eventually being absorbed into the tail bud.[WP]. the regional thickening of cells at the rostral tip of the vertebrate primitive streak through which gastrulating cells migrate anteriorally to form tissues in the future head and neck; this region organizes the formation of the three embryonic layers and establishes the longitudinal axis and the polarity of the embryo[MP].
This class groups together possibly disparate structures, following homology class in vHOG; early development terms need review
A signaling center that directs the development of the whole embryo or of part of the embryo.[AAO]
Embryonic structure that is a local accumulation of cells along the germ ring. The shield marks the dorsal side of the embryo[ZFIN:ZDB-PUB-961014-576].
The organizer is a central feature of vertebrate embryogenesis. It was first characterized in functional terms in amphibians by Spemann and Mangold (1924), and homologous tissues have since been identified in representatives of most other vertebrate classes, including mammals (the node), birds (Henson's node) and teleost fish (the embryonic shield).[well established][VHOG]
DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue.
TODO - check; developmental relationship to anterior hypoblast in ZFA?
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]
all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm').
Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43
The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements.
The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
Lateral neurogenic placodes positioned dorsal of the epibranchial placodes.
In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK].
Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991).
A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion.
The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]
The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]
The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA].
Consider adding subclasses for male and female specific variants
TODO - mesonephric portion of the nephric duct
Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]
In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts.
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA].
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO].
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia.
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]
Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively
in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)
The specialized glial structure (non-neuronal cells) situated at the ventral midline of the embryonic neural tube; this structure spans the anteroposterior axis from the midbrain to the tail regions, separating the left and right basal plates of the developing neural tube, and serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube.
Organizing center consisting of a small group of cells located at the ventral midline of the neural tube that influences the development of the nervous system, governing the specification of neuronal cell types and directing axonal trajectories.[AAO]
although this is classically defined as being located on the neural tube, in many AOs the floor plate continues post-embryonically after the neural tube has ceased to exist. Consider 'floor plate of neural tube'.
"A structure integral to the developing nervous system of vertebrate organisms. Located on the ventral midline of the embryonic neural tube, the floor plate is a specialized glial structure that spans the anteroposterior axis from the midbrain to the tail regions. It has been shown that the floor plate is conserved among vertebrates with homologous structures in invertebrates such as the fruit fly Drosophila and the nematode C. elegans. Functionally, the structure serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube."
TODO - add grouping class for the anterior end of the neural tube at all stages
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)
Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia].
Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
The ventral aorta is a blood vessel in a single-pass circulatory system that carries de-oxygenated blood from the heart to the gills. In a single-pass circulatory system blood passes once through the heart to supply the body once[GO].
Outflow artery from the heart to the aortic arches. Kimmel et al, 1995.[TAO]
The artery in vertebrate embryos that carries blood from the ventricle of the heart to the aortic arches. In adult fish it branches into afferent branchial arteries supplying the gills. In adult tetrapods it is represented by the ascending part of the aorta.
Taxon notes (via vHOG): "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them." Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.620. // in Reptiles, splits to form bases of 3 arteries: left aortic arch, right aortic arch and pulmonary trunk. In birds, the right systemic arch becomes predominant, the left never fully develops [Kardong]
Extension of the dorsal aorta in the tail.
Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO]
The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus.
Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator].
In all vertebrates the thyroid arises from the ventral aspect of the second pouch
Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm
Median fin located on the dorsal surface of the organism.
The narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain.
The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]
Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
Gonochoristic organism that can produce female gametes.
Gonochoristic organism that can produce male gametes.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Anatomical cluster that is a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO]
Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO]
relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO]
UBERONREF:0000007 has this as a syn for otic capsule
Anatomical cluster that forms the floor and sidewalls of the middle part of the cranium.
Anatomical cluster that forms the floor and sidewalls of the middle part of the neurocranium.[AAO]
Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ.
Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO]
Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO]
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus.
The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO]
in XAO, called branchial arch 1 and df VP3
Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus.
The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]
in XAO, called branchial arch 2 and df VP4
The third in a series of paired bars in the wall of the pharynx, within which are formed the third aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
A fifth arch never establishes itself in amniotes
in XAO, called branchial arch 3 and df VP5
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles.
The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
The vessels formed within the first pair of branchial arches in embryogenesis.
Disappears early in development in tetrapods
ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas
The vessels formed within the second pair of branchial arches in embryogenesis.
The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2].
The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO]
The vessels formed within the third pair of branchial arches in embryogenesis.
Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]
The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3].
The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]
The vessels formed within the fourth pair of branchial arches in embryogenesis.
The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]
The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4].
Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta
The vessels formed within the fifth pair of pharyngeal arches in embryogenesis.
The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]
The fifth arch disappears on both sides[WP][Wikipedia:Aortic_arches#Arch_5].
The fifth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 5 artery is paired and has a common trunk with aortic arch 6 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. Aortic arches 5 and 6 supply the trunk and tail with oxygenated blood.[AAO]
In humans the 5th arch disappears on both sides
The vessels formed within the sixth pair of branchial arches in embryogenesis.
The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]
The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].
the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries
The outermost extraembryonic membrane of amniotes.
The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]
The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252].
The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584]
This term refers to the amniote structure. It is distinct from the concept of chorion in insects
A structure directly adjacent to the outer surface of the plasma membrane of an ovum. It is composed mostly of protein fibers, with protein receptors needed for sperm binding, binding to sperm plasma membrane receptors. The species-specificity between these receptors contributes to prevention of breeding between different species [Wikipedia]. A protective layer around the egg[FBbt].
TODO - consider GO CC request. GO:0030704-vitelline membrane formation considered a subclass of CC organization
Thin membrane enclosing and immediately adjacent to the ovum. Produced in the ovary.[AAO]
relationship loss: part_of zygote (AAO:0010324)[AAO]
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
An elongated tube which carries air to and from the lungs.[AAO]
The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]
In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409
Upper portion of the skull that excludes the mandible (when present in the organism).
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
GO uses genitalia for the singular organ
A female organ involved in reproduction.
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
reproductive system organ of male organism
An organism at the prepupal stage. The prepupal stage is a life stage interposed between the larval and the pupal stages in insects that undergo a complete metamorphosis. The start of the pre-pupal stage is marked by pupariation, and the end is marked by pupation.
An organism at the pupal stage. A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
A simple visual organ of insects[GO]. Two ocelli appear on the vertical and one on the frontal plate[FBbt]. The multi-tissue structure that is located on the top of the head, composed of the corneal lens, pigment cell, rhabdoms and synaptic plexus[HAO]. Two evolutionary distinct ocellus types exist [2]: dorsal ocelli (or simply 'ocelli'), found in most insects, and lateral ocelli (or stemmata), which are found in the larvae of some insect orders. They are structurally and functionally very different. Simple eyes of other animals, e.g. cnidarians may also be referred to as 'ocelli', but again the structure and anatomy of these eyes is quite distinct from those of the dorsal ocelli of insects[Wikipedia].
Barrier in the choroid plexus located in the lateral, third, and fourth brain ventricles that controls the entrance of substances into the cerebrospinal fluid from the blood[MP].
Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912).
A sac-like structure that is found in the mature gland[GO].
Organ part that has the form of a hollow cavity[WP].
Anterior portion of the palate consisting of bone and mucous membranes [GO]. The hard palate is formed from bony processes of the maxilla, premaxilla and palatine bone [Kardong].
in FMA this is divided into bony parts and submucosa
Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO].
One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO].
A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]
When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]
Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"]
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462
Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits.
In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three
An epithelium that is part of a elbow [Automatically generated definition].
An epithelium that is part of a wrist [Automatically generated definition].
An epithelium that is part of a hip [Automatically generated definition].
An epithelium that is part of a knee [Automatically generated definition].
An epithelium that is part of a shoulder [Automatically generated definition].
An epithelium that is part of a upper jaw [Automatically generated definition].
epithelial tissue of palatoquadrate arch
An epithelium that is part of a lower jaw [Automatically generated definition].
epithelial tissue of ventral mandibular arch
ventral mandibular arch epithelial tissue
An epithelium that is part of an anterior semicircular canal [Automatically generated definition].
anterior semicircular canal epithelial tissue
epithelial tissue of anterior semicircular canal
epithelial tissue of superior semicircular canal
epithelium of anterior semicircular canal
superior semicircular canal epithelial tissue
epithelium of superior semicircular canal
An epithelium that is part of a posterior semicircular canal [Automatically generated definition].
epithelial tissue of posterior semicircular canal
posterior semicircular canal epithelial tissue
epithelium of posterior semicircular canal
An epithelium that is part of a lateral semicircular canal [Automatically generated definition].
epithelial tissue of lateral semicircular canal
lateral semicircular canal epithelial tissue
epithelium of lateral semicircular canal
The epithelial layer of the luminal surfaces of the mammary gland.
An epithelium that is part of a lower arm [Automatically generated definition].
An epithelium that is part of a footplate.
An epithelium that is part of a otic placode [Automatically generated definition].
check ZFA, placemeant, appears to refer to both adult structures and primordium
Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case.
Anatomical cluster that consists of more than one rib in an individual.[TAO]
The neck of the rib is the flattened portion which extends lateralward from the head; it is about 2.5 cm. long, and is placed in front of the transverse process of the lower of the two vertebrC& with which the head articulates. Its anterior surface is flat and smooth, its posterior rough for the attachment of the ligament of the neck, and perforated by numerous foramina. Of its two borders the superior presents a rough crest (crista colli costE) for the attachment of the anterior costotransverse ligament; its inferior border is rounded. On the posterior surface at the junction of the neck and body, and nearer the lower than the upper border, is an eminencebthe tubercle; it consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrC& to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs.
The portion of the yolk sac that is derived from endoderm and lines the yolk sac.
An endoderm that is part of a foregut [Automatically generated definition].
An endoderm that is part of a midgut [Automatically generated definition].
An endoderm that is part of a hindgut [Automatically generated definition].
An endoderm that is part of a thyroid primordium.
A calcareous tooth that is part of the upper jaw region. In mammals, the upper jaw teeth are attached to the maxilla.
Note that we follow EHDAA2 and consider teeth part of the jaw skeleton
A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary).
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones.
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
An endothelium that is part of a trachea.
The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum.
The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG]
A mesentery that is part of a esophagus [Automatically generated definition].
A mesentery that is part of a midgut [Automatically generated definition].
A meninx that is part of a midbrain [Automatically generated definition].
consider changing genus to subdivision of meninx
Meninges that are part of the midbrain. [Bgee_curator][VHOG]
A meninx that is part of a telencephalon [Automatically generated definition].
Meninges that are part of the telencephalon. [Bgee_curator][VHOG]
A meninx that is part of a diencephalon [Automatically generated definition].
Meninges that are part of the diencephalon. [Bgee_curator][VHOG]
A meninx that is part of a hindbrain [Automatically generated definition].
Meninges that are part of the hindbrain. [Bgee_curator][VHOG]
A meninx that is part of a spinal cord [Automatically generated definition].
Meninges that are part of the spinal cord. [Bgee_curator][VHOG]
A gland that is part of a foregut [Automatically generated definition].
Racemose mucous glands beneath the mucous membrane of the pharynx.
Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis.
A gland that is part of a integumental system [Automatically generated definition].
The mesencephalic roof plate, including the caudal and rostral part of the midbrain roof.
Roof plate that is part of the midbrain. [Bgee_curator][VHOG]
A roof plate that is part of a telencephalon [Automatically generated definition].
Roof plate that is part of the telencephalon. [Bgee_curator][VHOG]
A roof plate that is part of a diencephalon [Automatically generated definition].
Roof plate that is part of the diencephalon. [Bgee_curator][VHOG]
A roof plate that is part of a metencephalon [Automatically generated definition].
Roof plate that is part of the metencephalon. [Bgee_curator][VHOG]
A roof plate that is part of a medulla oblongata [Automatically generated definition].
Roof plate that is part of the medulla oblongata. [Bgee_curator][VHOG]
A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
A floor plate that is part of a neural tube [Automatically generated definition].
In summary, the available data for tunicates, amphioxus, and vertebrates indicate that a floorplate-like structure was already present in the proximate invertebrate ancestor of the vertebrates and that the genetic mechanisms for DV patterning of the nerve cord were also largely in place.[well established][VHOG]
although 'floor plate' is classically defined as being located on the neural tube, in many AOs the floor plate continues post-embryonically after the neural tube has ceased to exist. We introduce this class for the neural tube specific structure
A floor plate that is part of a midbrain [Automatically generated definition].
Floor plate that is part of the midbrain.[TAO]
relationship type change: subclass multi-tissue structure (CARO:0000055) CHANGED TO: develops_from multi-tissue structure (UBERON:0000481)[TAO]
relationship type change: subclass multi-tissue structure (CARO:0000055) CHANGED TO: part_of multi-tissue structure (UBERON:0000481)[TAO]
A floor plate that is part of a telencephalon [Automatically generated definition].
A floor plate that is part of a diencephalon [Automatically generated definition].
A floor plate that is part of a metencephalon [Automatically generated definition].
A floor plate that is part of a medulla oblongata [Automatically generated definition].
Mesenchyme that is part of a developing testis [Automatically generated definition].
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
Mesenchyme that is part of a developing ovary [Automatically generated definition].
female reproductive system gonad mesenchyme
female reproductive system gonada mesenchyme
gonad of female reproductive system mesenchyme
gonada of female reproductive system mesenchyme
mesenchyme of female reproductive system gonad
mesenchyme of female reproductive system gonada
mesenchyme of gonad of female reproductive system
mesenchyme of gonada of female reproductive system
The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme.
Mesenchyme that is part of a developing elbow [Automatically generated definition].
Mesenchyme of the carpal region that contributes to the carpal skeleton.
Mesenchyme that is part of a developing hip [Automatically generated definition].
Mesenchyme that is part of a developing knee [Automatically generated definition].
Mesenchyme that is part of a developing shoulder [Automatically generated definition].
Mesenchyme that is part of a developing upper jaw [Automatically generated definition].
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
Mesenchyme that is part of a developing pinna [Automatically generated definition].
EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation
Mesenchyme that is part of a developing mammary gland.
Mesenchyme that is part of a developing lower arm [Automatically generated definition].
We group two EMAPA classes here but these may need to be separated
A submucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically submucosa
submucosa of anal canal viewed anatomically
The submucous layer of the wall of the rectum.
A submucosa that is part of a colon [Automatically generated definition].
A submucosa that is part of a duodenum [Automatically generated definition].
A serous membrane that is part of a rectum [Automatically generated definition].
A serous membrane that is part of a colon [Automatically generated definition].
A serous membrane that is part of a duodenum [Automatically generated definition].
A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
A ganglion that is part of a central nervous system [Automatically generated definition].
this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia
A mucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically mucosa of organ
anal canal viewed anatomically mucous membrane
anal canal viewed anatomically organ mucosa
mucosa of anal canal viewed anatomically
mucosa of organ of anal canal viewed anatomically
mucosa of organ of anatomical anal canal
mucous membrane of anal canal viewed anatomically
mucous membrane of anatomical anal canal
organ mucosa of anal canal viewed anatomically
A mucosa that is part of a oral opening [Automatically generated definition].
A mucosa that is part of a rectum [Automatically generated definition].
A layer of epithelial cells on the surface of the mucosa.
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
An epithelium that is part of a hindgut [Automatically generated definition].
An epithelium that is part of a rectum [Automatically generated definition].
An epithelium that is part of a tongue [Automatically generated definition].
examples: tongue squamous epithelium, keratined, non-keratinized and parakeratinized epithelium, as well as gustatory epithelium. Note that not all these subtypes are named in individual anatomy ontologies.
An epithelium that is part of a soft palate [Automatically generated definition].
An epithelium that is part of a submandibular gland [Automatically generated definition].
epithelial tissue of submandibular gland
An epithelium that is part of a right lung [Automatically generated definition].
An epithelium that is part of a left lung [Automatically generated definition].
An epithelium that is part of a hard palate [Automatically generated definition].
An unilaminar epithelium that surrounds a pelvic appendage bud.
An unilaminar epithelium that surrounds a pectoral appendage bud.
An ectoderm that is part of a footplate.
An extraembryonic structure that develops_from a ectoderm and is part of a chorion.
A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition].
cardiac muscle tissue of heart right atrium
cardiac muscle tissue of right atrium of heart
textus muscularis of myocardium of right atrium
textus muscularis of myocardium of right atrium of heart
textus muscularis of myocardium of right cardiac atrium
A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition].
cardiac left atrium cardiac muscle tissue
textus muscularis of myocardium of cardiac left atrium
textus muscularis of myocardium of heart left atrium
textus muscularis of myocardium of left atrium
textus muscularis of myocardium of left atrium of heart
textus muscularis of myocardium of left cardiac atrium
A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of right ventricle
A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition].
cardiac muscle of interventricular septum
cardiac muscle tissue of interventricular septum
A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition].
Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi.
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition].
A mesothelium that is part of a pericardium [Automatically generated definition].
cavity of pericardial sac meso-epithelium
meso-epithelium of cavity of pericardial sac
mesothelium of cavity of pericardial sac
A mesothelium that is part of a diaphragm [Automatically generated definition].
A mesothelium that is part of a pleural cavity [Automatically generated definition].
A mesentery that is part of a urinary system [Automatically generated definition].
A mesentery that is part of a hindgut [Automatically generated definition].
A mesentery that is part of a rectum [Automatically generated definition].
A mesentery that is part of a colon [Automatically generated definition].
A mesentery that is part of a duodenum [Automatically generated definition].
A zone of skin that is part of a lower arm [Automatically generated definition].
A lobar bronchus that is part of a right lung [Automatically generated definition].
A lobar bronchus that is part of a left lung [Automatically generated definition].
A cartilage element that is part of a respiratory system [Automatically generated definition].
A gland that is part of a digestive tract [Automatically generated definition].
Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue.
Mesenchyme that is part of a pelvic appendage bud.
Mesenchyme that is part of a pectoral appendage bud.
Mesoderm that is part of the pectoral fin bud.[TAO]
Mesenchyme that is part of a developing tongue [Automatically generated definition].
Mesenchyme that is part of a developing soft palate [Automatically generated definition].
Mesenchyme that is part of a developing submandibular gland [Automatically generated definition].
A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP].
Mesenchyme that is part of a developing hard palate [Automatically generated definition].
A lymph node that is located in a kidney [Automatically generated definition].
Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland
An adipose tissue that is part of a dermis [Automatically generated definition].
The encapsulated adipose tissue in the abdomen.
The encapsulated adipose tissue associated with the ovaries or testes.
consider change relationship from part_of
Anatomical structure associated with the gonads which vary in form among amphibians but are primarily composed of adipose tissue and are thought to be a source of nutrients for the gonads.[AAO]
we place the amphibian structures here as their definitions state a gonadal association.
A nerve that is part of an abdomen [Automatically generated definition].
A nerve that is part of a neck [Automatically generated definition].
A nerve that is part of a leg [Automatically generated definition].
A nerve that is part of a chest [Automatically generated definition].
A nerve that is part of an arm [Automatically generated definition].
A nerve that is part of a wrist [Automatically generated definition].
A nerve that is part of a toe [Automatically generated definition].
digit of terminal segment of free lower limb nerve
nerve of digit of terminal segment of free lower limb
nerve of terminal segment of free lower limb digit
terminal segment of free lower limb digit nerve
A nerve that is part of a shoulder [Automatically generated definition].
added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea
A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk).
A nerve that is part of a limb [Automatically generated definition].
A nerve that is part of a forelimb [Automatically generated definition].
A nerve that is part of a hindlimb [Automatically generated definition].
A nerve that is located in a thoracic cavity [Automatically generated definition].
consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve
A nerve that is part of a pelvis [Automatically generated definition].
A nerve that is part of a foot [Automatically generated definition].
A nerve that is part of an ankle [Automatically generated definition].
A nerve that is part of a finger [Automatically generated definition].
digit of terminal segment of free upper limb nerve
nerve of digit of terminal segment of free upper limb
nerve of terminal segment of free upper limb digit
terminal segment of free upper limb digit nerve
A nerve that is part of a manus [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a trabecula carnea [Automatically generated definition].
cardiac muscle muscle tissue of trabecula carnea
cardiac muscle textus muscularis of trabecula carnea
cardiac muscle tissue of trabecula carnea
heart muscle muscle tissue of trabecula carnea
heart muscle textus muscularis of trabecula carnea
heart myocardium muscle tissue of trabecula carnea
heart myocardium textus muscularis of trabecula carnea
muscle of heart muscle tissue of trabecula carnea
muscle of heart textus muscularis of trabecula carnea
muscle tissue of cardiac muscle of trabecula carnea
muscle tissue of heart muscle of trabecula carnea
muscle tissue of heart myocardium of trabecula carnea
muscle tissue of muscle of heart of trabecula carnea
muscle tissue of myocardium of trabecula carnea
myocardium muscle tissue of trabecula carnea
myocardium textus muscularis of trabecula carnea
textus muscularis of cardiac muscle of trabecula carnea
textus muscularis of heart muscle of trabecula carnea
textus muscularis of heart myocardium of trabecula carnea
textus muscularis of muscle of heart of trabecula carnea
textus muscularis of myocardium of trabecula carnea
trabecula carnea cardiac muscle muscle tissue
trabecula carnea cardiac muscle textus muscularis
trabecula carnea heart muscle muscle tissue
trabecula carnea heart muscle textus muscularis
trabecula carnea heart myocardium muscle tissue
trabecula carnea heart myocardium textus muscularis
trabecula carnea muscle of heart muscle tissue
trabecula carnea muscle of heart textus muscularis
trabecula carnea muscle tissue of cardiac muscle
trabecula carnea muscle tissue of heart muscle
trabecula carnea muscle tissue of heart myocardium
trabecula carnea muscle tissue of muscle of heart
trabecula carnea muscle tissue of myocardium
trabecula carnea myocardium muscle tissue
trabecula carnea myocardium textus muscularis
trabecula carnea textus muscularis of cardiac muscle
trabecula carnea textus muscularis of heart muscle
trabecula carnea textus muscularis of heart myocardium
trabecula carnea textus muscularis of muscle of heart
trabecula carnea textus muscularis of myocardium
A Peyer's patch that is part of a large intestine.
solitary lymphatic follicle of large intestine
solitary lymphoid follicle of subdivision of large intestine
Nodular lymphoid structures on the serosal surface of the small intestine.
aggregated lymphoid follicle of small intestine
noduli lymphoidei aggregati intestini tenuis
A loop of Henle that is part of a inner medulla of kidney [Automatically generated definition].
A lymphatic vessel that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius lymphatic vessel
lymphatic vessel of apparatus respiratorius
A bone that is part of a head [Automatically generated definition].
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A bone that is part of a neck [Automatically generated definition].
A bone that is part of a chest [Automatically generated definition].
bone organ of anterolateral part of thorax
A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia.
A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods.
this is a forelimb bone in MA, but this would lead to part-disjointness violations.
A bone that is part of a facial skeleton [Automatically generated definition].
test whether 'facial bone' is an exact synonym
A bone that is part of a trunk [Automatically generated definition].
A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle).
the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc
A bone that is part of a lower arm [Automatically generated definition].
The ureteral branches of renal artery are small branches which supply the ureter.
An artery that is part of a respiratory system [Automatically generated definition].
The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose.
ramus labialis superior arteriae facialis
The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
ramus labialis inferior (arteria facialis)
ramus labialis inferior arteriae facialis
An artery that supplies blood to the cerebellum.
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
One of the arteries supplying a meninix[Automatically generated definition].
A vein that is part of a ureter [Automatically generated definition].
A vein that is part of a respiratory system [Automatically generated definition].
The inferior labial vein is the vein receiving blood from the upper lip.
The inferior labial vein is the vein receiving blood from the lower lip.
A vein that is part of a thoracic cavity [Automatically generated definition].
A vein that is part of a clitoris [Automatically generated definition].
A vein that is part of a tail [Automatically generated definition].
A portion of vein that is part of a trabecular bone tissue [Automatically generated definition].
A portion of lymphoid tissue that is part of a thymus [Automatically generated definition].
A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland.
A sebaceous gland that is part of a vagina [Automatically generated definition].
A holocrine gland of the dermis that secretes sebum into hair follicles.
A lactiferous gland that is part of the abdominal region [Automatically generated definition].
Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius blood capillary endothelium
apparatus respiratorius capillary endothelium
apparatus respiratorius capillary vessel endothelium
apparatus respiratorius endothelium of blood capillary
apparatus respiratorius endothelium of capillary
apparatus respiratorius endothelium of capillary vessel
blood capillary endothelium of apparatus respiratorius
blood capillary endothelium of respiratory system
capillary endothelium of apparatus respiratorius
capillary endothelium of respiratory system
capillary vessel endothelium of apparatus respiratorius
capillary vessel endothelium of respiratory system
endothelium of blood capillary of apparatus respiratorius
endothelium of blood capillary of respiratory system
endothelium of capillary of apparatus respiratorius
endothelium of capillary of respiratory system
endothelium of capillary vessel of apparatus respiratorius
endothelium of capillary vessel of respiratory system
respiratory system blood capillary endothelium
respiratory system capillary vessel endothelium
respiratory system endothelium of blood capillary
respiratory system endothelium of capillary
respiratory system endothelium of capillary vessel
respiratory system capillary endothelium
A venule that is part of a respiratory system [Automatically generated definition].
An arteriole that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a head [Automatically generated definition].
A blood vessel that is part of an abdomen [Automatically generated definition].
A blood vessel that is part of a heart [Automatically generated definition].
A blood vessel that is part of a brain [Automatically generated definition].
A blood vessel that is part of a cornea [Automatically generated definition].
A blood vessel that is part of a retina [Automatically generated definition].
blood vessel of tunica interna of eyeball
A blood vessel that is part of a neck [Automatically generated definition].
A blood vessel that is part of a leg [Automatically generated definition].
A blood vessel that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a trachea.
A blood vessel that is part of a chest [Automatically generated definition].
anterolateral part of thorax blood vessel
blood vessel of anterior thoracic region
blood vessel of anterolateral part of thorax
A blood vessel that is part of an arm [Automatically generated definition].
A blood vessel that is part of a toe [Automatically generated definition].
blood vessel of digit of terminal segment of free lower limb
blood vessel of terminal segment of free lower limb digit
digit of terminal segment of free lower limb blood vessel
terminal segment of free lower limb digit blood vessel
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A blood vessel that is part of a eyelid [Automatically generated definition].
A blood vessel that is part of a iris [Automatically generated definition].
A blood vessel that is part of a lung [Automatically generated definition].
A blood vessel that is part of a trunk [Automatically generated definition].
A blood vessel that is part of a limb [Automatically generated definition].
A blood vessel that is part of a forelimb [Automatically generated definition].
A blood vessel that is part of a hindlimb [Automatically generated definition].
A blood vessel that is part of a kidney [Automatically generated definition].
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
A blood vessel that is part of a pelvis [Automatically generated definition].
A blood vessel that is part of a foot [Automatically generated definition].
A blood vessel that is part of a finger [Automatically generated definition].
blood vessel of digit of terminal segment of free upper limb
blood vessel of terminal segment of free upper limb digit
digit of terminal segment of free upper limb blood vessel
terminal segment of free upper limb digit blood vessel
A blood vessel that is part of a manus [Automatically generated definition].
A blood vessel that is part of a tail [Automatically generated definition].
A capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius capillary vessel
blood capillary of apparatus respiratorius
capillary vessel of apparatus respiratorius
A capillary that is part of a kidney [Automatically generated definition].
A gray matter that is part of a brain [Automatically generated definition].
An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius endothelium of lymph vessel
apparatus respiratorius lymph vessel endothelium
apparatus respiratorius lymphatic vessel endothelium
endothelium of lymph vessel of apparatus respiratorius
endothelium of lymph vessel of respiratory system
lymph vessel endothelium of apparatus respiratorius
lymph vessel endothelium of respiratory system
lymphatic vessel endothelium of apparatus respiratorius
lymphatic vessel endothelium of respiratory system
respiratory system endothelium of lymph vessel
respiratory system lymph vessel endothelium
respiratory system lymphatic vessel endothelium
A zone of skin that is part of a toe [Automatically generated definition].
digit of terminal segment of free lower limb skin
skin of digit of terminal segment of free lower limb
skin of terminal segment of free lower limb digit
terminal segment of free lower limb digit skin
A zone of skin that is part of a forelimb [Automatically generated definition].
TODO - check free limb vs pectoral complex
A zone of skin that is part of a hindlimb [Automatically generated definition].
TODO - check free limb vs pelvic complex
A zone of skin that is part of a finger [Automatically generated definition].
digit of terminal segment of free upper limb skin
skin of digit of terminal segment of free upper limb
skin of terminal segment of free upper limb digit
terminal segment of free upper limb digit skin
A zone of skin that is part of a tail [Automatically generated definition].
An alveolar duct that is part of a right lung [Automatically generated definition].
An alveolar duct that is part of a left lung [Automatically generated definition].
A bronchiole that is part of a right lung [Automatically generated definition].
A bronchiole that is part of a left lung [Automatically generated definition].
A terminal bronchiole that is part of a right lung [Automatically generated definition].
A terminal bronchiole that is part of a left lung [Automatically generated definition].
A respiratory bronchiole that is part of a right lung [Automatically generated definition].
A respiratory bronchiole that is part of a left lung [Automatically generated definition].
The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.
A macula densa that is part of a distal convoluted tubule [Automatically generated definition].
A meninx that is part of a brain [Automatically generated definition].
Meninges that are part of the brain. [Bgee_curator][VHOG]
A meninx that is part of a forebrain [Automatically generated definition].
The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule.
The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]
A pia mater that is part of a forebrain [Automatically generated definition].
A pia mater that is part of a midbrain [Automatically generated definition].
Pia mater that is part of the midbrain. [Bgee_curator][VHOG]
A pia mater that is part of a telencephalon [Automatically generated definition].
Pia mater that is part of the telencephalon. [Bgee_curator][VHOG]
A pia mater that is part of a diencephalon [Automatically generated definition].
Pia mater that is part of the diencephalon. [Bgee_curator][VHOG]
mature diencephalon pia mater of neuraxis
pia mater of neuraxis of mature diencephalon
A pia mater that is part of a hindbrain [Automatically generated definition].
Pia mater that is part of the hindbrain. [Bgee_curator][VHOG]
A pia mater that is part of a spinal cord [Automatically generated definition].
An arachnoid mater that is part of a forebrain [Automatically generated definition].
arachnoid mater of neuraxis of forebrain
An arachnoid mater that is part of a midbrain [Automatically generated definition].
Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG]
An arachnoid mater that is part of a diencephalon [Automatically generated definition].
Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG]
arachnoid mater of neuraxis of between brain
arachnoid mater of neuraxis of diencephalon
arachnoid mater of neuraxis of interbrain
arachnoid mater of neuraxis of mature diencephalon
between brain arachnoid mater of neuraxis
diencephalon arachnoid mater of neuraxis
mature diencephalon arachnoid mater of neuraxis
An arachnoid mater that is part of a hindbrain [Automatically generated definition].
Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG]
arachnoid mater of neuraxis of hindbrain
An arachnoid mater that is part of a spinal cord [Automatically generated definition].
The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]
arachnoid mater of neuraxis of spinal cord
A dura mater that is part of a forebrain.
A dura mater that is part of a midbrain [Automatically generated definition].
Dura mater that is part of the midbrain. [Bgee_curator][VHOG]
A dura mater that is part of a telencephalon [Automatically generated definition].
A dura mater that is part of a diencephalon [Automatically generated definition].
Dura mater that is part of the diencephalon. [Bgee_curator][VHOG]
dura mater of neuraxis of mature diencephalon
mature diencephalon dura mater of neuraxis
A dura mater that is part of a hindbrain [Automatically generated definition].
Dura mater that is part of the hindbrain. [Bgee_curator][VHOG]
A portion of connective tissue that is part of a head [Automatically generated definition].
portion of connective tissue of adult head
A portion of connective tissue that is part of an abdomen [Automatically generated definition].
A portion of connective tissue that is part of a neck [Automatically generated definition].
neck (volume) portion of connective tissue
portion of connective tissue of neck (volume)
A portion of connective tissue that is part of a leg [Automatically generated definition].
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
A portion of connective tissue that is part of a trachea.
A portion of connective tissue that is part of a chest [Automatically generated definition].
anterior thoracic region connective tissue
anterior thoracic region portion of connective tissue
anterior thoracic region textus connectivus
anterolateral part of thorax connective tissue
anterolateral part of thorax portion of connective tissue
anterolateral part of thorax textus connectivus
connective tissue of anterior thoracic region
connective tissue of anterolateral part of thorax
front of thorax portion of connective tissue
portion of connective tissue of anterior thoracic region
portion of connective tissue of anterolateral part of thorax
portion of connective tissue of front of thorax
textus connectivus of anterior thoracic region
textus connectivus of anterolateral part of thorax
A portion of connective tissue that is part of an arm [Automatically generated definition].
A portion of connective tissue that is part of a elbow [Automatically generated definition].
A portion of connective tissue that is part of a wrist [Automatically generated definition].
A portion of connective tissue that is part of a hip [Automatically generated definition].
A portion of connective tissue that is part of a knee [Automatically generated definition].
A portion of connective tissue that is part of a toe [Automatically generated definition].
A portion of connective tissue that is part of a shoulder [Automatically generated definition].
portion of connective tissue of shoulder
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
connective tissue of lower respiratory tract
lower respiratory tract portion of connective tissue
lower respiratory tract textus connectivus
portion of connective tissue of lower respiratory tract
textus connectivus of lower respiratory tract
lower respiratory tract connective tissue
A portion of connective tissue that is part of a eyelid [Automatically generated definition].
A portion of connective tissue that is part of a nasopharynx [Automatically generated definition].
connective tissue of nasal part of pharynx
nasal part of pharynx portion of connective tissue
nasal part of pharynx textus connectivus
nasopharynx portion of connective tissue
portion of connective tissue of nasal part of pharynx
portion of connective tissue of nasopharynx
portion of connective tissue of rhinopharynx
rhinopharynx portion of connective tissue
textus connectivus of nasal part of pharynx
A portion of connective tissue that is part of a larynx [Automatically generated definition].
The fibrous supportive tissue of the mammary gland.
connective tissue of lobe of mammary gland
lactiferous gland portion of connective tissue
A portion of connective tissue that is part of a dermis [Automatically generated definition].
A portion of connective tissue that is part of a trunk [Automatically generated definition].
A portion of connective tissue that is part of a limb [Automatically generated definition].
A portion of connective tissue that is part of a forelimb [Automatically generated definition].
A portion of connective tissue that is part of a hindlimb [Automatically generated definition].
A portion of connective tissue that is part of a lobar bronchus [Automatically generated definition].
A portion of connective tissue that is part of a bronchus [Automatically generated definition].
bronchial trunk portion of connective tissue
portion of connective tissue of bronchial trunk
portion of connective tissue of bronchus
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
cavity of chest portion of connective tissue
cavity of thorax portion of connective tissue
chest cavity portion of connective tissue
pectoral cavity portion of connective tissue
portion of connective tissue of cavity of chest
portion of connective tissue of cavity of thorax
portion of connective tissue of chest cavity
portion of connective tissue of pectoral cavity
portion of connective tissue of thoracic cavity
thoracic cavity portion of connective tissue
A portion of connective tissue that is part of a pelvis [Automatically generated definition].
A portion of connective tissue that is part of a foot [Automatically generated definition].
connective tissue of terminal segment of free lower limb
A portion of connective tissue that is part of an ankle [Automatically generated definition].
A portion of connective tissue that is part of a finger [Automatically generated definition].
A portion of connective tissue that is part of a hand [Automatically generated definition].
connective tissue of terminal segment of free upper limb
A portion of connective tissue that is part of a tail [Automatically generated definition].
portion of connective tissue of post-vent region
post-vent region portion of connective tissue
A cartilage that is part of a neck [Automatically generated definition].
A cartilage that is part of a lower respiratory tract [Automatically generated definition].
The ring-shaped cartilaginous structures that support the trachea.
check whether to classify as part of splanchoncranium
in mammals the rings are incomplete, in avians the rings are complete.
A skin gland that is part of a camera-type eye [Automatically generated definition].
A long bone that is part of a limb [Automatically generated definition].
A long bone that is part of a forelimb [Automatically generated definition].
A long bone that is part of a hindlimb [Automatically generated definition].
The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall.
adult aorta textus connectivus elasticus
dorsal aorta textus connectivus elasticus
elastic connective tissue of adult aorta
elastic connective tissue of dorsal aorta
elastic connective tissue of trunk of aortic tree
textus connectivus elasticus of adult aorta
textus connectivus elasticus of dorsal aorta
textus connectivus elasticus of trunk of aortic tree
trunk of aortic tree elastic connective tissue
trunk of aortic tree textus connectivus elasticus
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
An elastic tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius elastic connective tissue
apparatus respiratorius textus connectivus elasticus
elastic connective tissue of apparatus respiratorius
elastic connective tissue of respiratory system
elastic tissue of apparatus respiratorius
respiratory system elastic connective tissue
respiratory system textus connectivus elasticus
textus connectivus elasticus of apparatus respiratorius
textus connectivus elasticus of respiratory system
An elastic tissue that is part of a circulatory system [Automatically generated definition].
cardiovascular system elastic connective tissue
cardiovascular system textus connectivus elasticus
circulatory system elastic connective tissue
circulatory system textus connectivus elasticus
elastic connective tissue of cardiovascular system
elastic connective tissue of circulatory system
textus connectivus elasticus of cardiovascular system
textus connectivus elasticus of circulatory system
Elastic tissue layer that lines a blood vessel layer.
blood vessel textus connectivus elasticus
elastic connective tissue of blood vessel
textus connectivus elasticus of blood vessel
Elastic tissue that is part of a lung [Automatically generated definition].
An elastic tissue that is part of a bronchus [Automatically generated definition].
bronchial trunk elastic connective tissue
bronchial trunk textus connectivus elasticus
elastic connective tissue of bronchial trunk
textus connectivus elasticus of bronchial trunk
textus connectivus elasticus of bronchus
An elastic tissue that is part of a trachea [Automatically generated definition].
cartilaginous trachea elastic connective tissue
cartilaginous trachea textus connectivus elasticus
elastic connective tissue of cartilaginous trachea
elastic connective tissue of vertebrate trachea
textus connectivus elasticus of cartilaginous trachea
textus connectivus elasticus of vertebrate trachea
textus connectivus elasticus of windpipe
vertebrate trachea elastic connective tissue
vertebrate trachea textus connectivus elasticus
The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers.
The innermost layer of the aorta, containing the endothelium and an inner elastic membrane.
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
respiratory system arterial blood vessel
An arterial blood vessel that is part of a kidney [Automatically generated definition].
A bone that is part of a mesopodial skeleton.
The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost
Any joint that is part of a (free) limb.
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses
Any muscle organ that is part of a hip [Automatically generated definition].
Any muscle organ that is part of a toe [Automatically generated definition].
digit of terminal segment of free lower limb muscle organ
muscle organ of digit of terminal segment of free lower limb
muscle organ of terminal segment of free lower limb digit
terminal segment of free lower limb digit muscle organ
The muscle in the orbit of the eye that lifts the upper eyelid[ncithesaurus:Eyelid_Muscle].
Any muscle organ that is part of a limb [Automatically generated definition].
Any muscle organ that is part of a forelimb.
FMA and MA class actually refer to muscles of entire pectoral complex
Any muscle organ that is part of a hindlimb [Automatically generated definition].
Any muscle organ that is part of a finger [Automatically generated definition].
digit of terminal segment of free upper limb muscle organ
muscle organ of digit of terminal segment of free upper limb
muscle organ of terminal segment of free upper limb digit
terminal segment of free upper limb digit muscle organ
A muscle organ that attaches to a tail vertebra [Automatically generated definition].
the BTO class may possibly refer to an invertebrate structure
A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl.
Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO]
The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition])
The muscles of the palate are the glossopalatine, palatoglossus, levator palati(ni), musculus uvulae, palatopharyngeus, and tensor palati(ni).
see also FMA:71438 ! set of muscles of soft palate and fauces
The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity).
in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity
Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture.
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].
Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]
Design pattern notes: check whether this fits the foramen design pattern
Any joint connecting the acromonion of the scapula and clavicle.
The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula.
Anatomical space in the abdominal cavity behind (retro) the peritoneum. It has no specific delineating anatomical structures. Organs are retroperitoneal if they only have peritoneum on their anterior side.
The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas.
The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted].
we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part
The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral.
we follow FMA in making these joints part of digits
The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles.
Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct.
includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct
Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct.
includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts
Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]
A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle.
In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis
The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava.
The cavernous sinus (or lateral sellar compartment), within the human head, is a large collection of thin-walled veins creating a cavity bordered by the temporal bone of the skull and the sphenoid bone, lateral to the sella turcica.
An irregularly shaped venous space in the dura mater at either side of the sphenoid bone[MESH:A07.231.908.224.334].
A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein.
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia.
All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers
A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch.
Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754].
recurrent laryngeal nerve from vagus nerve
vagus X nerve recurrent laryngeal branch
The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue.
The vestibular nerve is one of the two branches of the Vestibulocochlear nerve (the cochlear nerve being the other). It goes to the semicircular canals via the vestibular ganglion. It receives positional information. Axons of the vestibular nerve synapse in the vestibular nucleus on the lateral floor and wall of the fourth ventricle in the pons and medulla. It arises from bipolar cells in the vestibular ganglion, ganglion of Scarpa, which is situated in the upper part of the outer end of the internal auditory meatus. [WP,unvetted].
vestibulocochlear VIII nerve vestibular component
The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls.
The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted].
The central part of the thoracic cavity enclosed by the left and right pleurae.
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
A region of the fetal urogenital sinus epithelium destined to become the prostate[GO].
AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204]
The part of the forelimb between pectoral region and the elbow, corresponding to the humerus.
Segment of the hindleg corresponding to the humerus.[AAO]
anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. Naming conventions for pod terms under discussion within phenoscape group.
The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants.
FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion
A nerve that is part of a thorax [Automatically generated definition].
A nerve that is part of an abdominal segment of trunk [Automatically generated definition].
A bone that is part of a hindlimb stylopod [Automatically generated definition].
May be merged into femur. See https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376
A bone that is part of a thorax [Automatically generated definition].
A bone that is part of an abdominal segment of trunk [Automatically generated definition].
bone organ of abdominal segment of trunk
Any muscle tissue that is part of the urethra.
Any muscle organ that is part of a thorax [Automatically generated definition].
Any muscle organ that is part of a respiratory system [Automatically generated definition].
Any muscle organ that is part of a esophagus [Automatically generated definition].
A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition].
muscle organ of abdominal segment of trunk
A blood vessel that is part of a thorax [Automatically generated definition].
A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].
blood vessel of abdominal segment of trunk
A skin of body that is part of an abdominal segment of trunk [Automatically generated definition].
A portion of connective tissue that is part of a thorax [Automatically generated definition].
A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition].
abdominal segment of trunk connective tissue
abdominal segment of trunk portion of connective tissue
abdominal segment of trunk textus connectivus
connective tissue of abdominal segment of trunk
portion of connective tissue of abdominal segment of trunk
textus connectivus of abdominal segment of trunk
A limb joint that is part of a forelimb [Automatically generated definition].
A limb joint that is part of a hindlimb [Automatically generated definition].
A limb joint that is part of an autopod [Automatically generated definition].
joint of limb of distal free limb segment
An anatomical space that surrounded_by a neural tube.
Epithelium that is part of a developing tooth or dental organ.
In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)
An epithelium that is part of a thymus, forming a supporting framework[MP,modified].
An artery that supplies a thyroid gland.
Part of the external carotid which supplies blood to the thyroid gland.[AAO]
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a telencephalon.
Cranial neural crest that is part of the telencephalon.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a diencephalon.
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
Mesenchyme that is part of a developing gonad [Automatically generated definition].
Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla.
we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme
Mesenchyme enclosed by dental organ.[MP]
Mesenchyme enclosed by dental organ.[TAO]
Mesenchyme that is part of a developing forelimb [Automatically generated definition].
Mesenchyme that is part of a developing hindlimb [Automatically generated definition].
Posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine.
A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO]
Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO]
the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process)
relationship loss: develops_from basidorsal (TAO:0001060)[TAO]
(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]
tiny neural arches present in Hagfish (which lack a true vertebraal column).
The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270
A middle phalanx that is part of a finger [Automatically generated definition].
A distal phalanx that is part of a finger [Automatically generated definition].
This is typically proximally connected to the middle phalanx of manus, except in some cases such as the manual digit 1 (thumb) of many mammals such as humans, where it connects to the proximal phalanx. It always connects to some phalanx, by definition
A middle phalanx that is part of a toe [Automatically generated definition].
A distal phalanx that is part of a pedal digit [Automatically generated definition].
This is typically proximally connected to the middle phalanx of pes, except in some cases such as the pedal digit 1 (big toe) in many mammals such as humans, where it connects to the proximal phalanx. It always connects to some phalanx, by definition
A proximal phalanx that is part of a pedal digit [Automatically generated definition].
A presumptive structure that has the potential to develop into a ganglion.
A mesentery that is part of a uterus [Automatically generated definition].
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166
Initial section of the oviduct through which the ova pass from the ovary to the uterus.
Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].
Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]
Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]
In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]
Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559
Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.
A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP].
see also: protective structure surrounding some species of bacteria and fungi. Note that FMA has classes such as Articular capsule that are not subtypes of Capsule (which is undefined in FMA). GO has 'capsule' which is a fungal structure, and 'external encapsulating structure' which is restricted to cells
A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum.
consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ
One of the skeletal muscles of the head and neck, spine, and ribs.
A portion of skeletal muscle tissue in the trunk.
The part of the retina that contains neurons and photoreceptor cells[GO].
An epithelial and lymphoid organ that develops as a dorsal diverticulum of the proctodeal region of the cloaca in birds. The luminal (interior) surface of the bursa is plicated with as many as 15 primary and 7 secondary plicae or folds. These plicae have hundreds of bursal follicles containing follicle-associated epithelial cells, lymphocytes, macrophages, and plasma cells. Lymphoid stem cells migrate from the fetal liver to the bursa during ontogeny. In the bursa, these stem cells acquire the characteristics of mature, immunocompetent B cells[WP]. The bursa is an organ found in birds involved in B cell differentiation[GO].
Portion of extracellular matrix between the myocardium and the endocardium. The cardiac jelly plays a central role in the septation of the heart and comprises most of the thickness of the heart wall at early stages, but disappears as the heart differentiates.
The extracellular matrix between the myocardium and the endocardium. The cardiac jelly plays a central role in the septation of the heart and comprises most of the thickness of the heart wall at early stages, but disappears as the heart differentiates.[TAO]
An atrioventricular canal that is in the left side of a atrioventricular region.
An atrioventricular canal that is in the right side of a atrioventricular region.
Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP].
Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]
some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined).
endothelium of irregular blood filled space
The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue.
The CP epithelial layer is continuous with the ependymal cell layer that lines the ventricles, but unlike the ependyma, the epithelial layer has tight gap junctions between the cells on the side facing the ventricle (apical surface). These gap junctions prevent the majority of substances from crossing the cell layer into the CSF; thus the CP acts as a blood-CSF barrier
epithelial tissue of chorioid plexus of cerebral hemisphere
Tooth-like structure composed of chitin.
Hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
A mass of closely packed fat cells (adipose tissue) surrounded by fibrous tissue septa[TMD].
An accumulation of adipose tissue (fat cells) enclosed in fibrous tissue[BTO].
FMA says isa fascia organ. Note that XAO and AAO have structures called fat pad/body, but these are gonad-associated, so we place them with the gonad-specific subclass
An insect gland dorsal to the insect gut, with a function analogous to that of the vertebrate liver. It is a storage organ for fats, glycogen and protein and is a major site of intermediary metabolism.
A fatty tissue especially of nearly mature insect larvae that serves as a food reserve[BTO].
Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].
A blood vessel that carries blood from the capillaries toward the heart.
Embryonic structure that develops into pancreatic bud.
in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds
revisit after standardizing terms 'primordium', 'anlagen', 'bud'
The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID].
Pancreatic bud that gives rise to the accessory pancreatic duct.
The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]
In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]
DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)
Pancreatic bud that gives rise to the major pancreatic duct.
The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]
the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship.
A duct that is part of a digestive system [Automatically generated definition].
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
Endocardium that is part of the atrioventricular canal[ZFA,vetted].
White matter that is part of a diencephalon [Automatically generated definition].
predominantly white regional part of diencephalon
A cartilage element of chondrocranium. Example: neurocranial trabecula.
A cartilage element that is part of the cranial skeleton.
Cartilage which is part of the cranium.[TAO]
Mesenchyme that is part of a developing pectoral fin [Automatically generated definition].
Mesenchyme that is part of the pectoral fin.[TAO]
Mesenchyme that is part of a developing pelvic fin [Automatically generated definition].
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
The sensory system for the sense of touch and pain.
The neural tissue involved in the transmission of sensory signals
MP defines this in a may more appropriate to somatosensory cortex
The placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood.
Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively ... The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[DOI: 10.1073/pnas.96.14.8138 ]
The brain ventricles or their associated choroid plexuses.
TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted
The anterior segment of the lamellated connective tissue layer of the cornea.
The posterior segment of the lamellated connective tissue layer of the cornea.
The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins.
An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP].
add more specific classification e.g. anastomosing network - consider FMA:3726
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity.
The lymph nodes located outside the thoracic and abdominal cavities, such as the submandibular, prescapular, axillary, inguinal and popliteal lymph nodes.
Blood vessels of the layer of the placenta where embryonic and maternal blood vessels interdigitate.
The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina.
internal genitalia of female reproductive system
TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows.
Primordial follicles are indiscernible to the naked eye and develop to primary, secondary, and finally mature vesicular follicles.
A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP].
Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO]
Kardong says absent in adult tetrapods, check AAO
we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally
The funnel-like expansion of the abdominal extremity of the uterine tube[MP].
The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube].
In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct.
The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells.
A sac-like structure comprising a sebaceous gland.
Missing definition for term UBERON:0004001. Please replace it using linked reference.
cytoarchitectural part of olfactory bulb
The connection between the embryo proper and extraembryonic tissues.
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
The structure of the outer structural layer of the rodent placenta[MP].
restriction to Rodentia may be too strong - we apply it for now as we are inheriting the MP definition
Forms a compact layer of non-syncytial cells between the labyrinth and the outer giant cells
In the absence of direct lineage analysis, it has been assumed, from histological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP].
contributes significantly in building up the GABAergic cortical cell population[WP]
That portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate.
The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate.
The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects
The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone.
The nodules of small undifferentiated B lymphocytes and follicular dendritic cells located in the spleen white pulp.
FMA:15843 is classified as primary follicle so it belongs here
The nodules of antigen-activated, differentiating B cells, follicular dendritic cells, antigen-presenting T cells and macrophages in the spleen white pulp.
The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands.
consider splitting genitalia from genital organ
One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP].
In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule)
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter.
The region of the mantle layer of the neural tube that lies dorsal to the sulcus limitans and contains primarily sensory neurons and interneurons involved in communication of sensory impulses; the alar plate develops into the dorsal horn in the grey matter of the spinal cord.
TODO - merge with UBERON:0003054 roof plate?
The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons.
The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout.
The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it.
The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it.
Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity.
The nucleus composed of the globose and emoliform nuclei of the cerebellum; in some mammalian species the globose nucleus is not distinguishable.
The interposed nucleus is a deep nucleus of the cerebellum and is composed of the globose nuclei and the emboliform nuclei. It is located in in the roof (dorsal aspect) of the fourth ventricle, lateral to the fastigial nucleus. It receives its afferent supply from the anterior lobe of the cerebellum and sends output via the superior cerebellar peduncle to the red nucleus.
modulates muscle stretch reflexes of proximal limb muscles[WP]
One of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid.
Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356].
FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies.
Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present.
note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye
The middle of the face including the nose and its associated bony structures[MW].
this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface.
Joint cavity shared by all the joints of the elbow. The elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis. All three share a joint cavity which is highly sinuated/scalloped/coved. Joint spaces of the elbow summarizes the joint cavity shared by all three adjoining joints of the elbow joint.
The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone.
One of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP].
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
A muscle of the tympanic cavity that attaches to an auditory ossicle.
attenuate low-frequency sounds, reduce masking of high-frequency sounds by low-frequency sounds, frequency-selection filter
Small cavity surrounding the bones of the middle ear.
A blood vessel that is part of a tympanic cavity [Automatically generated definition].
anatomical cavity of middle ear blood vessel
blood vessel of anatomical cavity of middle ear
blood vessel of middle ear anatomical cavity
middle ear anatomical cavity blood vessel
A nerve that is part of a tympanic cavity [Automatically generated definition].
nerve of anatomical cavity of middle ear
An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches.
Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO]
EMAPA also includes a distinct pouch endoderm
The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389]
A vasculature that is part of a iris [Automatically generated definition].
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633
Any of the layers of the myocardium. Example: compact layer, trabecular layer.
The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA].
The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO]
Outer dense layer of the myocardium uniting the epicardium and myocardium[MP].
A myocardium trabecular layer that is part of a cardiac ventricle.
The outer layer the ventricular myocardium, muscle fibers are arranged in a compact form and involved the entire ventricle.
The outer layer the ventricular myocardium, muscle fibers are arranged in a compact form and involved the entire ventricle.[TAO]
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
Cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo.
cytoarchitectural part of the cerebellar cortex
The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. The nucleus is divided into three parts, from rostral to caudal (top to bottom in humans): * The mesencephalic nucleus * The chief sensory nucleus (or pontine nucleus or main sensory nucleus or primary nucleus) * The spinal trigeminal nucleus[WP].
TODO - check ZFA link. note this is part of medulla in ZFA, but we do not include this link here as it leads to inconsistencies
Missing definition for term UBERON:0004133. Please replace it using linked reference.
In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO].
TODO - ensure definition works across species.
The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments.
The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules.
TODO - check for applicability across species
The somitomeric trunk muscle is derived from somitomeric mesoderm. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle. An example of this process is found in Mus musculus.[GO].
TODO - find N+S conditions. SMT & develops_from somite is not specific enough (all SMT develops_from somite)
The first recognizable structure derived from the heart field.
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
The outflow tract septum is a partition in the outflow tract.
The outflow tract is the portion of the heart through which blood flows into the arteries.
Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]
The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.
the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles.
Vein of heart that drains the myocardium.
A heart valve located between the ventricle and bulbus arteriosus.
Vestigial cardiac valve which is continuous with the valve of the inferior vena cava[FMA].
A cardiac chamber surrounds an enclosed cavity within the heart.
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
The bulbus arteriosus is an elastic heart chamber[GO]. Multi-tissue structure that consists of three layers and through which the blood exits the heart. The bulbus arteriosus is a pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches[ZFA].
A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]
replaces conus arteriosis in cartilaginous fish
Endocardial cushions project into the atrial canal, and, meeting in the middle line, unite to form the septum intermedium which divides the canal into two channels, the future right and left atrioventricular orifices[Gray's via WP].
In the developing heart, the cavity of the primitive atrium becomes subdivided into right and left chambers by a septum, the septum primum, which grows downward into the cavity. The increasingly smaller gap below it (before it fuses with the endocardial cushion) is known as the ostium primum. The septum primum eventually fuses with the endocardial cushion, closing the ostium primum off completely. Meanwhile, perforations appear in the superior part of the septum primum, forming the ostium secundum. This will eventually form part of the fossa ovalis.
The first of the two membranous sheets which partially separate the two atria during embryonic development. [TFD][VHOG]
Missing definition for term UBERON:0004155. Please replace it using linked reference.
The second of the two membranous sheets which partially separate the two atria during embryonic development. [TFD][VHOG]
The septum secundum, semilunar in shape, grows downward from the upper wall of the atrium immediately to the right of the primary septum and ostium secundum. Shortly after birth it fuses with the septum primum, and consequently the foramen ovale is closed, but sometimes the fusion is incomplete and the upper part of the foramen remains patent. The limbus fossae ovalis denotes the free margin of the septum secundum.
Missing definition for term UBERON:0004159. Please replace it using linked reference.
An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium.
Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum
The pulmonary myocardium is the myocardial tissue present in the pulmonary vein.
A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves.
The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707].
It has been hypothesized that Haikouella must have been powered by branchiomeric muscles, as in living craniates, rather than by water moving through the pharynx via ciliary currents, as in lancelets[http://icb.oxfordjournals.org/content/42/4/743.full]
Missing definition for term UBERON:0004166. Please replace it using linked reference.
check ZFA structures superior reticular formation medial column & tegmentum
The region of the cerebral cortex covering the basal surface of the frontal lobes; this region normally controls emotion and decision making.
The band of nerve fibers which cross the midline of the spinal cord ventral to the central canal and posterior grey commissure[MP]. The anterior (or ventral) white commissure, also known as the alba anterior medullae spinalis, is a bundle of nerve fibers which cross the midline of the spinal cord just anterior to the gray commissure. A N4 fibers and C fibers carrying pain sensation in the spinothalamic tract contribute to this commissure, as do fibers of the anterior corticospinal tract, which carry motor signals from the primary motor cortex[WP].
anterior white commissure of spinal cord
commissura alba anterior medullae spinalis
The trigeminothalamic tract is one of the major routes of nociceptive and temperature signaling from the face.
Axon tract that carries efferent (outgoing) action potentials from the cell body in the pons towards target cells in the spinal cord.
Axon tract that carries efferent (outgoing) action potentials from the cell body in the medulla towards target cells in the spinal cord[GO].
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals.
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
The external genitalia are the outer sex organs, such as the penis or vulva in mammals.
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
The nonstriated, involuntary muscle tissue located in the wall of the aorta.
A saclike structure of the prostate gland, comprised of at least three cell layers: an innermost layer of secretory columnar luminal epithelium, a middle layer of squamous basal epithelium that also contains neuroendocrine cells, transit amplifying cells, and stem cells, and an outer layer of smooth muscle intermixed with other stromal cells.
the muscle layer is implicitly treated as outside the acinus
Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]
The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts.
The solid cord of epithelial cells that emerges from the mammary bud and grows down from the primary mammary mesenchyme and into a second stromal compartment, the fat pad precursor, beneath the dermis.
in female mouse embryos, the primary mammary cord (aka 'mammary sprout') is formed between E15.5 and E16.5; once the primary cord reaches the adipocytes of the fat pad (around E16), it begins to branch in a characteristic dichotomous fashion to form the initial ductal tree
The embryonic vessels grow through the layer to come in close contact with the maternal blood supply.
blood vessel of labyrinthine layer of placenta
labyrinthine layer of placenta blood vessel
The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland.
TODO - check also FMA Stroma of glandular part of prostate
A portions of the gut that is derived from endoderm.
The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer.
NIF divides this into main and accessory
olfactory bulb main mitral cell body layer
The Harderian gland is an anterior orbital gland usually associated with the nictitating membrane, and produces and secretes a variety of substances to the eye, depending upon the species[GO].
In mouse the HG appears in the posterior part of eye region, in the form of nonluminated tubules between the sixteenth and eighteenth days of gestation. At birth it is still not differentiated histologically. In birds the HG originates from the conjunctival epithelium at a late embryonic stage. In the English sparrow, Passer domesticus (incubation period of about 13 days), it appears between the seventh and the eighth days of incubation. In the chick embryo (incubation period of about 21 days) it originates between the eleventh and the twelfth days.[PMID:9156609]
In the limbless, burrowing amphibian Apoda (Caecilians) the harderian gland is very large, filling much of the orbit and lubricating a retractile sensory tentacle rather than the eye (Walls, 1942; Wolff, 1948).
In mammals, the gland excretes an oily substance used to preen the fur[WP]
In some animals it acts as an accessory to the lacrimal gland, secreting fluid that eases movement of the nictitating membrane[WP]
The functions attributed to the gland are many and diverse. Amongst these, it has been held to be a site of immune responses, a source of thermoregulatory lipids, a source of pheromones, a photoprotective organ and part of a retinal-pineal axis. It is arguably the last remaining large organ of widespread dis- tribution among the vertebrates to which we cannot confidently ascribe a confirmed function.
The harderian gland may be compound tubular (MacLeod, 1880; Paule, 1957) or compound tubuloacinar/tubuloalveolar (Aureli, 1957; Hoffman, 1971).
The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.
TODO - check - GO says outer, BTO says inner. Make this a superclass
The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus.
The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.
A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water.
ascending limb thin segment of loop of Henle
loop of Henle ascending limb thin segment
Long nephrons are associated with juxtamedullary glomeruli and extend to the inner medulla.
Short nephrons are associated with mid-cortical glomeruli, and have no short ascending limb, so the limb is situated in the outer medulla.
The S1 portion is the initial portion of the proximal convoluted tubule and is responsible for avid reabsorption of water and solutes[GO].
The S2 portion of the tubule is involved in reabsorption of water and sodium chloride[GO].
The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron.
The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron.
Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.
not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)
The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules.
The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules.
The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex.
The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla.
The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla.
The long descending thin limb bend is a part of the descending thin limb of a long nephron that lies beyond the prebend segment.
The prebend segment is a part of the descending thin limb that lies before the bend and exhibits robust sodium chloride reabsorption.
Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron.
The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]
The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.
note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap
The nephron epithelium is a tissue that covers the surface of a nephron.
The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus.
Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]
A nerve that is part of a hindlimb stylopod [Automatically generated definition].
A nerve that is part of a back [Automatically generated definition].
A nerve that is part of a lower arm [Automatically generated definition].
A nerve that is part of a forelimb stylopod [Automatically generated definition].
A nerve that is part of a lower leg [Automatically generated definition].
A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition].
A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition].
MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa
A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition].
A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition].
A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition].
A muscular coat that is part of a vas deferens [Automatically generated definition].
TODO - check MA and FMA classes mean the same thing
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition].
smooth muscle tissue of gastrointestinal system
The smooth muscle tissue surrounding the urothelium of the kidney pelvis.
A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition].
A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition].
involuntary muscle of neck of urinary bladder
involuntary muscle of urinary bladder neck
neck of urinary bladder involuntary muscle
neck of urinary bladder non-striated muscle
neck of urinary bladder smooth muscle tissue
non-striated muscle of neck of urinary bladder
non-striated muscle of urinary bladder neck
smooth muscle of neck of urinary bladder
smooth muscle tissue of neck of urinary bladder
smooth muscle tissue of urinary bladder neck
urinary bladder neck non-striated muscle
urinary bladder neck smooth muscle tissue
A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum involuntary muscle
anal part of perineum non-striated muscle
anal part of perineum smooth muscle tissue
involuntary muscle of anal part of perineum
non-striated muscle of anal part of perineum
smooth muscle tissue of anal part of perineum
A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition].
smooth muscle tissue of lymphatic vessel
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
involuntary muscle of lower respiratory tract
lower respiratory tract involuntary muscle
lower respiratory tract non-striated muscle
lower respiratory tract smooth muscle tissue
non-striated muscle of lower respiratory tract
smooth muscle of lower respiratory tract
smooth muscle tissue of lower respiratory tract
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
A portion of smooth muscle tissue that is part of a mammary gland [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
Smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition].
A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition].
A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition].
A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition].
A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition].
A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition].
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
A bone that is part of the dorsal region of an animal.
this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93
A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids.
A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids.
A bone that is part of a forelimb stylopod [Automatically generated definition].
May be merged into humerus. See: https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376
A bone that is part of a lower leg [Automatically generated definition].
bone of inferior member middle limb segment
bone of intermediate segment of free lower limb
bone of lower extremity middle limb segment
bone of middle limb segment of hind limb
bone of middle limb segment of inferior member
bone of middle limb segment of lower extremity
bone organ of hind limb middle limb segment
bone organ of hindlimb middle limb segment
bone organ of inferior member middle limb segment
bone organ of intermediate segment of free lower limb
bone organ of lower extremity middle limb segment
bone organ of middle limb segment of hind limb
bone organ of middle limb segment of hindlimb
bone organ of middle limb segment of inferior member
bone organ of middle limb segment of lower extremity
bone organ of zeugopod of inferior member
bone organ of zeugopod of lower extremity
hind limb middle limb segment bone organ
inferior member middle limb segment bone
inferior member middle limb segment bone organ
intermediate segment of free lower limb bone
intermediate segment of free lower limb bone organ
lower extremity middle limb segment bone
lower extremity middle limb segment bone organ
middle limb segment of hind limb bone organ
middle limb segment of hindlimb bone organ
middle limb segment of inferior member bone
middle limb segment of inferior member bone organ
middle limb segment of lower extremity bone
middle limb segment of lower extremity bone organ
Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition].
Any muscle organ that is part of a skin of body [Automatically generated definition].
review as part of general integumentary system review - part of skin, or more generally, integumental system
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
Any muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition].
Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition].
the FMA class 'muscle of arm' belongs here, do not move
See notes on UBERON:0001460 for possible terminological confusion over term 'arm'
Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition].
the FMA class 'muscle of leg' belongs here, do not move[cjm]
See notes on UBERON:0000978 for possible terminological confusion over term 'leg'
A blood vessel that is part of a hindlimb stylopod [Automatically generated definition].
A blood vessel that is part of a back [Automatically generated definition].
A blood vessel that is part of a lower arm [Automatically generated definition].
A blood vessel that is part of a forelimb stylopod [Automatically generated definition].
A blood vessel that is part of a lower leg [Automatically generated definition].
A zone of skin that is part of a hindlimb stylopod [Automatically generated definition].
A zone of skin that is part of a forelimb stylopod [Automatically generated definition].
A zone of skin that is part of a lower leg [Automatically generated definition].
A myocardium that is part of a outflow tract [Automatically generated definition].
(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]
PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)
A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition].
A portion of connective tissue that is part of a back [Automatically generated definition].
A portion of connective tissue that is part of a lower arm [Automatically generated definition].
A portion of connective tissue that is part of a forelimb stylopod [Automatically generated definition].
A portion of connective tissue that is part of a lower leg [Automatically generated definition].
A pericardium that is part of a outflow tract [Automatically generated definition].
A cranial suture that is part of a cartilaginous joint [Automatically generated definition].
articulatio cartilaginea cranial sutures
articulatio cartilaginea cranial sutures set
articulatio cartilaginea suture of cranium
cranial suture of articulatio cartilaginea
cranial sutures of articulatio cartilaginea
cranial sutures set of articulatio cartilaginea
cranial sutures set of cartilaginous joint
cranium suture of articulatio cartilaginea
suture of cranium of articulatio cartilaginea
suture of cranium of cartilaginous joint
A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle
chorioid plexus of cerebral hemisphere epithelium of lateral ventricle
choroid plexus epithelial tissue of lateral ventricle
choroid plexus epithelium of lateral ventricle
epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle
epithelial tissue of choroid plexus of lateral ventricle
epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle
epithelium of choroid plexus of lateral ventricle
lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue
lateral ventricle chorioid plexus of cerebral hemisphere epithelium
lateral ventricle choroid plexus epithelial tissue
lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere
lateral ventricle epithelial tissue of choroid plexus
lateral ventricle epithelium of chorioid plexus of cerebral hemisphere
lateral ventricle epithelium of choroid plexus
lateral ventricle choroid plexus epithelium
A choroid plexus epithelium that is part of a third ventricle [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue of third ventricle
chorioid plexus of cerebral hemisphere epithelium of third ventricle
choroid plexus epithelial tissue of third ventricle
choroid plexus epithelium of third ventricle
epithelial tissue of chorioid plexus of cerebral hemisphere of third ventricle
epithelial tissue of choroid plexus of third ventricle
epithelium of chorioid plexus of cerebral hemisphere of third ventricle
epithelium of choroid plexus of third ventricle
third ventricle chorioid plexus of cerebral hemisphere epithelial tissue
third ventricle chorioid plexus of cerebral hemisphere epithelium
third ventricle choroid plexus epithelial tissue
third ventricle epithelial tissue of chorioid plexus of cerebral hemisphere
third ventricle epithelial tissue of choroid plexus
third ventricle epithelium of chorioid plexus of cerebral hemisphere
third ventricle epithelium of choroid plexus
third ventricle choroid plexus epithelium
A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition].
chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle
chorioid plexus of cerebral hemisphere epithelium of fourth ventricle
choroid plexus epithelial tissue of fourth ventricle
choroid plexus epithelium of fourth ventricle
epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle
epithelial tissue of choroid plexus of fourth ventricle
epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle
epithelium of choroid plexus of fourth ventricle
fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue
fourth ventricle chorioid plexus of cerebral hemisphere epithelium
fourth ventricle choroid plexus epithelial tissue
fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere
fourth ventricle epithelial tissue of choroid plexus
fourth ventricle epithelium of chorioid plexus of cerebral hemisphere
fourth ventricle epithelium of choroid plexus
fourth ventricle choroid plexus epithelium
A muscle that is part of the eye region.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart.
It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]
A nerve that is part of a parasympathetic nervous system [Automatically generated definition].
An endothelium that is part of a glomerular capillary.
A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle of lymph vessel of respiratory system
respiratory system lymphatic vessel smooth muscle
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle tissue of blood vessel of respiratory system
respiratory system blood vessel smooth muscle
In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans.
A phalanx located between proximal and distal phalanges.
consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit
Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin
in some groups such as whales, there are multiple intermediate phalanges
Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)
Upper part of skull, consisting of parietals, frontals, post-parietals, and in some species the squamosal and a portion of the alisphenoid.
We follow http://www.ncbi.nlm.nih.gov/pubmed/11523816 (Morriss-Kay) in definingenumerating the components of the skull vault. Note that there is a conflict with Kardong; e.g. in fig 7.10, Kardong places the squamosal in the temporal series. We cannot place the vault as entirely part of the dermatocranium as it has a small splanchnocranium contribution and a sclerotomal contribution
The earliest tetrapods arose from rhipidistian ancestors and retained many of their skull features, including most of the bones of the dermatocranium.[well established][VHOG]
Terminology notes. we include calvarium as a synonym, but Gray's Anatomy's list includes the Ethmoid and Sphenoid bone in the Calvaria. Some books (and HPO) state that calvaria consists of just the frontal bone, parietal bone, temporal bone, and occipital bone. Note vault may not be precisely equivalent to calvaria
small pharyngeal arch and sclerotomal contribution
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]
a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)]
part_of embryo in EHDAA2 - note differences in humans
The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP].
(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]
VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826
primitive streak - blastopore - germ ring
PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139
Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition.
distinction between trophectoderm and trophoblast unclear/inconsistent in many sources
The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]
(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG]
BTO has this has part of the trophoblast
ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106
An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Early outgrowth of presumptive limb.[AAO]
developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm
The embryonic structure that gives rise to the corneal ectoderm.
Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
note that media, dorsal fins etc have AERs.
Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]
Proliferative region that is part of the developing fin fold or fin.[TAO]
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold
maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries.
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP].
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta.
derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast.
Blood vessel that is connected to the yolk sac.
A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].
Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]
The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
Vascular network that is connected to the yolk sac.
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
A bone that is part of a fin [Automatically generated definition].
A metaphysis that is in the proximal side of a diaphysis.
An epiphysis that is on the proximal side of the bone.
The collection of all skeletal elements in an individual limb.
Skeletal subdivision that is part of the limb.[VSAO]
EHDAA2 considers hip and shoulder joints part of limb skeleton.
An epiphysis that is part of a humerus [Automatically generated definition].
An epiphysis that is part of a tibia [Automatically generated definition].
An epiphysis that is part of a femur [Automatically generated definition].
An epiphysis that is part of a phalanx of a manus [Automatically generated definition].
An epiphysis that is part of a fibula [Automatically generated definition].
An epiphysis that is part of a metatarsal bone [Automatically generated definition].
An epiphysis that is part of a metacarpal bone [Automatically generated definition].
A portion of bone tissue that is part of a epiphysis [Automatically generated definition].
A portion of bone tissue that is part of a proximal epiphysis [Automatically generated definition].
The upper extremity of the humerus (proximal humerus) consists of a large rounded head joined to the body by a constricted portion called the neck, and two eminences, the greater and lesser tubercles.
A proximal epiphysis that is part of a femur [Automatically generated definition].
A proximal epiphysis that is part of a phalanx of manus [Automatically generated definition].
A proximal epiphysis that is part of a metatarsal bone [Automatically generated definition].
A proximal epiphysis that is part of a metacarpal bone [Automatically generated definition].
An epiphysis that is part of a phalanx [Automatically generated definition].
A proximal epiphysis that is part of a phalanx [Automatically generated definition].
One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain.
Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO]
in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required
A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra.
In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar)
it's not clear if the XAO class belongs here or below
A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted].
A metapodium region that is part of a manus.
Note that along with FMA we treat this as a limb segment rather than a purely skeletal element
Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
Mesopodial segment of the pes, including the tarsal skeleton and associated tissues.
this term refers to the limb segment. See also: tarsal bones and tarsal skeleton
MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin).
Sum of all sensory systems in an organism.
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376
Any collection of muscles that is part of a body wall [Automatically generated definition].
define generically to encompass both vertebrates and invertebrates
Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition].
Any collection of muscles that is part of a thorax [Automatically generated definition].
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
Any collection of muscles that is part of a neck [Automatically generated definition].
Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition].
see notes on UBERON:0000978 for possible confusion over the term 'leg'. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class)
The collection of muscles that acts on the pharynx.
Any collection of muscles that is part of a back [Automatically generated definition].
Any collection of muscles that is part of a pelvic girdle [Automatically generated definition].
A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles.
Any collection of muscles that is part of a face.
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
Any collection of muscles that is part of an arm [Automatically generated definition].
The collection of muscles that form attachments to the hip skeleton.
The collection of muscles that form attachments to the shoulder skeleton.
The collection of muscles that are part of the larynx.
currently defined by location rather than attachment
Any collection of muscles that is part of a trunk [Automatically generated definition].
Any collection of muscles that is part of a limb [Automatically generated definition].
Any collection of muscles that is part of a forelimb [Automatically generated definition].
Any collection of muscles that is part of a hindlimb [Automatically generated definition].
Any collection of muscles that is part of a lower arm [Automatically generated definition].
Any collection of muscles that is part of a foot [Automatically generated definition].
Any collection of muscles that is part of a manus [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging.
A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition].
interatrial septum cardiac muscle tissue
cardiac muscle tissue of interatrial septum
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Note placement of MA class based on parthood relationship
A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a deltoid [Automatically generated definition].
skeletal muscle tissue of deltoid muscle
A portion of skeletal muscle tissue that is part of a trapezius [Automatically generated definition].
skeletal muscle tissue of trapezius muscle
A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition].
A portion of smooth muscle tissue that is part of a terminal bronchiole [Automatically generated definition].
smooth muscle tissue of terminal bronchiole
A portion of smooth muscle tissue that is part of a respiratory bronchiole [Automatically generated definition].
smooth muscle tissue of respiratory bronchiole
A muscle that is attached to a vertebra of the vertebral column.
A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition].
A vasculature that is part of a muscle organ [Automatically generated definition].
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of trabecula carnea of right ventricle
A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
cardiac muscle tissue of trabecula carnea of left ventricle
The thickened ridge of bone that contains the tooth sockets on the maxilla.
In humans, the tooth-bearing bones are the maxilla and the mandible. The mineral content of alveolar bone is mostly hydroxyapatite, which is also found in enamel as the main inorganic substance
A projection or outgrowth of tissue from a larger body or organ.
should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]
Anatomical projection that is composed of bone tissue.
A testis that is in the left side of the genitalia [Automatically generated definition].
A testis that is in the right side of the genitalia [Automatically generated definition].
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451
A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.
A vascular network consisting of blood vessels.
A kidney that is part of a left side of organism [Automatically generated definition].
A kidney that is part of a right side of organism [Automatically generated definition].
The layer of secretory cells which lines the epididymis.
An eye that is part of a left side of organism [Automatically generated definition].
An eye that is part of a right side of organism [Automatically generated definition].
An artery that is part of a digit [Automatically generated definition].
check part_of - do we need term for digit + metacarpal/tarsal bones?
A digital artery that is part of a forelimb [Automatically generated definition].
A digital artery that is part of a hindlimb [Automatically generated definition].
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
The part of the cardiovascular system consisting of all arteries.
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
The part of the venous system that drains the general body tissues[Kardong].
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
The capsule surrounding the inner ear mechanism.
developmental relationships need to be checked
Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO]
The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG]
relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO]
relationship loss: part_of otic and occipital (AAO:0000993)[AAO]
Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG]
in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235, DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart.
The blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism.
The connective tissue that surrounds the spleen.
The epithelial lining of the luminal space of the urinary bladder.
5-7 cell layers thick in contracted bladder, 2-3 cells thick in distended bladder; lines renal pelvis, ureters, bladder, most of urethra but not distal urethra
transitional epithelium of urinary bladder
The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein.
should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP]
The process projecting downward from either side of the sphenoid bone, in vertebrates divided into two plates, an inner and an outer (sometimes called the lateral and medial); the posterior nares pass through the space, called the pterygoid fossa, between the processes.
TODO - check AAO:0000521-pterygoid and MA:0001471-pterygoid bone. MA also has 'inner plate of pterygoid process' as a syn for MA:0001471, FMA has lateral/medial plates. Seems likely inner = lateral (see MP:0004452).
Process that projects from posterior margin of commissure into subocular space.[AAO]
relationship loss: part_of anterior quadratocranial commissure (AAO:0010061)[AAO]
processus pterygoideus ossis sphenoidalis
A keratinized stratified squamous epithelium that is part of a tongue.
The body or shaft of the humerus is almost cylindrical in the upper half of its extent, prismatic and flattened below, and has three borders and three surfaces.
An anatomical wall that is part of an aorta, enclosing the luminal space.
The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers.
A muscular coat that is part of a seminal vesicle [Automatically generated definition].
The membranous portion of the wall between the two lower chambers of the heart.
The membranous septum is the upper part of ventricular septum[GO:0003149].
membranous part of interventricular septum
membranous portion of interventricular septum
pars membranacea (septi interventricularis)
pars membranacea septi interventricularis
The muscular portion of the wall between the two lower chambers of the heart.
The muscular septum is the lower part of the ventricular septum[GO]
muscular part of interventricular septum
pars muscularis (septi interventricularis)
pars muscularis septi interventricularis
One of: the 4th ventricle median or lateral apertures.
A nerve root that extends_fibers_into a trigeminal nerve.
A nerve root that extends_fibers_into a facial nerve.
A nerve root that extends_fibers_into a hypoglossal nerve.
The molecular layer of the dentate gyrus that is bounded by the pial surface superficially and the dentate gyrus granule cell layer deep. It is divided into 2 or more sublayers.
The sensory system for the sense of balance.
The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system].
FMA and NIF have no part information for this class. This is a GAT in FMA
The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane.
we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei'
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
An epithelium that is part of an external naris [Automatically generated definition].
The specialized epithelial layer covering the entire Peyer's patch, including both the follicular and interfollicular areas and forming part of the gut-associated lymphoid tissue.
An epithelium that is part of a Harderian gland [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
Area of the Peyer's patch where B cells proliferate and differentiate into plasma cells.
An endothelium that is part of a vena cava [Automatically generated definition].
An endothelium that is part of a outflow tract [Automatically generated definition].
It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]
DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)
An endothelium that is part of an arterial system [Automatically generated definition].
An endothelium that is part of a venous system [Automatically generated definition].
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
respiratory system blood vessel endothelium
TODO. http://www.ncbi.nlm.nih.gov/pubmed/8167659
Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO]
General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here
A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches.
TODO - check relationship to bulbus arteriosus
A chordate developmental stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities.
Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)
An appendage that is part of an appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues.
While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]
DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule.
The subdivision of the laminated olfactory cortex with only three main layers that receive monosynaptic input from the olfactory bulb via the lateral olfactory tract; it is located bilaterally in the ventrolateral forebrain and is commonly divided into anterior and posterior regions.
Piriform cortical regions are present in the brains of amphibians, reptiles and mammals. The piriform cortex is among three areas that emerge in the telencephalon of amphibians, situated caudally to a dorsal area, which is caudal to a hippocampal area. Farther along the phylogenic timeline, the telencephalic bulb of reptiles as viewed in a cross section of the transverse plane extends with the archipallial hippocampus folding toward the midline and down as the dorsal area begins to form a recognizable cortex. As mammalian cerebrums developed, volume of the dorsal cortex increased in slightly greater proportion, as compared proportionally with increased overall brain volume, until it enveloped the hippocampal regions. Recognized as neopallium or neocortex, enlarged dorsal areas envelop the paleopallial piriform cortex in humans and Old World monkeys. Among taxonomic groupings of mammals, the piriform cortex and the olfactory bulb become proportionally smaller in the brains of phylogenically younger species. The piriform cortex occupies a greater proportion of the overall brain and of the telencephalic brains of insectivores than in primates. The piriform cortex continues to occupy a consistent albeit small and declining proportion of the increasingly large telencephalon in the most recent primate species while the volume of the olfactory bulb becomes less in proportion
A nerve in the head that carries signals from the cochlea of the inner ear to the brain. It is part of the vestibulocochlear nerve, the 8th cranial nerve which is found in higher vertebrates; the other portion of the 8th cranial nerve is the vestibular nerve which carries spatial orientation information from the semicircular canals. The cochlear nerve is a sensory nerve, one which conducts to the brain information about the environment, in this case acoustic energy impinging on the tympanic membrane. The cochlear nerve arises from within the cochlea and extends to the brainstem, where its fibers make contact with the cochlear nucleus, the next stage of neural processing in the auditory system[WP].
vestibulocochlear VIII nerve cochlear component
vestibulocochlear nerve cochlear component
Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
A metameric segment of the central nervous system.[ZFA]
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
An organ subunit that is part of a hindbrain [Automatically generated definition].
We explicitly merge the NCITA terms here
Glomerulus of the mature vertebrate kidney, or metanephros.
A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition].
Juxtaglomerular apparatus of the mature vertebrate kidney, or metanephros.
juxtaglomerular apparatus of metanephros
The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment.
a glomus differs from a glomerulus in that each vascular glomus services several tubules
Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO]
The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG]
GO treats glomus and pronephric glomerulus differently
PMID:9806915 Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].
Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]
Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]
relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]
Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]
In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248
A tooth- or denticle-covered plate which is attached to the sphenoid stem[Palaeos].
Azygous, dermal bone of intramembranous origin that underlies the ventral surface of the braincase in anurans and salamanders. In caecilians, the parasphenoid and other bones are fused to form the Os basale.[AAO]
Dermal bone that forms part of the base of the skull and the lateral walls of the braincase through its ascending processes. It may articulate with the vomer anteriorly, the prootics and exoccipitals laterally, and the basioccipital posteriorly. The parasphenoid is an elongate median bone.[TAO]
relationship loss: overlaps parasphenoid-basioccipital joint (TAO:0001832)[TAO]
relationship loss: overlaps parasphenoid-pterosphenoid joint (TAO:0002217)[TAO]
A small, circular, white spot (approximately 2-3 mm across) on the surface of the yellow yolk of an egg that has been laid. The nucleus of the egg is in the germinal disc.
A layer of cells formed at one pole of macrolecithal eggs such as the yolky egg of birds. The yolk prevents the division from taking place through the egg, resulting in meroblastic cleavage during the many cleavage divisions. At the animal pole (containing less yolk than the vegetal pole), the zygote divides and subdivides, forming the blastoderm, which gradually spreads around the yolk and forms the embryo. The blastoderm is composed of two layers, the epiblast and the hypoblast, which enclose the fluid-filled blastocoel cavity.
Skeletal element that consists of the scapula and the coracoid[VSAO, modified].
todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present
Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO]
Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO]
either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos]
relationship loss: part_of scapular area (AAO:0000935)[AAO]
ZFA defines as precursor to scapula and coracoid. Cartilage in TAO
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
taken from version of VSAO used in TAO and used directly in Uberon
Dermis-derived entity that is made of skeletal tissue.
An evagination of the terminal portion of the intestine that is capable of secreting high concentrations of excess sodium chloride.
shark liver produces copious amounts of urea, making the shark hyperosmotic to seawater, & thus a shark acts like a fresh water fish, constantly gaining water. Excess salts are concentrated by the rectal gland and secreted
An organ for excreting excess salts. It is found in elasmobranchs, seabirds, and some reptiles.[WP].
In sharks, salt glands are found in the rectum, but in birds and reptiles, they are found in or on the skull, in the area of the eyes, nostrils or mouth. In crocodiles, the salt is excreted through the tongue. Such glands work by active transport via sodium-potassium pump that moves salt from the blood into the gland, where it can be excreted as a concentrated solution. Salt glands function to keep salt balance, and allow marine vertebrates to drink seawater
A salt gland located in the cranium or head region.
A gland that is part of an anal canal [Automatically generated definition].
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
cartiligionous skeletal structure of skull
Replacement bone tissue that forms within cartilage[VSAO, modified].
the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Tooth that is attached to the vomer.[TAO]
relationship type change: OBO_REL:part_of vomer (TAO:0000308) CHANGED TO: attaches_to vomer (UBERON:0002396)[TAO]
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular.
Do not manually classify under here - bones are automatically classified
Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified].
Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA].
The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis].
Anatomical system that consists of all the joints of the body.
Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP].
One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Opening between the nasal cavity and the nasopharynx.[AAO]
The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]
Fish don't have choanae, instead they have two pairs of external nostrils
In addition to tetrapods, the lungfish has internal nostrils too. In tetrapods the exhalant nostril (choana) empties into the buccal cavity.
The tarsi (tarsal plates) are two comparatively thick, elongated plates of dense connective tissue, about 2.5 cm. in length; one is found in each eyelid, and contributes to its form and support. They directly abut the lid margins.
In most taxa (birds, mammals, lizards), the tarsal plate is described as a dense, fibrous connective tissue, possibly including cartilage, present within one or both of the upper and lower eyelids (Gau- thier et al., 1988; Rieppel, 2000). In humans, the tarsal plate of the upper eyelid is composed of collagens types I, III, and V, as well as glycosaminogly- cans (chondroitin sulphate 4 and 6), aggrecan, and cartilage oligomeric matrix proteins but lacks collagen type II as well as chondrocytes (Milz et al., 2005). Thus, for humans, the upper tarsal plate represents neither a truly fibrous nor a truly cartilagi- nous element but instead one that is composed of a unique transitional tissue (Milz et al., 2005). In many birds, lizards, and Sphenodon (the tuatara), the upper eyelid has lim- ited mobility and a putative tarsal plate is instead found within the lower eyelid (Underwood, 1970; Gau- thier et al., 1988).
A submucosa that is part of a respiratory system [Automatically generated definition].
A submucosa that is part of a larynx [Automatically generated definition].
A lamina propria that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius lamina propria mucosa
lamina propria mucosa of apparatus respiratorius
lamina propria mucosa of respiratory system
lamina propria of apparatus respiratorius
respiratory system lamina propria mucosa
A lamina propria that is part of a gastrointestinal system.
A lamina propria that is part of a gallbladder [Automatically generated definition].
A serous membrane that is part of a digestive system [Automatically generated definition].
serous membrane of gastrointestinal system
A serous membrane that is part of a gallbladder [Automatically generated definition].
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
anatomical wall of lower chamber of heart
The mucous membrane lining the respiratory tract.
TODO - split respiratory tract mucosa from respiratory system mucosa
mucosa of organ of apparatus respiratorius
mucous membrane of apparatus respiratorius
A mucosa that is part of a gastrointestinal system.
The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
An urothelium that is part of a urethra [Automatically generated definition].
The epithelial lining of the luminal space of the kidney pelvis.
transitional epithelium of kidney pelvis
A mucous gland that is part of a larynx [Automatically generated definition].
A mucous gland that is part of the skin.
The thymic connective tissue which extends into the parenchyma.
A secretion that is part of a endocrine pancreas [Automatically generated definition].
A secretion that is part of a exocrine pancreas [Automatically generated definition].
A secretion that is part of a esophagus [Automatically generated definition].
A secretion that is part of a pancreas [Automatically generated definition].
A bodily secretion that is produced by the prostate gland.
Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline.
A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20-30% of the volume of the semen along with spermatozoa and seminal vesicle fluid [Wikipedia:Prostate#Secretions]
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
An epithelium that is part of a uterine cervix [Automatically generated definition].
The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium
The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi.
An epithelium that is part of a penis [Automatically generated definition].
An epithelium that is part of a oviduct [Automatically generated definition].
in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label
columnar epithelium of the fallopian tube
An epithelium that is part of a seminal vesicle [Automatically generated definition].
An epithelium that is part of a vas deferens [Automatically generated definition].
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
An epithelium that is part of a digestive system [Automatically generated definition].
epithelial tissue of gastrointestinal system
gastrointestinal system epithelial tissue
An epithelium that is part of a salivary gland [Automatically generated definition].
The cellular avascular layer of the renal tubule luminar surfaces.
See https://github.com/obophenotype/uberon/issues/1305
An epithelium that is part of an endometrium [Automatically generated definition].
In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial)
epithelium of tunica mucosa of endometrium
The stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule.
epithelial tissue of seminiferous tubule
epithelial tissue of seminiferous tubule of testis
epithelium of seminiferous tubule of testis
An epithelium that is part of a upper respiratory tract [Automatically generated definition].
epithelial tissue of upper respiratory tract
upper respiratory tract epithelial tissue
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
epithelial tissue of lower respiratory tract
lower respiratory tract epithelial tissue
An epithelium that is part of a larynx [Automatically generated definition].
composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0]
An epithelium that is part of a lacrimal gland [Automatically generated definition].
The cellular avascular layer of the kidney luminar surfaces.
Any epithelium that lines one of the bile ducts.
The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium.
The epithelial layer of the alveoli[MP]. The layer of cells covering the lining of the tiny air sacs at the end of the bronchioles[BTO].
An epithelium that is part of a extrahepatic bile duct [Automatically generated definition].
epithelial tissue of extrahepatic bile duct
extrahepatic bile duct epithelial tissue
An epithelium that is part of a intrahepatic bile duct [Automatically generated definition].
epithelial tissue of intrahepatic bile duct
intrahepatic bile duct epithelial tissue
A medulla that is part of a thyroid [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
respiratory system skeletal muscle tissue
skeletal muscle of apparatus respiratorius
skeletal muscle tissue of apparatus respiratorius
skeletal muscle tissue of respiratory system
A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition].
Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal
A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum skeletal muscle tissue
skeletal muscle of anal part of perineum
skeletal muscle tissue of anal part of perineum
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips
Smooth muscle tissue in all or part of a hepatic duct.
A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition].
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius arterial endothelium
apparatus respiratorius artery endothelium
apparatus respiratorius endothelium of artery
arterial endothelium of apparatus respiratorius
arterial endothelium of respiratory system
artery endothelium of apparatus respiratorius
artery endothelium of respiratory system
endothelium of artery of apparatus respiratorius
endothelium of artery of respiratory system
respiratory system endothelium of artery
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius endothelium of vein
apparatus respiratorius vein endothelium
apparatus respiratorius venous endothelium
endothelium of vein of apparatus respiratorius
endothelium of vein of respiratory system
vein endothelium of apparatus respiratorius
venous endothelium of apparatus respiratorius
venous endothelium of respiratory system
An endothelium that is part of a lymph node [Automatically generated definition].
The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall.
endothelium of trunk of systemic arterial tree
trunk of systemic arterial tree endothelium
An endothelium that is part of the cardiovascular system.
A mesentery that is part of a digestive system [Automatically generated definition].
A connective tissue that surrounds a skeletal muscle tissue.
connective tissue of skeletal muscle tissue
portion of connective tissue of skeletal muscle
portion of connective tissue of skeletal muscle tissue
skeletal muscle portion of connective tissue
skeletal muscle tissue connective tissue
skeletal muscle tissue portion of connective tissue
skeletal muscle tissue textus connectivus
textus connectivus of skeletal muscle tissue
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
An alveolus that is part of a right lung [Automatically generated definition].
An alveolus that is part of a left lung [Automatically generated definition].
A vasculature that is part of a retina [Automatically generated definition].
Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye.
note that the AAO and ZFA class is a cavity
Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP].
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
splanchnic layer of lateral plate mesoderm
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP].
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
sources differ as to whether this is part-of or develops-from the LPM
A portion of the urogenital ridge which is the source of much of the urinary system[WP].
part_of or develops_from urogenital ridge?
One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].
Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]
The central region of trunk mesoderm. This tissue forms the notochord.
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
The mass of tissue made up of mesenchymal cells in the lung.
The mass of tissue composed of mesenchymal cells in the lobar bronchus..
Vasculature that is composed of the tubule structures that carry blood or lymph in the lungs.
A the thin septum that separates adjacent pulmonary alveoli, containing connective tissue constituents of the respiratory tissue and the capillary network of the blood supply of the lung.
Alveolar smooth muscle is a type of non-striated muscle, found within the walls of the alveolus.
The right lung lobar bronchus mesenchyme is a type of tissue made up of loosely-packed mesenchymal cells in the right lung lobar bronchus.
The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra.
we follow EHDAA2 in dividing the UGS into epithelium and lumen
A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila.
for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)
neuron projection bundle connecting eye with brain
Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition].
MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus
after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct.
Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO]
One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct.
Muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP].
musculus sphincter ampullae hepatopancreatica
A sphincter muscle that is part of a anal region.
A sphincter muscle surrounding the urethra.
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A mitotically active layer of cells surrounding the brain ventricles in the adult that consists of migrating neuroblasts, astrocytes and transitory amplifying progenitor cells[MP].
A paired brain structure situated throughout the lateral walls of the lateral ventricles. It has been associated with having four distinct layers of variable thickness and cell density, as well as cellular composition[WP][Wikipedia:Subventricular_zone].
The subventricular zone (SVZ) is a paired brain structure situated throughout the lateral walls of the lateral ventricles. Along with the subgranular zone of dentate gyrus, subventricular zone serves as a source of neural stem cells in the process of adult neurogenesis. It harbors the largest population of proliferating cells in the adult brain of rodents, monkeys and humans. Neurons generated in SVZ travel to the olfactory bulb via the rostral migratory stream[BTO:0003090].
The subventricular zone (SVZ) is one of two sources of adult-born neurons in the mammalian brain, the other being the subgranular zone (SGZ) of the hippocampus. In most adult mammals, the SVZ is a three-layered sheath that lies along the lateral wall of the lateral ventricle and consists of type A, B, and C cells. Type A rest along the ventricle wall and are neuronal precursor cells, Type B are adjacent astrocytes, and Type C are immature precursors to the Type A neuroblasts. The neuronal precursor cells travel along the rostral migratory stream ensheathed in a tube of Type B astrocytes, until they reach the olfactory bulb. There they integrate into the existing cellular network and mature into local interneurons. While the majority become adult-born granule cells, a subset become periglomerular cells. Interestingly, the human SVZ differs from other mammals' in several ways. It consists of four layers rather than three: ependymal cells (layer I), a hypo cellular gap (layer II), a ribbon of astrocytes (layer III), and a transitional zone (layer IV). The astrocytes are capable of differentiating into many kinds of tissue including new neurons. However, there is no evidence that the proliferating neurons travel along the rostral migratory stream in a chain to populate the olfactory bulb with new interneurons, as is the case for other mammals[NLX:144262].
A part of a wall of an organ that forms a layer.
The tissue underlying the tunica mucosa of the pharynx.
A submucosa that is part of a cystic duct [Automatically generated definition].
A submucosa that is part of a cecum [Automatically generated definition].
A submucosa that is part of an ascending colon [Automatically generated definition].
A submucosa that is part of a transverse colon [Automatically generated definition].
A submucosa that is part of a descending colon [Automatically generated definition].
A submucosa that is part of a sigmoid colon [Automatically generated definition].
A submucosa that is part of a body of stomach [Automatically generated definition].
corpus gastricum (ventriculare) submucosa
submucosa of corpus gastricum (ventriculare)
A submucosa that is part of a pyloric antrum [Automatically generated definition].
A submucosa that is part of a pylorus [Automatically generated definition].
A submucosa that is part of a biliary tree [Automatically generated definition].
A submucosa that is part of a common bile duct [Automatically generated definition].
submucosa of ductus choledochus (biliaris)
A submucosa that is part of a common hepatic duct [Automatically generated definition].
A submucosa that is part of a right hepatic duct [Automatically generated definition].
A submucosa that is part of a left hepatic duct [Automatically generated definition].
The submucous layer of the wall of the urinary bladder.
A submucosa that is part of a neck of urinary bladder [Automatically generated definition].
A submucosa that is part of a lobar bronchus [Automatically generated definition].
A submucosa that is part of a segmental bronchus [Automatically generated definition].
A submucosa that is part of a bronchiole [Automatically generated definition].
A mucosa that is part of a ureter [Automatically generated definition].
A mucosa that is part of a vagina [Automatically generated definition].
A mucosa that is part of a seminal vesicle [Automatically generated definition].
A mucosa that is part of a ejaculatory duct [Automatically generated definition].
A mucosa that is part of a vas deferens [Automatically generated definition].
A mucosa that is part of a cystic duct [Automatically generated definition].
A mucosa that is part of an ascending colon [Automatically generated definition].
A mucosa that is part of a transverse colon [Automatically generated definition].
A mucosa that is part of a descending colon [Automatically generated definition].
A mucosa that is part of a sigmoid colon [Automatically generated definition].
A mucosa that is part of a body of stomach [Automatically generated definition].
corpus gastricum (ventriculare) mucosa of organ
corpus gastricum (ventriculare) mucous membrane
corpus gastricum (ventriculare) organ mucosa
mucosa of corpus gastricum (ventriculare)
mucosa of organ of corpus gastricum (ventriculare)
mucous membrane of corpus gastricum (ventriculare)
organ mucosa of corpus gastricum (ventriculare)
A mucosa that is part of a pyloric antrum [Automatically generated definition].
mucosa of organ of stomach pyloric antrum
mucous membrane of stomach pyloric antrum
A mucosa that is part of a pylorus [Automatically generated definition].
mucosa of organ of pyloric part of stomach
mucosa of organ of stomach pyloric region
mucous membrane of pyloric part of stomach
mucous membrane of stomach pyloric region
A mucosa that is part of a biliary tree [Automatically generated definition].
A mucosa that is part of a common bile duct [Automatically generated definition].
ductus choledochus (biliaris) mucosa of organ
ductus choledochus (biliaris) mucous membrane
ductus choledochus (biliaris) organ mucosa
mucosa of organ of ductus choledochus (biliaris)
mucous membrane of ductus choledochus (biliaris)
organ mucosa of ductus choledochus (biliaris)
A mucosa that is part of a common hepatic duct [Automatically generated definition].
A mucosa that is part of a right hepatic duct [Automatically generated definition].
A mucosa that is part of a left hepatic duct [Automatically generated definition].
A mucosa that is part of a right ureter [Automatically generated definition].
A mucosa that is part of a left ureter [Automatically generated definition].
A mucosa that is part of a renal pelvis [Automatically generated definition].
A mucosa that is part of a neck of urinary bladder [Automatically generated definition].
mucosa of organ of neck of urinary bladder
mucous membrane of neck of urinary bladder
A mucosa that is part of a right uterine tube [Automatically generated definition].
A mucosa that is part of a left uterine tube [Automatically generated definition].
A mucosa that is part of a male urethra [Automatically generated definition].
A mucosa that is part of a female urethra [Automatically generated definition].
A mucosa that is part of a palate [Automatically generated definition].
A mucosa that is part of a tongue [Automatically generated definition].
A mucosa that is part of a nasopharynx [Automatically generated definition].
mucosa of organ of nasal part of pharynx
mucous membrane of nasal part of pharynx
A mucosa that is part of a soft palate [Automatically generated definition].
A mucosa that is part of a middle ear [Automatically generated definition].
A mucosa that is part of a upper lip [Automatically generated definition].
A mucosa that is part of a lower lip [Automatically generated definition].
A mucosa that is part of a gallbladder [Automatically generated definition].
A mucosa that is part of a lobar bronchus [Automatically generated definition].
A mucosa that is part of a segmental bronchus [Automatically generated definition].
A mucosa that is part of a bronchiole [Automatically generated definition].
A mucosa that is part of a terminal bronchiole [Automatically generated definition].
mucosa of organ of bronchiolus terminalis
mucous membrane of bronchiolus terminalis
A mucosa that is part of a respiratory bronchiole [Automatically generated definition].
bronchiolus respiratorius mucosa of organ
bronchiolus respiratorius mucous membrane
mucosa of organ of bronchiolus respiratorius
mucosa of organ of respiratory bronchiole
mucous membrane of bronchiolus respiratorius
mucous membrane of respiratory bronchiole
organ mucosa of bronchiolus respiratorius
A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane.
tympanic membrane external middle ear cavity epithelial component
inner epithelial layer of tympanic membrane
A mucosa that is part of a hard palate [Automatically generated definition].
A mucosa that is part of a fallopian tube [Automatically generated definition].
A mucosa that is part of a uterine tube infundibulum [Automatically generated definition].
mucosa of infundibulum of fallopian tube
mucosa of organ of uterine tube infundibulum
mucous membrane of uterine tube infundibulum
organ mucosa of uterine tube infundibulum
uterine tube infundibulum mucosa of organ
uterine tube infundibulum mucous membrane
The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP].
A cluster of neurons that is the most prominent longitudinally extending condensed part of a nervous system.
some species have multiple longitudinal nerve cords; this class refers to the most prominent one, which is dorsal in chordates and ventral in others.
A nerve cord in the dorsal mid-line that is the most prominent nerve cord.
An organ part that is part of a long bone [Automatically generated definition].
An external genitalia that is part of a female reproductive system [Automatically generated definition].
in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]
external genitalia of female reproductive system
An organ that is part of a immune system [Automatically generated definition].
A gland that is part of a hemolymphoid system [Automatically generated definition].
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
Missing definition for term UBERON:0005063. Please replace it using linked reference.
Missing definition for term UBERON:0005064. Please replace it using linked reference.
Missing definition for term UBERON:0005065. Please replace it using linked reference.
Missing definition for term UBERON:0005066. Please replace it using linked reference.
Amphid sensory organs are the sensory organs of nematodes[GO].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
The median hinge point extends for the entire length of the neural tube, and the lateral hinge points do not form in the spinal cord region of the neural tube[GO].
The neuropore at the anterior (rostral) end of the neural tube.
Anterior site of neural tube closure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.378, see_Kardong_KV][VHOG]
The neuropore at the posterior (caudal) end of the neural tube.
Posterior site of neural tube closure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.378, see_Kardong_KV][VHOG]
An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain.
The boundary between the diencephalon and the mesencephalon.[TAO]
relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO]
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
A temporary opening leading from the central canal of the embryonic neural tube to the exterior.
The anterior-most (rostral) portion of the wall of the neural tube, formed by closure of the anterior neuropore; the median strip of the anterior wall of the prosencephalon, which persists in a relatively unchanged state as the cerebral hemispheres grow out forward beyond the original anterior end of the prosencephalon.
A product of the somatic follicle cell epithelium and a structure that supports the egg in a hostile environment, minimizing water loss whilst allowing gas exchanges essential for embryonic respiration[GO].
The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO].
The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO].
A circular ingrowth of the epidermis around the region of the mammary sprout[GO].
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO].
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate.
An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO].
An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO].
Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO]
In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs.
A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO].
An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO].
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003
A simple mucus-secreting structure that is positioned at the front of the embryo, attaches the newly hatched embryo to a support before the hatchling can swim well or feed, and marks the anterior-most dorsal ectoderm[XAO].
A simple mucus-secreting structure that is positioned at the front of the embryo, attaches the newly hatched embryo to a support before the hatchling can swim well or feed, and marks the anterior-most dorsal ectoderm.[AAO]
The avian beak is an external anatomical structure, in the head region, that is adapted for feeding self and young, catching prey, probing, etc. It encompasses, but is not restricted to, the maxilla, mandible, maxillary ramaphotheca, mandibular ramaphotheca, nostril, nasal fossa, nasal bones, egg tooth and rictus[GO]. The beak, bill or rostrum is an external anatomical structure of birds which is used for eating and for grooming, manipulating objects, killing prey, probing for food, courtship and feeding young.
The term beak is also used to refer to a similar mouthpart in some Ornithischian dinosaurs, monotremes, cephalopods, cetaceans, pufferfishes, turtles, Anuran tadpoles and sirens
Missing definition for term UBERON:0005095. Please replace it using linked reference.
class added for consistency with GO - consider merging with kidney mesenchyme.
The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO].
thin descending limb of the loop of Henle
The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO].
The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology[GO].
The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla[GO].
The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive[GO].
The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO].
An epithelium that is part of a mesonephros [Automatically generated definition].
Missing definition for term UBERON:0005104. Please replace it using linked reference.
Missing definition for term UBERON:0005105. Please replace it using linked reference.
A metanephric tubule is an epithelial tube that is part of the metanephros[GO].
The metanephric cap is formed by the condensation of metanephric mesenchymal cells surrounding the ureteric bud tip[GO]. Mesenchyme closely apposed to the tips of the buds is called cap mesenchyme; it will later go on to form nephrons etc[GUDMAP].
An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO].
Any smooth muscle tissue that is part of a metanephros.
A metanephric nephron is the functional unit of the metanephros[GO].
The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG]
DOI:10.1093/icb/34.4.542 Ruppert EE, Evolutionary Origin of the Vertebrate Nephron. Integrative and Comparative Biology (1994)
Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO].
The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent[GO].
The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO].
It extends to the tip of the metanephric loop of Henle[GO].
The metanephric distal convoluted tubule is a portion of the metanephric nephron tubule that connects the metanephric loop of Henle to the collecting duct[GO].
The metanephric early distal convoluted tubule contains metanephric DCT cells and is vasopressin-insensitive[GO].
metanephric early distal convoluted tubule
The metanephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the metanephros, which helps to support the capillary loops in a renal glomerulus[GO].
The metanephric late distal convoluted tubule contains metanephric DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO].
metanephric late distal convoluted tubule
The metanephric long descending thin limb bend is a part of the descending thin limb of a long nephron that lies beyond the prebend segment in the metanephros[GO].
metanephric long descending thin limb bend
The metanephric macula densa is an area of specialized cells in the distal tubule of the metanephros that makes contact with the vascular pole of the glomerulus[GO].
The metanephric prebend segment is a part of the metanephric descending thin limb that lies before the bend and exhibits permeabilities characteristic of the ascending limb, especially negligible water permeability[GO].
The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule[GO].
The metanephric proximal straight tubule is the part of the metanephric descending limb that extends from the metanephric proximal convoluted tubule to the metanephric descending thin tubule[GO].
TODO - place mammalian xrefs here rather than at parent
The S1 portion is the initial portion of the metanephric proximal convoluted tubule and is responsible for avid reabsorption of water and solutes[GO].
At the macula densa, the thick ascending limb connects to the distal convoluted tubule[GO].
The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule[GO].
The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros[GO].
Long nephrons are associated with juxtamedullary glomeruli and extend into the inner medulla in the metanephros[GO].
The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO].
The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO].
A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros[GO].
The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros[GO].
The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO].
Short nephrons are associated with mid-cortical and superficial glomeruli, are situated entirely in the outer medulla, and have no thin ascending limb[GO].
The metanephric short descending thin limb is the descending thin limb of a short nephron in the metanephros that has a squamous epithelial morphology[GO].
This process pertains to the initial formation of a structure from unspecified parts[GO].
The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO].
A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO].
The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO].
The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO].
The metanephric connecting tubule is a tubular segment of the metanephric nephron; it connects the distal convoluted tubule to the collecting duct in the metanephros[GO].
The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology[GO].
A bud is a protrusion that forms from an epithelial sheet by localized folding.
A cord of epithelial cells without a lumen and usually several cells thick.
An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster.
Any anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
The functional tissue of the central nervous system consisting of neurons and glial cells.
A structure consisting mainly of cell components, rather than complete cells.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
Such a structure may contain some complete cells in addition to partial cells (e.g., glia in nervous system regions).
The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP].
TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule
Connective tissue between the cellular elements of a structure.
A layer of the ovarian follicle that consists of granulosa cells.
At one part of the mature follicle the cells of the membrana granulosa are collected into a mass which projects into the cavity of the follicle. This is termed the discus proligerus. [Wikipedia:Membrana_granulosa, Wikipedia:Membrana_granulosa]
granulosa cell layer of ovarian follicle
Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion).
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same
A duct that carries bile from the liver to the small intestine.[TAO]
The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG]
The hepatic duct is the duct that leads from the liver to the bile duct[GO].
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
An organ that is part of a chest [Automatically generated definition].
A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth.
A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO]
NOT develops_from NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation
. Alternate definition: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
The portion of the collecting duct that resides in the renal medulla.
An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP].
A vein that is part of a thorax [Automatically generated definition].
A vein that is part of a vas deferens [Automatically generated definition].
A germinal center that is part of the spleen. The spleen germinal center is located in a secondary B follicle in the white pulp of the spleen.
A mammary gland that is part of a cervical region.
mice have a single pair of cervical mammary glands
A lactiferous gland that is located in the thoracic region/breast.
Most primates have one pair of mammary glands, which are thoracic.
A macula densa that is part of an ascending limb of loop of Henle [Automatically generated definition].
TODO - unify terminology - check DST = TAL? Note EMAPA class appears to refer to this segment
A tubuloacinar seromucous gland that is located principally in the submucosa of the trachea. Excretory ducts from this gland pass through the lamina propria to the tracheal lumen.
These glands secrete mucus, lysozyme, defensins, and other agents that help protect the lungs from particles and infectious agents.
A gland that is part of a larynx submucosa [Automatically generated definition].
Stromal matrix surrounding blood vessels within the choroid plexus.
A valve that is part of a right atrium [Automatically generated definition].
Tissue surrounding the loop of Henle in the renal medulla.
It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct.
The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS..
A portion of interstitial tissue that is part of a outer medulla of kidney [Automatically generated definition].
A portion of interstitial tissue that is part of a inner medulla of kidney [Automatically generated definition].
The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.
See https://sourceforge.net/p/geneontology/ontology-requests/10941/
The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment.
The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue.
A subarachnoid space that is part of a midbrain [Automatically generated definition].
Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG]
A subarachnoid space that is part of a diencephalon [Automatically generated definition].
Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG]
A subarachnoid space that is part of a hindbrain [Automatically generated definition].
Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG]
A parenchyma that is part of a right lobe of liver [Automatically generated definition].
A parenchyma that is part of a left lobe of liver [Automatically generated definition].
An epithelium that is part of a hindlimb stylopod [Automatically generated definition].
An epithelium that is part of a toe [Automatically generated definition].
An epithelium that is part of a finger [Automatically generated definition].
An epithelium that is part of a forelimb stylopod [Automatically generated definition].
An epithelium that is part of a lower leg [Automatically generated definition].
An ectoderm that is part of a medial nasal prominence [Automatically generated definition].
An ectoderm that is part of a optic eminence [Automatically generated definition].
The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]
An endocardium that is part of a interventricular septum [Automatically generated definition].
interventricular septum endocardial tissue
A myocardium that is part of a bulbus cordis [Automatically generated definition].
A renal pelvis that is part of a metanephros.
The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG]
An anatomical cavity that is part of a yolk sac [Automatically generated definition].
In mammals, the yolk sac cavity contains fluid rather than platelets
in EHDAA2, there are separate primary and secondary yolk sac cavities
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition].
Mesenchyme that is part of a developing toe [Automatically generated definition].
Mesenchyme that is part of a developing trunk.
Mesenchyme that is part of a developing finger [Automatically generated definition].
In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation
Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition].
Mesenchyme that is part of a developing lower leg [Automatically generated definition].
A cardiac jelly that is part of an atrium [Automatically generated definition].
Cardiac jelly that is part of the atrium. [Bgee_curator][VHOG]
A cardiac jelly that is part of a ventricle [Automatically generated definition].
Cardiac jelly that is part of the ventricle. [Bgee_curator][VHOG]
A cardiac jelly that is part of a outflow tract [Automatically generated definition].
Cardiac jelly that is part of the outflow tract. [Bgee_curator][VHOG]
An artery that supplies the renal cortex.
Artery that receives blood from the renal cortex[MP, modified].
A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells.
In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c.
A dorsal skin of digit that is part of a manual digit.
this class is explicitly the union of the two FMA classes
subdivision of skin of dorsal part of finger
A dorsal skin of digit that is part of a pedal digit.
subdivision of skin of dorsal part of toe
A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP].
TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity'
ventricular system of central nervous system
A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm].
Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447].
Vascularized tela choroidea is choroid plexus.
Note that the structure in ZFA may be different
Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP].
Tela chorioidea that lines the fourth ventricle.[TAO]
Tela chorioidea that lines the third ventricle[ZFA]. The part of the choroid plexus in relation to the body of the ventricle forms the vascular fringed margin of a triangular process of pia mater, named the tela chorioidea of the third ventricle, and projects from under cover of the lateral edge of the fornix. Blood is supplied by branches from the superior cerebellar artery[WP].
Tela chorioidea that lines the third ventricle.[TAO]
Tela chorioidea that lines the telencephalic ventricle.
tela chorioidea of telencephalic ventricle
tela choroidea of telencephalic ventricle
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
A portion of tissue that is part of an embryo.
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
The elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary.
TODO - check developmental relationships. merge with urogenital ridge?
in eutherians, SRY transforms the indifferent gonad into testes
Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female.
Structures that develop from sex cords in the female. After further development they become the ovarian follicles.
TODO check secondary vs cortical vs ovary
The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP].
A zone of skin that is part of a clitoris [Automatically generated definition].
An eggshell that contains chorion. An example of this is found in Drosophila melanogaster.
The nephrostome is the opening of the pronephros into the body cavity[GO].
A pronephric nephron is the functional unit of the pronephros[GO].
The structure that is the basic functional unit of the pronephros.[AAO]
The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO].
Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO]
The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO].
in mouse, five pairs of symmetrically positioned mammary placodes (three thoracic and two inguinal) form at reproducible locations along the mammary line at E11.5; the individual pairs develop asynchronously and in a distinct order; pair 3 is first, followed by pair 4, then by pairs 1 and 5 (which develop together), and finally by pair 2; the orientation of placodal cells is not uniform, suggesting that placodes are formed by migration of cells from the mammary line; between E11.5 and E12.5, each mammary placode expands and invaginates into the underlying mesenchyme to form an early bulb-shaped mammary bud[MP]
Missing definition for term UBERON:0005312. Please replace it using linked reference.
A unique club-shaped epithelial structure that develops at the tip of the mammary duct at the onset of puberty under the action of circulating hormones.
terminal end buds (TEBs) consist of an outer layer of undifferentiated myoepithelial progenitor cells ('cap cells'), and a multilayered inner core of luminal epithelial cells ('body') fated to form the walls of the ductal lumen; both layers have high rates of mitosis, consistent with a motile organ dedicated to ductal morphogenesis
TEBs proliferate, ramify, and actively invade the fad pad to allow the formation of a complex branching structure; this process of branching morphogenesis concludes at ~10-12 weeks of age in mice, when TEBs have traversed the length of the fat pad and a fully developed ductal tree has formed
A primary alveolar septum is a specialized epithelium that surrounds the saccule as it forms[GO].
TODO - check UBERON:0004893 interalveolar septum
A secondary alveolar septum is a specialized epithelium that subdivides the initial saccule[GO].
The endothelial lining of the endocardium.
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO].
The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO].
Missing definition for term UBERON:0005321. Please replace it using linked reference.
A nephron that is part of a mesonephros.
The structure that is the basic functional unit of the kidney.[AAO]
Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO].
The mesonephric macula densa is an area of specialized cells in the distal tubule of the mesonephros that makes contact with the vascular pole of the glomerulus[GO].
The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO].
A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO]
In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG]
XAO/AAO class belongs here, as it refers to mesonephric structure
ISBN:978-0127224411 Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3
The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus[GO].
A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros[GO].
The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO].
A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros[GO].
The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO].
The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO].
The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO].
A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland.
produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts
A lamina propria that is part of a mucosa of oral region.
A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP].
An outflow tract that is part of a aorta.
A fiber tracts that connect the dorsal region of the two cerebral hemispheres and span the longitudinal fissure, including the corpus callosum and hippocampal commissure[MP].
The fiber tracts that connect the ventral region of the two cerebral hemispheres and span the longitudinal fissure, including the anterior and the habenular commissures[MP].
The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP].
A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047]
in humans develops into cortical layers II-VI
The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP].
A pouch of ectoderm that grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland[MP]. In embryogenesis, Rathke's pouch is a depression in the roof of the developing mouth in front of the buccopharyngeal membrane. It gives rise to the anterior pituitary (adenohypophysis), a part of the endocrine system[WP].
A depression that forms in the roof of the mouth of an embryo, anterior to the buccopharyngeal membrane. The walls of the diverticulum develop into the anterior lobe of the pituitary gland. [TFD][VHOG]
median funnel­-shaped invagination of ectoderm, the nasohypophyseal pouch. It will contribute to the formation of the pituitary gland of the adult lamprey and is homologous to Rathke's pouch and perhaps to Hatschek 's pit (amphioxus).
EHDAA2 distinguishes between the adenohypophyseal pouch and it's precursor Rathke's pouch epithelium.
A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord.
region of wall of ventricular system of neuraxis
The group of sensory neuron cell bodies associated with the vagus nerve.
The lobe at the anterior part of each cerebral hemisphere, responsible for olfactory functions.
Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180].
TODO - check this. The granule layer is typically in the dentate gyrus, under some definitions of hippocampus, the DG is included, thus making this layer a hippocampal layer
The wedge-shaped fiber bundle of white matter in the dorsomedial side of the spinal cord that is made up of the fasciculus gracilis and fasciculus cuneatus; it is part of the ascending posterior column-medial lemniscus pathway that is important for well-localized fine touch and conscious proprioception.
The dorsolateral ridge of gray matter in each lateral half of the spinal cord. [TFD][VHOG]
The dorsal column is a part of the spinal cord which is responsible for transporting sensory input from the body to the cerebral cortex. This part of the spinal cord is key in perceiving fine touch, such as that used to distinguish textures, along with vibration. The dorsal column also contributes to the body's system of proprioception, used to orient the body in space and to coordinate muscle movements, given information about the body's position
Granule cell layer is also called the DG principal cell layer. This one of the three layers of dentate gyrus that lies deep to the molecular layer and is made of densely packed layer that is four to eight granule cells thick.
Dorsal components of the striatum comprising the caudate nucleus and the putamen, in species that have distinct nuclei; the caudoputamen in species which don't.
According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum
According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (putamen and the globus pallidus) and the caudate nucleus
It may also refer to both the basal ganglia and the internal capsule collectively.
It may also refer to the putamen and caudate collectively.
The term dorsal striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes most of the striatum ( Heimer-1995 ). The boundary between this structure and the ventral striatum is indistinct in sections stained for Nissl substance.
Regional part of telencephalon in some species, e.g., rodent, equivalent to the dorsal striatum (caudate nucleus and putamen). Unlike the dorsal striatum of primates, for example, the caudoputamen is not split into separate nuclei by the fibers of the internal capsule. Rather, the internal capsule splits into fiber bundles which course through the structure.
we do not currently place rodent-specific taxon constraints here as this would cause taxon violations. There is an argument for merging this into dorsal striatum and treating the distinction as phenotypic
In the human, histologically the caudate nucleus and putamen are identically and share a common embryological origin[ISBN:0123813611]
An epithelium that lines the nasal cavity.
this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism
That portion of the nasal mucosa containing the sensory endings for olfaction; the organ of smell[MESH].
The olfactory mucosa is located in the upper region of the nasal cavity and is made up of the olfactory epithelium and the underlying lamina propria, connective tissue containing fibroblasts, blood vessels, Bowman's glands and bundles of fine axons from the olfactory neurons. The mucus protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP][Wikipedia:Olfactory_mucosa].
An array of photoreceptors and any supporting cells found in an eye.
A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.
directing or focusing light onto light receptors
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries
Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]
An arachnoid mater that surrounds a brain.
A sex gland that is part of a female reproductive system.
A sex gland that is part of a male reproductive system.
An arachnoid mater that is part of a telencephalon.
A gray matter that is part of a cerebral hemisphere.
BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon
A composite structure of the telencephalon that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the anterior perforated substance, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance (Heimer-1995; adapted from Brain Info).
The term ventral striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the olfactory tubercle, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance ( Heimer-1995 ).
A suture between frontal and nasal bones.
articulation of the nasal bone with frontal bone
Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow.
All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330)
CVOs contain neural tissue and are an integral part of neuroendocrine function; all of the CVOs, besides the subcommissural organ, contain extensive vasculature and fenestrated capillaries which leads to a leaky BBB at the site of the organs; the lack of a BBB allows CVOs to act as an alternative route for peptides and hormones in the neural tissue to the peripheral blood stream, while still protecting it from toxic substances
The part of the digestive system that excludes the hepatobiliary system.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
alimentary part of gastrointestinal system
ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3
An otic capsule endochondral element that is composed primarily of cartilage tissue.
Bilaterally paired cartilage encasing the semicircular canals of the inner ear.[TAO]
In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans). todo - check EMAPA
The cartilage or bony capsule surrounding the inner ear mechanism.
In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)
A limb bud that develops into a forelimb.
Genes: Tbx5 specifies forelimbs. Wnt2b restricts Fgf10 in chick // In tetrapods, the position of the forelimb is associated with the anterior expression border of Hoxc6 in the paraxial mesoderm (Burke et al., 1995)
A limb bud that develops into a hindlimb.
The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO]
Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick.
A limb bud that develops into a forelimb or pectoral fin.
Fin bud that develops into the pectoral fin.[TAO]
at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future
A limb bud that develops into a hindlimb or pelvic fin.
Fin bud that develops into the pelvic fin.[TAO]
at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future
An apical ectodermal ridge that is part of a pectoral appendage bud.
An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]
Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]
apical ectodermal ridge pectoral fin bud
pectoral appendage apical ectodermal ridge
An apical ectodermal ridge that is part of a pelvic appendage bud.
An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]
pelvic appendage apical ectodermal ridge
Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium.
presumptive retinal pigmented epithelium
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
Portion of tissue that gives rise to the lens.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]
In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates.
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine), pancreas, and gall bladder. It arises from the celiac artery and has the following branches: the hepatic artery proper, the gastroduodenal artery and the right gastric artery.
A segment of autopod that is part of a pes.
The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.
A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG]
It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG]
PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976)
A segment of autopod that is part of a manus.
A three-dimensional arrangement formed by plates of hepatocytes, usually one cell thick, that radiates from the center of the liver lobule; hepatic laminae are highly branched, irregular structures bordered by endothelial lined vascular spaces called hepatic sinusoids.
The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side.
Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO]
One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary]
relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO]
A thymus lobe that is in the left side of a thymus.
A vitelline vein that is in the left side of a multicellular organism.
An axial muscle that originates in the cervical vertebraae inserts on the scapula.
cervical nerve and dorsal scapular nerve
Posterior tubercles of transverse processes of C1 - C4 vertebrae
Superior part of medial border of scapula
A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae.
A thymus lobe that is in the right side of a thymus.
A vitelline vein that is in the right side of a multicellular organism.
A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD].
neural tube lateral wall sulcus limitans
Either of the two lateral lobes that constitute the thymus.
each lobe of the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. Each lobe is composed of numerous lobules held together by delicate areolar tissue; the entire organ being enclosed in an investing capsule of a similar but denser structure. The primary lobules vary in size from that of a pin's head to that of a small pea, and are made up of a number of small nodules or follicles.[WP]
A valve leaflet that is part of a tricuspid valve.
Leaf of caridac valve which has as its parts the anterior, posterior and septal leaflets that is is attached to the chorda tendinea of the right ventricle and the fibrous ring of tricuspid valve.
The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[uncertain][VHOG]
A venous channel found between layers of dura mater in the brain. Receives blood from internal and external veins of the brain, receive cerebrospinal fluid (CSF) from the subarachnoid space, and ultimately empty into the internal jugular vein.
The paired veins that carry blood from the yolk sac back to the embryo.
One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO]
Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG]
check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460
Cranial neural crest which gives rise to the glossopharyngeal ganglion.
Portion of tissue on the side of the lumen of the neural tube.
todo - epidermis? todo - track down EHDAA2 class in new release
In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]
After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998).
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
Hindbrain segment or neuromere. Kimmel et al, 1995.[TAO]
A neural tube lateral wall that is part of a rhombomere.
The third transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order.
The fourth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order.
The fifth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order.
The sixth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order.
The seventh transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order.
The eighth transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order.
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID].
we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution.
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]
variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals
Cranial neural crest which gives rise to the trigeminal ganglion.
todo - compare ZFA and EHDAA2 representation
Portion of tissue that gives rise to the immature gonad.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
Cranial neural crest that gives rise to the facio-acoustic ganglion.
A rhombomere lateral wall that is part of a rhombomere 1.
A rhombomere roof plate that is part of a rhombomere 1.
The second transiently divided segment of the developing rhombencephalon; rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates; rhombomeres are numbered in caudal to rostral order.
A rhombomere lateral wall that is part of a rhombomere 2.
A rhombomere roof plate that is part of a rhombomere 2.
A rhombomere lateral wall that is part of a rhombomere 3.
A rhombomere roof plate that is part of a rhombomere 3.
A rhombomere lateral wall that is part of a rhombomere 4.
A rhombomere roof plate that is part of a rhombomere 4.
A rhombomere lateral wall that is part of a rhombomere 5.
A rhombomere roof plate that is part of a rhombomere 5.
A rhombomere lateral wall that is part of a rhombomere 6.
A rhombomere roof plate that is part of a rhombomere 6.
A rhombomere lateral wall that is part of a rhombomere 7.
A rhombomere roof plate that is part of a rhombomere 7.
A rhombomere lateral wall that is part of a rhombomere 8.
A rhombomere roof plate that is part of a rhombomere 8.
Somite located in the head region, caudal to the otic vesicle.
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]
Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery.
this is an extremely loose and flexible grouping class that is the superclass of the mammalian common iliac and its main brahces, together with analagous structures in other tetrapods
we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific
Any of the three veins including the common, external and internal iliac veins.
A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]
Contributes to the arch of aorta in humans
ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
Arteries which arise from the abdominal aorta and distribute to most of the intestines.
includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries
A vein that returns blood from the intestines.
In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein
The outgrowths of the embryonic maxillary prominences that come together during prenatal development to form the secondary palate.
consider splitting into embryonic/fully formed
The outgrowths of the embryonic maxillae that come together during prenatal development to form the secondary palate. [TFD][VHOG]
The part of the palate formed from the intermaxillary segment.
The shelf separating the oral and nasal cavities that is formed during early embryonic development from protrusions of tissue between the olfactory pits. [TFD][VHOG]
Early tetrapod possessed a primary palate that included the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. Therapsid evolved a partial secondary palate formed by the medial extension of the premaxilla and maxilla. Mammals have a secondary palate that, in addition to extensions of the premaxilla and maxilla, includes part of the palatine bone[VHOG]
The valves that gate the flow of blood from the ventricles into the aorta and pulmonary trunk.
Artery that supplies blood to the adrenal glands.
The cavity formed by the tubotympanic recess epithelium.
Portion of ventral mesentery closest to the stomach.
The mesentery that originates from the ventral side of the peritoneal cavity.[TAO]
The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG]
"The primitive gut is enveloped by a mesentery that has a dorsal and a ventral aspect. The ventral mesentery degenerates during development with the exception of the foregut ventral mesentery, which develops into specialized structures (see foregut embryology)." [http://sprojects.mmi.mcgill.ca/embryology/gi/pgm.htm]. todo - check
A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part.
In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system].
Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)]
An epithelium that is part of a pylorus.
An epithelium that is part of a anterior chamber of eyeball.
An epithelium that is part of a lens vesicle.
An epithelium that is part of a secondary palatal shelf.
An epithelium that is part of a primary palate.
An ectoderm that is part of a pharyngeal arch 2.
In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]
An ectoderm that is part of a pharyngeal arch 3.
An ectoderm that is part of a pharyngeal arch 4.
An endoderm that is part of a pharyngeal arch 2.
An endoderm that is part of a pharyngeal arch 3.
An endoderm that is part of a pharyngeal arch 4.
A mesothelium that is part of a peritoneal cavity.
we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood
An endothelium that is part of a right lung.
An endothelium that is part of a left lung.
An orbitosphenoid endochondral element that is composed primarily of cartilage tissue.
An anatomical cavity that is part of a lens vesicle.
Mesenchyme that is part of a pharyngeal arch 2.
Mesenchyme that is part of a pharyngeal arch 3.
Mesenchyme that is part of a pharyngeal arch 4.
Mesenchyme that is part of a optic eminence.
Mesenchyme that is part of a developing secondary palatal shelf.
Mesenchyme that is part of a developing primary palate.
A mesentery of duodenum that is part of a foregut.
A mesentery of duodenum that is part of a midgut.
An apical ectodermal ridge that is part of a footplate.
A venous system that is part of a hindbrain.
A mesoderm that has the potential to develop into a pronephros.
Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]
the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney
A multi-tissue structure that is part of a spinal cord and is part of a floor plate.
A tissue that is part of a spinal cord and is part of a roof plate.
Roof plate that is part of the spinal cord. [Bgee_curator][VHOG]
A sensory system that is capable of olfaction (the sensory perception of smell).
consider splitting into main and accessory. See also: vomeronasal organ
we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system
The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system].
The sensory system used for olfaction (the sense of smell).[AAO]
In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].
A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme.
Embryonic region that develops into the pectoral fin bud.[TAO]
pectoral appendage field of lateral plate mesoderm
A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme.
Embryonic region that develops into the pelvic fin bud.[TAO]
pelvic appendage field of lateral plate mesoderm
A limb/fin field that has_potential_to_developmentally_contribute_to a paired fin bud.
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
limb/fin field of lateral plate mesoderm
A ring of cells capable of forming a limb.
the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995)
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].
A tunica intima that is part of a artery.
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).
An opening in the skull through which cranial nerve II passes.[MP].
An aperture in the root of the lesser wing of the sphenoid bone transmitting the optic nerve. [TFD][VHOG]
Foramen in the orbital region of the neurocranium for the passage of the optic nerve (cranial nerve II).[TAO]
The short canal through the orbitosphenoid bone at the apex of the orbit that gives passage to the optic nerve and the opthalmic artery
In teleost fishes the opening is wider that in mammals. Due to the longer and deeper shape in mammals, this is usually called the optic canal; sometimes the term optic foramen may be used for the opening of the canal, but here we use this term to denote the entire space together with surrounding bone surface.
The capillary loops of the kidney that normally function as a filtration unit[MP].
...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus
The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.
The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.
An acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter.
Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]
Layer of the glomerular basement membrane adjacent to the glomerular capillary.
internal layer of glomerular basement membrane
lamina interna of glomerular basement membrane
Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions.
TODO - check ridge vs cord vs nephrogenic cord vs blastema
Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle.
The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP].
Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]
The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch
relationship loss: part_of axial vasculature (TAO:0001073)[TAO]
In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP].
A bone tissue that is part of a long bone.
A round nodule, small eminence, or warty outgrowth on an anatomical surface, such as bones, skin, or within the lungs (in the case of tuberculosis). They are also found on the leading edge of Humpback Whale's flippers, improving fluid flow over the flipper's surface[WP].
A vertebral arch that is part of the first cervical vertebra.
A group of axons that are from neurons involved in proprioception from the lower trunk and lower limb[GO]. The fasciculus gracilis (tract of Goll) is a bundle of axon fibres in the dorsomedial spinal cord that carries information about fine touch, vibrations, and conscious proprioception from the lower part of the body to the brain stem. It is part of the posterior column of the spinal cord, which also contains the fasciculus cuneatus, which carries the same information from the upper part of the body. This tract and its continuation in the brain stem is often referred to as the posterior column-medial lemniscus pathway. The fasciculus gracilis is wedge-shaped on transverse section and lies next the posterior median septum, its base being at the surface of the medulla spinalis, and its apex directed toward the posterior gray commissure. It increases in size from below upward, and consists of long thin fibers that are derived from the posterior nerve roots, and ascend as far as the medulla oblongata, where they end in the nucleus gracilis. The tract of Goll was named after Swiss neuroanatomist Friedrich Goll[WP].
distinction between axon tract and fasicle is unclear
A gracile fasciculus that is part of a spinal cord.
spinal cord segment of fasciculus gracilis
spinal cord segment of gracile fasciculus
An axon tract in the spinal cord and medulla which primarily transmits information from the forelimb and trunk. It is part of the dorsal column-medial lemniscus pathway.
we assign the synonym 'Burdachs tract' to the subclass. sometimes the term 'cuneate fasciculus' refers specifically to cuneate fasiculus of spinal cord. We use the term more broadly here.
An axon tract in the spinal cord which primarily transmits information from the forelimb and trunk. It is part of the posterior column-medial lemniscus pathway.
check ontology structure, isa parentage to fasciculus of spinal cord should be inferred. TODO - change definition to be the *whole* of the CF in the SC
A fascicle that is part of a spinal cord.
This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term
A spinal cord segment that adjacent_to a caudal region.
segmenta coccygea medullae spinalis [1-3]
for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned
A delimited region of dense mesenchyme within looser mesenchyme.
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
isa cell condensation in VSAO; has_part chondroblast in AEO
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip.
The paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw.
An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO].
we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode
By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit].
A groove that is situated between the 1st and 2nd pharyngeal arch.
In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]
DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)
A groove that is situated between the 2nd and 3rd pharyngeal arch.
A groove that is situated between the 3rd and 4th pharyngeal arch.
A groove that is situated between the 4th and 5th pharyngeal arch.
The embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin.
The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG]
embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP]
In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG]
All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris[PMID:24960313]
GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771]
we assume the EMAPA class is the undifferentiated form based on TS timings
DOI:10.1242/dev.036830 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009)
An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches.
Note we use overlaps as the relationship to the arches
EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former
A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis.
encompasses digits and prepollex. requires review
The mantle layer of the neural tube that lies dorsal to the sulcus limitans and contains primarily sensory neurons and interneurons involved in communication of sensory impulses.
A subdivision of skeleton that supports pharyngeal arch 2.
it's not clear where AAO:'hyobranchial skeleton' belongs
The epithelial lining of the surface of the coelom.
EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium'
A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx.
An appendage of an insect thoracic segment. It is primarily used for locomotion but may have additional functions in some species, such as digging, grasping, grooming, or silk production (Chapman 1998).
A bone that is part of the manus skeleton. Note that this includes the carpal bones.
A bone that is part of the pes skeleton.
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP].
ductus excretorius glandulae vesiculosae
Any of the ducts that are part of a male reproductive system.
this class groups the individual ducts in a variety of species
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA].
A serous sac which is the aggregate of the conjunctiva plus the conjunctival space.
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA].
A naris that provides one of the small external openings of the head that give passage to air for breathing.
Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO]
relationship loss: subclass nasal opening (AAO:0000316)[AAO]
In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG]
Fish have two pairs of external nostrils.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
An outflow tract that is part of a cardiac atrium.
Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk.
Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta.
Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA].
An outflow tract of atrium that is part of a left atrium.
A pore-like structure surrounding the entire circumference of the anterior chamber of the eye through which aqueous humor circulates[MP].
ligamentum pectinatum anguli iridocornealis
Any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain.
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain[MP]
A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong].
The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium.
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation.
The supporting bundles of muscular fibers lining the walls of the atrial myocardium.
The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve.
The three fibrous triangular components and associated flap of the aortic valve.
The fibrous ring of the aortic valve that attaches the cusps of aortic valve to the wall of left ventricle, and which consists of portions of the fibrous scallops of the posterior, right anterior and left anterior cusps.
The three fibrous triangular components and associated flap of the pulmonary valve.
The fibrous ring of the pulmonary valve that attaches the cusps of pulmonary valve to the wall of right ventricle, and which consists of portions of the fibrous scallops of the anterior, right posterior and left posterior cusps.
The tendinous strands that connect the papillary muscles on the wall of the ventricles to the leaflets of the atrioventricular valves; the chordae tendineae serve to prevent the AV valves from prolapsing back into the atria.
The fibrous ring of the mitral valve that attaches the cusps of mitral valve to the heart, and which consists of portions of the fibrous scallops of the anterior and posterior cusps.
The two fibrous components and associated flaps of the mitral valve.
The fibrous ring of the tricuspid valve that attaches the cusps of tricuspid valve to the heart, and which consists of portions of the fibrous scallops of the anterior cusp (infundibular cusp), the posterior cusp (marginal cusp), and the septal cusp (medial cusp).
The three fibrous triangular components and associated flaps of the tricuspid valve.
check whether we need to separate cusp/leaflet/valve
cuspis septalis valvae atrioventricularis dextrae
septal cusp of right atrioventricular valve
septal leaflet of right-sided tricuspid valve
The paired arteries that carry blood to the yolk sac from the dorsal aorta.
Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664]
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices.
TODO - compare with ZFA atrioventricular ring, part of the conduction system
The part of the heart valves that serves to seal the heart valves when closed. There are three cusps for each valve except for the mitral valve, which has only two (hence its alternate name, 'bicuspid valve'). 'Nodules' are located at the tip of the valve, to form a tighter seal[WP].
A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses).
One of the cartilaginous structures surrounding the embryonic spinal cord, formed by the dorsal growth of the dorsolateral arcualia; it is the primordium of the vertebral arch.
Any collection of muscles that is part of a hindlimb zeugopod.
A bone that is part of a post-anal tail.
MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future.
Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this.
This region is reduced in humans and corresponds to the coccyx
We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud
That portion of the spine comprising the cervical vertebrae. The neck area of the spine.
Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO]
That part of the spine comprising the thoracic vertebrae.
Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]
Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae.
Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO]
in AAO, this is posterior to the caudal-sacral region
A collection of all skeletal elements in some subdivision of the vertebral column.
The deep nuclei of telencephalic origin found in the basal region of the forebrain.
A funiculus of neuraxis that is part of a spinal cord.
The cerebrospinal nerves consist of numerous nerve fibers collected together and enclosed in membranous sheaths. A small bundle of fibers, enclosed in a tubular sheath, is called a funiculus; if the nerve is of small size, it may consist only of a single funiculus; but if large, the funiculi are collected together into larger bundles or fasciculi, which are bound together in a common membranous investment. Examples include: Anterior funiculus of the spinal cord Lateral funiculus of the spinal cord Posterior funiculus of the spinal cord Funiculus solitarius of the medulla Funiculus separans.
A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system.
Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH).
consider adding link to UBERON:0002316 ! white matter of neuraxis
http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin
The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue.
A hollowed out area on the medial margin of the kidney. The renal sinus opens at the renal hilum; it contains the renal aa. and vv., major calyces and renal pelvis, perirenal fat.
The rectal diverticulum is an outgrowth of the cloaca and links the pronephric kidney to the exterior.
The pronephric sinus is an ill-defined capillary network that lies between the pronephric tubules.
TODO - check relationship to renal sinus, improve definition
The mesonephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the mesonephros, which helps to support the capillary loops in a renal glomerulus.
Missing definition for term UBERON:0006183. Please replace it using linked reference.
The mesonephric connecting tubule is a tubular segment of the mesonephric nephron; it connects the distal tubule to the collecting duct in the mesonephros.
The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule.
The mesonephric proximal tubule extends from the capsule to the distal tubule.
A renal sinus that is part of a right kidney.
A renal sinus that is part of a left kidney.
A renal sinus that is part of a mesonephros.
TODO - check relationship to renal sinus, add definition
Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP].
The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions.
A collection of protruberances derived from pharyngeal arches 1 and 2 that develop into the folds of the pinna and gradually shift upwards and backwards to their final position on the head.
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
A cartilaginous condensation that has the potential to develop into a carpal bone.
A pre-cartilage condensation that has the potential to develop into a carpal bone.
The posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system.
The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]
dorsal part of alar plate of metencephalon
The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.
A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]
In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]
PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)
The foremost region of the future forebrain that develops into the diencephalon.
consider obsoleting, the ethmoid is endochondral?
facio-acoustic VII-VIII preganglion complex
A differentiated genital tubercle that is part of a female reproductive system.
A femur endochondral element that is composed primarily of a pre-cartilage condensation.
An anatomical junctions that overlaps the foregut and midgut.
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
A tendon that has the potential to develop into a central tendon.
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm.
cranial derivative of septum transversum
A presumptive structure that has the potential to develop into a forebrain.
TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)
A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops.
A humerus endochondral element that is composed primarily of cartilage tissue.
A humerus endochondral element that is composed primarily of a pre-cartilage condensation.
Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG]
the collection consisting of the two lateral swellings and the medial swelling
A differentiated genital tubercle that is part of a male reproductive system.
An anatomical junctions that overlaps the mouth and foregut.
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
Either of two openings transmitting nerves and blood vessels to or from the orbit.
The pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles.
A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG]
Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity.
Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG]
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
presumptive cardiac ventricle heart tube
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
Future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle.
A rib endochondral element that is composed primarily of cartilage tissue.
A rib endochondral element that is composed primarily of a pre-cartilage condensation.
A scapula endochondral element that is composed primarily of cartilage tissue.
A scapula endochondral element that is composed primarily of a pre-cartilage condensation.
the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005).
this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness
A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP].
check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme
A primordium that has the potential to develop into a submandibular gland.
See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model
A segment of the eyeball that is filled with refractive media.
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
The superior oblique muscle, or obliquus oculi superior, is a fusiform muscle in the upper, medial side of the orbit whose primary action is downward, lateral rotation of the eye. One of the extraocular muscles, the superior oblique is the only muscle innervated by the trochlear nerve (the fourth cranial nerve).
Cranial nerve IV innervated; dorsal in the obliquus group.[AAO]
A muscle in the orbit that depresses, adducts, and helps extort (rotate laterally) the eye. The inferior rectus muscle is the only muscle that is capable of depressing the pupil when it is in a fully abducted position.
A nucleus of brain that is part of a brainstem.
One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.
One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]
relationship loss: develops_from posterior lateral line primordium (TAO:0001157)[TAO]
relationship loss: part_of posterior lateral line system (TAO:0001471)[TAO]
A choroid plexus stroma that is part of a lateral ventricle.
definitions should be fixed to use generic stroma class
A choroid plexus stroma that is part of a third ventricle.
A choroid plexus stroma that is part of a fourth ventricle.
An artery that connects two larger arteries.
The unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species.
found in most mammals, with the exception of humans
The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals.
A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart).
Part of what are called the basal ganglia of the brain which consist of the globus pallidus and the ventral pallidum.
A lobe of lung that is part of a right lung.
4 in mice, divided into 3 in human by two interlobal fissures
System pertaining to a bronchus and alveoli.
A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended.
this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted)
we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid
This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation
seminal fluid may have a role in sperm capacitation, sperm motility
CURATOR NOTE A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs.
The muscles that move the eye. Included in this group are the medial rectus, lateral rectus, superior rectus, inferior rectus, inferior oblique, superior oblique, musculus orbitalis, and levator palpebrae superioris.
we follow MA in making this a subclass of extra-ocular muscle but the distinction is not clear
Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble.
A portion of organism substance that secreted_by a zone of skin.
A portion of organism substance that is secreted by a male reproductive gland.
male reproductive system fluid/secretion
A portion of organism substance that is secreted by a female reproductive gland.
female reproductive system fluid/secretion
A portion of organism substance that secreted_by a respiratory system.
A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards.
A loop of Henle that is part of a kidney outer medulla inner stripe.
outer medulla inner stripe loop of Henle
A loop of Henle that is part of a kidney outer medulla outer stripe.
outer medulla outer stripe loop of Henle
A tube in the kidney that collect and transport urine.
in ZFA this is defined as part of mesonephros
A tube that is part of a excretory system.
An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.
in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system
An organ system subdivision that is the part of the lymphoid system that excludes the lymphatic vessels..
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA].
A urethral meatus that is part of a female urethra[Automatically generated definition].
The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts.
ostium urethrae externum (urethra feminina)
A myocardium that is part of a left ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of aorta.
A myocardium that is part of a right ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk.
A nucleus of brain that is part of a hypothalamus.
A nucleus of brain that is part of a diencephalon.
A trabecula carnea that is part of a heart right ventricle.
A trabecula carnea that is part of a heart left ventricle.
trabeculae carneae (ventriculus sinister)
The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:.
FMA also has FMA:29321 but it's not clear how this differs
An organ that is part of a vestibular system.
Presumptive structure of the blastula that will develop into endoderm.
Portion of embryonic tissue determined by fate mapping to become a structure.
Tissue is fated to develop into the hypochord.
Tissue along the lateral edges of the shield that is fated to develop into the hypochord[ZFA:curator].
Unlike in frogs and axolotl, the hypochord does not appear to be endodermally derived[ZFA]
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified].
this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints
Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO]
in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible
A large vein or channel for the circulation of venous blood.
check if it is valid to group ZFA class here.
An external ear that is in the right side of a multicellular organism.
An external ear that is in the left side of a multicellular organism.
An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic.
A muscle layer that is part of a fallopian tube.
An adventitia that is part of a epididymis.
A muscle layer that is part of a epididymis.
An adventitia that is part of a vas deferens.
An adventitia that is part of a seminal vesicle.
Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP].
Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure.
Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO]
The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans
FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself
to be revised after scapulocoracoid fixes
A joint that connects one phalanx to another along a proximodistal axis.
Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint].
A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis.
currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)
An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO].
typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle.
On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP].
The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers.
In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]
A fat pad that is part of a orbital region.
An anatomical boundary that adjacent_to a epithelium.
The hypoglossal canal is a bony canal in the occipital bone of the skull.
A vein that is part of a vertebral column.
A vasculature that is part of a cerebellum.
The mammillary axonal complex is formed by the axons from the lateral, medial mammillary and the dorsal premammillary nuclei which share a branching pattern. Every neuron gives off one axonal stem that bifurcates into 2 branches. One of the branches is directed dorsally to the thalamus and another caudally to the midbrain[GO].
A fiber pathway that originates from neurons in the posterior hypothalamic region and projects to various nuclei of the anterior nuclear group of the thalamus. It is a composite structure that consists of the mammillothalamic tract of the hypothalamus and the mammillothalamic tract of the thalamus (Carpenter-1983). (from Brain Info.org).
The mammillothalamic tract is the collection of axons that connects the two major subdivisions of the diencephalon (hypothalamus and thalamus) and closes the diencephalic circuit[GO][GO:0061374].
The mammillothalamic fasciculus arises from cells in both the medial and lateral nuclei of the mammillary body and by fibers that are directly continued from the fornix. The Mammillothalamic fasciculus then connects the mammillary body to the dorsal tegmental nuclei, the ventral tegmental nuclei, and the anterior thalamic nucleus [WP]
The mammillotectal tract is the collection of axons that connects the ventral diencephalon to the superior colliculus.
The mammillotegmental tract is the collection of axons that connects the ventral diencephalon to the tegmentum and pons.
The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus).
The collection of all skeletal elements in an autopodium region.
Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]
The central cone shaped core of spongy bone about which turns the spiral canal.
During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's].
The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview]
During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line.
The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm.
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
Layer of nonkeratinized squamous epithelium lining the conjunctiva, overlying scleral tissue.
Embryologic structure that is formed by two longitudinal eminences, one on each alar plate of the midbrain. These eminences become the superior colliculus and inferior colliculus ( Carpenter-1983 )].
The term "tectal plate" (or "quadrigeminal plate") is used to describe the junction of the gray and white matter in the embryo. (NeuroNames ancil-453)
The microstructure of the optic tectum / superior colliculus varies across species. As a general rule, there is always a clear distinction between superficial layers, which receive input primarily from the visual system and show primarily visual responses, and deeper layers, which receive many types of input and project to numerous motor-related brain areas. The distinction between these two zones is so clear and consistent that some anatomists have suggested that they should be considered separate brain structures. In mammals, neuroanatomists conventionally identify seven layers[WP].
The tectum in lampreys has more layers than the tectum in hagfishes, likely related to the fact that vision is less well developed in hagfishes. tectal lamination is almost identical in reptiles and birds and is more restricted in mammals[http://icb.oxfordjournals.org/content/42/4/743.full]
cytoarchitectural part of superior colliculus
A central nervous system gray matter layer that is part of a superior colliculus.
gray matter layer of superior colliculus
A central nervous system white matter layer that is part of a superior colliculus.
predominantly white regional part of superior colliculus
white matter layer of superior colliculus
The outermost layer of the superior colliculus.
grouping teleost assuming homology of superior colliculus and optic tectum; however, this is dubious as tectal layers vary so widely. See: http://icb.oxfordjournals.org/content/42/4/743/T1.expansion.html
superficial layer of superior colliculus
A layer of superior colliculus that lies between the superficial layer and the deep layer.
intermediate layer of superior colliculus
The innermost layer of the superior colliculus.
This grouping class is primarily to accommodate GO
visual processing part of nervous system
An epithelium that is composed primarily of secretory cells.
consider splitting epithelium from epithelial tissue
Structural framework that provides support to the nasal sacs and ducts.
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]
The supporting bundles of muscular fibers lining the walls of the atria[MP].
Not present in any AO. Note that WP states that trabecular carnea are ventricular and 'They should not be confused with the pectinate muscles, which are present in the right and left atria only'
An anatomical space that surrounded_by a trachea.
A subdivision of a the reproductive tract in a female organism that is the site of embryo development.
Vein that is central to a lobule in the liver.
The initial segment of a cranial nerve, leaving the central nervous system.
recommend asserting under this class rather than relying on inference, as relations may change
Surface groove is modelled as immaterial - see https://github.com/obophenotype/uberon/issues/2667 for discussion
Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage.
Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583].
Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO]
relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO]
present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals.
chick scapula is of dual origin and segmentally organized
A region of nephron tubule that is part of a cortex of kidney.
A muscular coat that is part of a ureter.
This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO].
keep this grouping class so long as it is required for GO
Embryonic structure that forms from the anterior gut epithelium at the level of the second somite that then matures to form the swim bladder.
A thin membranous, sometimes alveolated sac in the dorsal portion of the abdominal cavity. Contains a varying mixture of gases, not identical to the composition of air. May be one, two or three chambered. May be connected to the gut by a tube, the ductus pneumaticus (then called physostomous) or unconnected (then called physoclistous).
Cavitated compound organ that is double-chambered, located in the coelom and used to maintain buoyancy and may function as an acoustic resonator.[TAO]
Found in Actinopterygii. Often lacking in bottom fishes
May function as one or more of: hydrostatic organ, sound producing organ, sound receptor, respiratory organ
Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these.
The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate
A diaphysis that is part of a femur[Automatically generated definition].
The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur].
A proximal metaphysis that is part of a femur.
The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.
The distal elements of the developing limb of vertebrates that will give rise to the pes (foot).
EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER
An apical ectodermal ridge that is part of a handplate.
The distal elements of the developing limb of vertebrates that will give rise to the manus (hand).
the EHDAA2 term and the FMA term may not be exact equivalents - check
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
Mesenchyme that is part of a mandibular prominence.
The darker-colored muscle tissue of some mammals, composed of slow twitch muscle fibers.
check if relationship to cell types should be more specific type I cells
The fast and slow skeletal muscles are different in terms of twitching speed (Fitts 1994), and they are believed to be derived from distinct myogenic precursors (Stockdale 1992)
check if CALOHA term is for fiber or tissue.
An anatomical space that surrounded_by a digestive tract.
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA].
A non-keratinized stratified squamous epithelium that is part of a tongue.
A squamous epithelium that is part of a tongue.
this is a singleton subclass of tongue epithelium in MA
A squamous epithelium that is part of a esophagus.
MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass
A squamous epithelium that is part of a stomach.
The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane.
A squamous epithelium that is part of a vagina.
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland.
Any gland that is part of the digestive system.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA].
Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
stomach glandular region glandular mucous membrane
An epithelium that is part of a vestibular labyrinth.
inner ear vestibular component epithelium
Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue.
note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical
The epithelial cells lining the capsule and trabeculae of the thymus.
TODO - check whether this is part of the thymus or borders it
The epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals.
The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis.
Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO]
There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis
A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra.
we use this as a generic grouping class for a number of taxa
in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct
An epithelium that is part of a efferent duct.
epithelium of efferent ductule of testis
The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands.
An epithelium that is part of a submandibular gland primordium.
submaxillary gland primordium epithelium
submandibular gland primordium epithelium
The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis.
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A capillary that is part of the coronary system.
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
A multicellular organism that is at the juvenile stage.
Whole organism that is not fully grown or sexually mature.[TAO]
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
Whole organism that is fully grown or sexually mature.[TAO]
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
Cranial neural crest that migrates into the mandibular arch.
Cranial neural crest that migrates into the hyoid arch.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively
The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present.
The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward.
A pharyngeal pouch that is between pharyngeal arches 1 and 2.
The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery
we use adjacency relations rather than part_of, as in EHDAA2.
A pharyngeal puch that is between the pharyngeal arches 2 and 3.
A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG]
Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]
the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract.
Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve
A pharyngeal pouch that between pharyngeal arches 3 and 4.
A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG]
Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]
The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve
A pharyngeal pouch between pharyngeal arch 4 and arch 5 or 6 (a fifth arch never establishes in amniotes).
A pouch that is situated between the 4th and 5th pharyngeal arch. [ISBN:0124020607][VHOG]
Fourth of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]
Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands.
Portion of tissue that consists of the precursors of the pronephric glomus or glomerulus; derived from the medial portion of the pronephric intermediate mesoderm.
Teleost head kidney consists of fused bilateral lobes located in the anterior part of the kidney. It is analogous to the mammalian bone marrow and the primary site of definitive hematopoiesis[ZFA,modified].
The zebrafish head kidney consists of fused bilateral lobes located in the anterior part of the kidney. It is analogous to the mammalian bone marrow and the primary site of definitive hematopoiesis. Davidson and Zon 2004.[TAO]
in GO, head kidney isa pronephros. Modified the ZFA relationships - the HK is derived from the anterior part of the pronephros and persists until adulthood
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
An internal carotid artery that branching_part_of a left common carotid artery plus branches.
An internal carotid artery that branching_part_of a right common carotid artery plus branches.
An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail.
By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx).
An anatomical cavity that surrounded_by a midgut.
An anatomical cavity that surrounded_by a hindgut.
A valve leafleft that is part of a mitral valve.
Leaf of cardiac valve which has as its parts the anterior, and posterior leaflets that is attached to the chorda tendinea of left ventricle and to the frbrous ring of mitral valve.
An anatomical cavity that surrounded_by a anal canal.
An anatomical cavity that surrounded_by a colon.
The inferior petrosal sinus, within the human head, is an area beneath the brain, which allows blood veins to span the area, from the center of the head downward. It drains from the cavernous sinus (beneath the brain) to the sigmoid sinuses above the internal jugular vein.
The lateral border (or axillary border, or margin) is the thickest of the three borders of the scapula. It begins above at the lower margin of the glenoid cavity, and inclines obliquely downward and backward to the inferior angle. Immediately below the glenoid cavity is a rough impression, the infraglenoid tuberosity, about 2.5 cm. in length, which gives origin to the long head of the Triceps brachii; in front of this is a longitudinal groove, which extends as far as the lower third of this border, and affords origin to part of the Subscapularis. The inferior third is thin and sharp, and serves for the attachment of a few fibers of the Teres major behind, and of the Subscapularis in front.
The medial border of the scapula (vertebral border, medial margin) is the longest of the three borders, and extends from the medial to the inferior angle. It is arched, intermediate in thickness between the superior and the axillary borders, and the portion of it above the spine forms an obtuse angle with the part below. This border presents an anterior and a posterior lip, and an intermediate narrow area. The anterior lip affords attachment to the Serratus anterior; the posterior lip, to the Supraspinatus above the spine, the Infraspinatus below; the area between the two lips, to the Levator scapulC& above the triangular surface at the commencement of the spine, to the Rhomboideus minor on the edge of that surface, and to the Rhomboideus major below it; this last is attached by means of a fibrous arch, connected above to the lower part of the triangular surface at the base of the spine, and below to the lower part of the border.
consider merging with UBERON:1500000 scapular blade, depending on https://github.com/obophenotype/uberon/issues/339. See also http://www.ncbi.nlm.nih.gov/pubmed/20136669
An angle of the scapula formed by the union of the vertebral and axillary borders; its dorsal surface affords attachment to the Teres major and frequently to a few fibers of the Latissimus dorsi.[WP,unvetted].
A lamina propria that is part of a colonic mucosa.
lamina propria of colonic mucous membrane
A serous membrane that is part of a uterine tube infundibulum.
serosa of infundibulum of fallopian tube
A muscle layer that is part of a uterine tube infundibulum.
muscle layer of infundibulum of fallopian tube
muscularis of infundibulum of uterine tube
muscle layer of infundibulum of uterine tube
A mesothelium that is part of a serous pericardium.
The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis.
The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells.
Multicellular organism that can produce both male and female gametes.
An anatomical structure present only in hermaphrodites.
The vasculature consisting of brachiocephalic arteries and veins.
Mesenchyme that develops_from a cranial neural crest.
head mesenchyme from cranial neural crest
mesenchyme derived from head neural crest
Mesenchyme that develops_from a trunk neural crest.
mesenchyme derived from trunk neural crest
An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
The osseous cochlea is the bony foundation that forms the small shell arrangement for the cochlear nerve.
TODO - check this. in MA, cochlea is not part of the bony labyrinth
A cranial nucleus for the vestibular nerve. [WP,unvetted].
vestibular nucleus of eighth cranial nerve
See comments for 'vestibular nuclear complex.
relationship to Meckel's cartilage to be added
relationship to palatoquadrate to be added
A tunica media that is part of a artery.
A tunica adventitia that is part of a artery.
A tunica adventitia that is part of a vein.
The inferior olivary nucleus is the largest nucleus situated in the olivary body, part of the medulla oblongata.
Gray matter of the central nervous system which is a collection of clustered nuclei.
Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei.
this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future.
A pre-cartilage condensation that is part of a trachea.
Any collection of muscles that is part of a pectoral appendage.
Any collection of muscles that is part of a pelvic appendage.
Musculature that is part of the pelvic fin.[TAO]
Any collection of muscles that is part of an appendage.
Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle.
The collection of all skeletal elements in a pelvic appendage region.
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
Portion of tissue that is part of the heart tube and will become the sinus venosus.
A presumptive structure that has the potential to develop into a atrioventricular canal.
Portion of tissue that is part of the heart tube and will become the atrioventricular canal.[TAO]
A presumptive structure that has the potential to develop into a endocardium.
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
A presumptive structure that has the potential to develop into a primitive knot.
Presumptive structure fated to become the shield. Defined by fate mapping[ZFIN:curator].
A presumptive structure that has the potential to develop into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
The part of the blastula that has the potential to develop into a paraxial mesoderm.
A presumptive structure that has the potential to develop into a floor plate.
A presumptive structure that has the potential to develop into a bulbus arteriosus.
Portion of tissue that is part of the heart tube and will become the bulbus arteriosus.[TAO]
A presumptive structure that has the potential to develop into a forebrain-midbrain boundary.
A presumptive structure that has the potential to develop into a rhombomere 1.
A presumptive structure that has the potential to develop into a rhombomere 3.
A presumptive structure that has the potential to develop into a rhombomere 4.
A presumptive structure that has the potential to develop into a rhombomere 5.
A presumptive structure that has the potential to develop into a rhombomere 6.
A presumptive structure that has the potential to develop into a rhombomere 7.
A presumptive structure that has the potential to develop into a rhombomere 8.
A presumptive structure that has the potential to develop into a rhombomere 2.
A presumptive structure that has the potential to develop into a pronephric mesoderm.
A proximal convoluted tubule that is part of a pronephros.
A blood vessel that is part of a pectoral appendage.
A blood vessel that is part of a limb/fin.
A vasculature that is part of a pectoral appendage.
A vasculature that is part of a chordate pharynx.
A vasculature that is part of a limb/fin.
A glomerular capillary that is part of a pronephros.
A glomerular basement membrane that is part of a pronephros.
pronephric glomerular filtration membrane
Either of two main superficial veins of the leg, one larger than the other, that begin at the foot.
A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans.
In mice many lobules lack islets, in contrast to other mammals including humans
A duct that collects and carries secretions of the exocrine pancreas to the intestine.
this class groups together accessory (dorsal) and main (ventral) pancreatic ducts
Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms
An anatomical surface that is part of a tongue.
The upper (superior) side of the tongue.
The lower (inferior) side of the tongue.
A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones.
check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food.
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
A lymphatic vessel that is part of a limb/fin.
A lymphatic vessel that is part of a pectoral appendage.
A lymphatic vessel that is part of a pelvic appendage.
A cartilage tissue that is part of a paired limb or fin.
Cartilage which is part of one of the paired fins.[TAO]
A cartilage tissue that is part of a pectoral appendage.
Cartilage which is part of the pectoral fin.[TAO]
A cartilage tissue that is part of a pelvic appendage.
Cartilage which is part of the pelvic fin.[TAO]
A nucleus of brain that spans a midbrain tegmentum.
this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species
A nucleus of midbrain tegmentum that is part of a midbrain reticular formation.
Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6).
A neural decussation that is part of a diencephalon.
A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified.
Acellular anatomical structure whose predominant constituent is keratin.
should all structures composed primarily of keratin be classified here? At what stage of cornification are keratin-filled cells no longer considered cells
Acellular anatomical structure whose predominant constituent is chitin.
An epithelial tube that is open at one end only.
An epithelial tube open at both ends that allows fluid flow.
A collection of connected epithelial tubes with a single portal.
A ring of smooth muscle cells whose contraction closes the opening of the ring.
A ring of striated muscle cells whose contraction closes the opening of the ring.
Mesenchyme with little extracellular matrix.
Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix.
this class will be an important part of the NC reorganization
An anatomical structure that is undergoing regeneration.
we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure.
A portion of tissue that is regrowing after damage or amputation.[TAO]
A ciliated columnar epithelium that is part of a oviduct.
A cuboidal epithelium that is part of a oviduct.
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA].
In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system
Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]
Epithelium bearing vibratile cilia on the free surface.
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together
A neural nucleus that is part of a medulla oblongata.
The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP].
in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate.
A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes.
A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx.
decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx
the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d
The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx.
The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer).
An anatomical structure that connects two structures.
A sphincter that is part of an esophagus.
check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here
Functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule.
consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts
Region of the embryo into the area in which the kidney rudiment will develop.
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
Endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP].
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project.
A nucleus of brain that is part of a thalamus.
TODO - consider splitting nucleus and complex
An axon tract that is part of a spinal cord.
the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts
A tract that originates from neurons in the spinal central gray and projects to various somatosensory nuclei of the thalamus. It is formed in the medulla by merger of the anterior spinothalamic tract and lateral spinothalamic tract (adapted from Braininfo.org).
a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the spinal cord towards target cells in the thalamus. This axonal process is a member of those that make up the spinothalamic tract, one of the major routes of nociceptive signaling[GO][GO:0021963].
A bone that is part of a reproductive organ.
The interphalangeal articulations of the foot (articulations of the phalanges) are ginglymoid joints, and each has a plantar and two collateral ligaments. The arrangement of these ligaments is similar to that in the metatarsophalangeal articulations: the Extensor tendons supply the places of dorsal ligaments.
The interphalangeal articulations of hand are hinge-joints of the phalanges of the hand. There are two sets (except in the thumb): 'proximal interphalangeal joints' (PIP), those between the first (also called proximal) and second (intermediate) phalanges 'distal interphalangeal joints' (DIP), those between the second and third (distal) phalanges A similar group of articulations also function in the toes.
consider renaming: 'finger' is ambiguous as the term in some usages excludes the thumb (we include it)
An endothelium that is part of a umbilical artery.
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces.
characteristically low in protein and cellular content (unless there has been secondary concentration)
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord.
TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels
A vasculature that is part of a connecting stalk.
Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots.
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton.
Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO]
Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO]
present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species)
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
Mesentery that is located in the peritoneum.
External part of the nose containing the external nares.
Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515].
A bone that is part of a appendage girdle region.
A bone that is part of a pectoral girdle region.
A bone element or fused bone that is part of pelvic girdle.
check sacrum, coccyx (MA does NOT include these)
typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone
A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons.
Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]
Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]
The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]
Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]
Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts
A spinal cord ventral commissure that is part of a cervical spinal cord.
cervical spinal cord anterior commissure
A spinal cord ventral commissure that is part of a thoracic spinal cord.
thoracic spinal cord anterior commissure
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
Intramembranous bone that forms deep in the organism.[TAO]
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
dense regular collagenous connective tissue
typus regularis (textus connectivus collagenosus compactus)
A bone that is part of a craniocervical region.
A sesamoid bone that is part of a manus.
The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid.
A skeletal joint that is part of a appendage girdle region.
An anatomical surface that is part of a cartilage element.
A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].
subclasses of this should be checked for taxonomic consistency
Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]
Any muscle organ that is part of a pectoral girdle region.
EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate
in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone
The part of the ventral body cavity that is within the pelvis.
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax.
A muscle of back that is part of a dorsal thoracic segment of trunk.
A clavicle that is in the right side of a entire appendicular skeleton.
A clavicle that is in the left side of a entire appendicular skeleton.
The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO].
The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html].
The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21].
FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA
A knoblike tooth primordium that develops into the mature tooth and consists of enamel organ, dental papilla, and dental sac enclosing them.
An endothelium that is part of a heart [Automatically generated definition].
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
With numerous vascular spaces that may become engorged with blood.
Examples: corpus cavernosum or penis or clitoris
A smooth muscle tissue that is part of a clitoris.
An epithelium that is part of a duodenum.
Epithelium pertaining to the trachea and bronchi.
The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions.
epithelium of proximal convoluted tubule
An epithelium that is part of a distal tubule.
A ridge of epidermal cells that will form the mammary placodes.
consider splitting ridge (precursor) and milk line
These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development
The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. After initial development of the milk lines they go into remission.
in mouse, mammary gland development begins shortly after mid-gestation (about E10.5); epidermal cells within the milk line become columnar and multilayered, defining a ridge that protrudes above and below the plane of the single-layered primitive epidermis or periderm; by E11.5, five pairs of lens-shaped placodes form along the mammary line at the site of each future nipple.[MP]
A neural arch that is part of a cervical vertebra.
A neural arch that is part of a thoracic vertebra.
Intertarsal articulations are the joints of the tarsus. The specific intertarsal articulations are: Talocalcaneal articulation Talocalcaneonavicular articulation Calcaneocuboid articulation Cuneonavicular articulation Cuboideonavicular articulation Intercuneiform articulation Cuneocuboid articulation.
Any muscle organ that is part of an nose.
pectoral girdle and thoracic body wall skeletal muscle
A muscle tissue that is part of a prostate gland.
A proximal epiphysis that is part of a tibia.
A proximal epiphysis that is part of a fibula.
The upper extremity or head of the fibula is of an irregular quadrate form, presenting above a flattened articular surface, directed upward, forward, and medialward, for articulation with a corresponding surface on the lateral condyle of the tibia. On the lateral side is a thick and rough prominence continued behind into a pointed eminence, the apex, which projects upward from the posterior part of the head. The prominence, at its upper and lateral part, gives attachment to the tendon of the Biceps femoris and to the fibular collateral ligament of the knee-joint, the ligament dividing the tendon into two parts. The remaining part of the circumference of the head is rough, for the attachment of muscles and ligaments. It presents in front a tubercle for the origin of the upper and anterior fibers of the Peronæus longus, and a surface for the attachment of the anterior ligament of the head; and behind, another tubercle, for the attachment of the posterior ligament of the head and the origin of the upper fibers of the Soleus[Wikipedia:Head_of_fibula].
An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers.
The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5.
An epiblast (generic) that develops_from a blastodisc.
The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation. Kimmel et al, 1995.[TAO]
relationship type change: subclass embryonic structure (VSAO:0000178) CHANGED TO: develops_from embryonic structure (UBERON:0002050)[TAO]
relationship type change: subclass embryonic structure (VSAO:0000178) CHANGED TO: part_of embryonic structure (UBERON:0002050)[TAO]
part of blastodisc in BTO; indirect development in ZFA: df DEL df deep blastomere isa blastomere po blastodisc
The dorsal venous arch of the foot is a superficial vein that connects the small saphenous vein and the great saphenous vein. Anatomically, it is defined by where the dorsal veins of the first and fifth digit, respectively, meet the great saphenous vein and small saphenous vein.
A limb segment that is part of a hindlimb.
A limb segment that is part of a forelimb.
Any of the three large depressions in the posterior, middle, and anterior aspects of the floor of the cranial cavity.
todo - review the relationships for this and its subclasses; the relation should be bounded rather than part of, and contains should be used for the brain parts contained by the fossae
The gingival sulcus is an area of potential space between a tooth and the surrounding gingival tissue and is lined by sulcular epithelium. The depth of the sulcus (Latin for groove) is bounded by two entities: apically by the gingival fibers of the connective tissue attachment and coronally by the free gingival margin.
A branch of that maxillary nerve that innervates the mucous membrane of the hard palate.
An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP].
this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition
Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
An endoderm that is part of a thymus primordium.
A brain that develops_from a neural tube.
a reasoner should automatically classify all the vertebrate ontology brain classes here
Any duct branching of of the main epididymis duct.
A substance formed by type II alveolar cells composed of surface-active lipoprotein complex (phospholipoprotein).
An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10
The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
A ligament that does not connect two skeletal elements.
Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625].
this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus.
Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified].
logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]
Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624].
Closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals.
The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines.
the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two
The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter.
The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP].
The network of intersecting plates and spicules in cancellous bone which form a meshwork of intercommunicating spaces filled with blood vessels and marrow; in mature bone, the trabeculae are aligned in parallel with the lines of major compressive or tensile force.
consider revision - we have 3 classes, the tissue itself, the network, and the spaces.
The distinguishing cell types of the lung alveolar tissue, including pulmonary epithelial cells (pneumocytes), alveolar capillary endothelial cells, interstitial cells (fibroblasts) and alveolar macrophages.
The largest lung subunit in which all airways participate in gas exchange, and it is composed of the parenchyma of the respiratory bronchioles, alveolar ducts, and alveoli.
Any skeletal muscle organ in the hypodermis / superficial fascia.
We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this
Unique telencephalic subventricular zones that extend from the lateral ventricles into the olfactory bulbs. Newly produced GABAergic interneurons migrate along the RMS and settle in the bulb.
The rostral migratory stream (RMS) or rostral migratory pathway is a pathway, found in the brain of some animals, along which neuronal precursors that originated in the subventricular zone (SVZ) of the brain migrate to reach the main olfactory bulb, where they differentiate into interneurons. Neurogenesis has been shown to occur in the SVZ into adulthood[WP]
The transient structure formed by neurons migrating from the subventricular zone into the olfactory bulb[MP:0004279]s
In rodents, the anterior region of the SVZ produces neuroblasts that migrate in chain toward the olfactory bulb along the so-called rostral migratory stream (RMS)
The nerve fiber tracts that span the midline of the spinal cord.
Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.
Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO]
Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n
Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA.
A putamen that is part of a left cerebral hemisphere.
A putamen that is part of a right cerebral hemisphere.
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]
The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus.
Subdivision of endoskeleton derived from pharyngeal arches.
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235
A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher.
Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO]
An external projection of an aquatic animal as a fish used in propelling or guiding the body[BTO].
Surface structure involved in locomotion.[TAO]
Surface structure involved in locomotion.[VSAO]
This class groups together various structures that may have arisen through convergent evolution, including, for example, the dorsal fin of a cetacean
Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements.
Type of mechanoreceptive organ of the lateral line which are arranged in lines on the body surface. These organs are constituted by hair cells and supporting cells and it is located in the epidermis with its hair cells exposed to the surface. Absent in some caecilians. These receptors receive afferent and efferent innervations.[AAO]
Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]
relationship loss: part_of lateral line receptor organ (AAO:0001001)[AAO]
relationship loss: subclass lateral line receptor (AAO:0010705)[AAO]
Cranial nerves that carry afferent and efferent fibers for the lateral line system.
Any of the sensory nerves that innervate mechano- and electroreceptors of the lateral line system. The lateral line nerves may be separated in two components, anterior and posterior, in relation to the position of its roots with respect to the otic capsule. These nerves develop from lateral line placodes.[AAO]
relationship loss: innervates lateral line receptor organ (AAO:0001001)[AAO]
relationship type change: part_of_proxy lateral line system (AAO:0000975) CHANGED TO: part_of lateral line system (UBERON:0002540)[AAO]
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
Bone element that is adjacent to the notochord.
We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA
Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]
Bone element that is located on the surface of a cartilage element.
Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]
include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
A lobe of lung that is part of a left lung.
1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure
A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder.
A sac containing the developing tooth and its odontogenic organ. The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts, cementoblasts and fibroblasts. They develop into the alveolar bone, the cementum with Sharpey's fibers and the periodontal ligament fibers respectively.
Any exocrine gland whose cells bud their secretions off through the plasma membrane producing membrane-bound vesicles in the lumen; the apical portion of the secretory cell of the gland pinches off and enters the lumen; it loses part of its cytoplasm in their secretions; apocrine secretion is functional during hormonal stress or puberty; an example of true apocrine glands are mammary glands, responsible for secreting breast milk.
Mammary glands are modified apocrine glands present in both humans and mice; unlike humans, mice do not have axillary apocrine sweat glands[MGI:anna]
The functional tissue of the kidney, consisting of the nephrons.
One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed.
Either of the two neural nuclei within the habenula.
Four accumulations of gray substance embedded in the white substance of the cerebellum, comprising the nucleus dentatus, nucleus emboliformis, nucleus globosus, and nucleus fastigii.
One or more deep cerebellar nuclei appear in agnathans, sharks, ropefishes, lungfishes, Latimeria, and amphibians. Reptiles have two nuclei (a medial and a lateral), and birds and mammals have three nuclei (a medial, a lateral, and an interposed nucleus). The medial nucleus of mammals is known as the fastigial nucleus, and the lateral nucleus is known as the dentate nucleus.[BgeeDb][ISBN:0471888893]
System pertaining to blood vessels in the brain.
Any portion of tissue that surrounds a urethra.
A zone of skin that is part of a dorsal thoracic segment of trunk.
An artery that supplies blood to the urinary bladder.
Either the internal or external pudendal vein, running from the genital-vulvar area and abdomen and down the leg.
Vein that drains left lung and returns blood to the heart.
A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].
Vein that drains right lung and returns blood to the heart.
A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].
Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble.
A germinal center that is located in a lymph node.
The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses.
A neural nucleus that is part of the solitary tract nuclear complex. The solitary tract and nucleus are structures in the brainstem that carry and receive visceral sensation and taste from the facial (VII), glossopharyngeal (IX) and vagus (X) cranial nerves. [WP,unvetted].
nucleus tractus solitarii medullae oblongatae
An organism containing a developing embryo, fetus, or unborn offspring within the body.
A mature thymus that is entirely part of the cervical region.
A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN:0781714125]
A mature thymus that is entirely part of thoracic region.
A gonad prior to differentiating into a definitive testis or ovary.
typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321]
The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary.
consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm
Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke's pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke's pouch, the anlage of the adenohypophysis. Rathke's pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009)
Rostralmost epibranchial placode. Associated with 1st branchial cleft.
Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to geniculate ganglion
Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft.
Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion
Cranial ganglion which develops from an epibranchial placode.
Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
An ectodermal placode that will develop into the components of the lateral line system.
Specialized series of dorsolateral ectodermal placodes.[AAO]
Endocardium that is part of the right atrium.
A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities.
A vein that is part of a craniocervical region.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation.
sphenoid bone pre-cartilage condensation
A sphenoid endochondral element that is composed primarily of cartilage tissue.
Any suture between cranial and/or facial bones.
we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA
The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium.
A nephric duct is a tube that drains a primitive kidney[GO].
Mesenchyme that is part of a medial nasal prominence.
Mesenchyme that is part of a lateral nasal prominence.
An ectoderm that is part of a lateral nasal prominence.
A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo.
In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG]
each membrane is initially composed of an inner layer formed by the endodermal lining of a branchial pouch and an outer layer formed by the ectodermal lining of the branchial groove; later, these two layers become separated by a thin layer of mesoderm; only the first branchial membrane contributes to the formation of an adult structure, i.e. the tympanic membrane (aka eardrum); the second, third, and fourth membranes are obliterated[MP]
ISBN:978-0124020603 Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72
A pharyngeal membrane that separates the first pharyngeal cleft from the first pharyngeal pouch.
check EMAPA - 3 terms appear to match. We follow EMAPA in making each membrane part of the arch with the same number, though in fact it is between these arches
medial or lateral; in EHDAA2 also frontonasal or intermaxillary
The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis).
The axilla is the area directly under the joint where the forelimb connects to the shoulder.
Mesenchyme that is part of a otic placode.
An ectoderm that is part of a buccopharyngeal membrane.
An endoderm that is part of a buccopharyngeal membrane.
Mesenchyme that is part of a foregut-midgut junction.
associated mesenchyme of foregut-midgut junction
A mesentery that is part of a foregut-midgut junction.
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
An epithelium that is part of a foregut-midgut junction.
Anatomical region that surrounds the otic vesicle.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head.
Mesenchyme that is part of a developing hindgut.
Mesenchyme that is part of a developing trachea.
Mesenchyme that is part of a developing middle ear.
Also 1st arch maxillary mesenchyme in EHDAA2
An endoderm that is part of a anal region.
An epithelium that is part of a lateral lingual swelling.
Mesenchyme that is part of a maxillary prominence.
A vascular plexus that is part of a left lung.
A vascular plexus that is part of a right lung.
Mesenchyme that is part of a submandibular gland primordium.
submaxillary gland primordium mesenchyme
mesenchyme of submandibular gland primordium
A hepatic sinusoid that is part of a left lobe of liver.
A hepatic sinusoid that is part of a right lobe of liver.
An endoderm that is part of a foregut-midgut junction.
A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium).
Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults
A segment of the manual digit containing the distal phalanx.
A segment of the pedal digit containing the distal phalanx. Note this class represents a digit segment and thus includes tissues in addition to bone.
A skeletal joint that connects a mesopodium bone and connects a proximal phalanx.
We include these joints as being part of the digits; this is consistent with the FMA, and makes classification easier. Note that digit and metapodial regions are part-disjoint
A submucosa that is part of a intestine.
Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions.
thoracolumbar region of vertebral column
A sulcus limitans of neural tube that is part of a future spinal cord.
spinal cord lateral wall sulcus limitans
In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate.
A cerebrospinal fluid-filled space that runs longitudinally through the length of the entire spinal cord. The central canal is contiguous with the ventricular system of the brain. The central canal represents the adult remainder of the neural tube.
A sulcus limitans of neural tube that is part of a future medulla oblongata.
A sulcus limitans of neural tube that is part of a future metencephalon.
A sulcus limitans of neural tube that is part of a future myelencephalon.
Mesenchyme that is part of a 1st arch mandibular component.
mesenchymal region of mandibular component of first pharyngeal arch
Mesenchyme that is part of a developing left lung.
Mesenchyme that is part of a developing right lung.
A neural plate that develops_from a future forebrain.
A neural plate that develops_from a presumptive midbrain.
A neural plate that develops_from a presumptive hindbrain.
TODO - developmental relationships for lines
midbrain-hindbrain boundary neural plate
midbrain hindbrain boundary neural plate
A presumptive structure that has the potential to develop into a midbrain.
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
A major contributor to neurocranium [PMID:16313393]
A proximal straight tubule that is part of a pronephros.
The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule.
ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS)
A spinal nerve root that is part of a thoracic nerve.
merge with sphenoid lesser wing cartilage element?
One of the two epithelia which make up the tympanic membrane (along with the fibrous layer).
An eyelid connective tissue that is part of a hypodermis.
A basement membrane that is part of a nephron tubule.
A basement membrane that is part of a bronchus.
MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108
A basement membrane that is part of a trachea.
An artery that supplies oxygenated blood to the ear.
A nucleus of brain that is part of a telencephalon.
Ventral mesentery is the part of the peritoneum closest to the navel.
degenerates during development except foregut portion
An anatomical space that surrounded_by a embryonic cloaca.
An anatomical space that surrounded_by a rectum.
Anatomical cluster consisting of adjacent teeth constituting a row.
A tooth row that is part of a skeleton of lower jaw.
A tooth row that is part of a skeleton of upper jaw.
Any endocardium that is part of the right ventricle of the heart.
Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk.
Any endocardium that is part of the left ventricle of the heart.
Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta.
The primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate.
requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip
An anatomical cavity that surrounded_by a stomodeum.
The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels.
Lymph flows into the medullary sinuses from cortical sinuses, and into efferent lymphatic vessels. Medullary sinuses contain histiocytes (immobile macrophages) and reticular cells.[WP]
The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node.
The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures.
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas.
A ganglion that is part of a abdominal segment of trunk.
An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx.
An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx.
A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.
this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules
A nuclear complex of the medullary reticular formation that can be divided into three subnuclei: the parvocellular, magnocellular and the subtrigeminal[WP,modified].
lateral group of medullary reticular formation
lateral reticular formation of the medulla oblongata
The lateral reticular nucleus, of the funiculus, can be divided into three subnuclei, the parvocellular, magnocellular and the subtrigeminal. As is typical of the reticular formation, none of these are very distinct subnuclei, but rather blurred distinctions between cell types and location. The lateral reticular nucleus sends all of its projections to the cerebellum. The parvocellular portion of the LRN and the immediately adjacent magnocellular portion send most their projections to the vermis of the cerebellum. The rest of the magnocellular subnucleus sends its projections to the hemisphere regions of the cerebellum. The subtrigeminal nucleus sends its projections to the flocculonodular lobe. All of these efferent pathways are projected in an ipsilateral manner to the cerebellum, the most abundant of which are those to the vermis. This nucleus is also involved in the mediation of inspiration (in-breathing) with a part of the ventral r. nucleus. The afferent pathways to the LRN come from the spinal cord and higher brain structures. Most of the afferents come from the ipsilateral dorsal horn of the spinal cord and project exclusively to the parts of the LRN that do not receive input from the cortex. The spinal cord projections terminate mostly in the parvocellular region along with the adjacent magnocellular cells. This implies that most input from the spinal cord is relayed into the vermis[WP]
A nucleus of brain that is part of a intermediate reticular formation.
A serous sac that has the pleura and the pleural cavity as parts.
despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
Complexity is conferred on the prostate during a postnatal development phase known as branching morphogenesis. Solid cords of prostate epithelium formed in utero elongate postnatally and their tips are bifurcated into primary, secondary, and tertiary branches in a pattern that is unique for each prostate lobe. Branching morphogenesis proceeds differentially for each of the three mouse prostate lobes (ventral, dorsolateral, and anterior) and is completed by about postnatal day 20 in mice, providing each lobe with unique glandular architecture [5]. It is important to note that the developing human prostate undergoes a similar series of morphogenetic events especially during prostatic bud formation, but gives rise to a mature glandular prostate that is unique from the rodent and features peripheral, central, and transitional zones[PMID:18977204]
An anatomical space that surrounded_by a primitive urogenital sinus.
Mesenchyme that surrounds primitive urogenital sinus.
Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth
An epithelium that is part of a embryonic cloaca.
A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop.
A narrow stripe of cells that lies between the prospective dorsal and ventral thalami. This boundary contains signals that pattern the prethalamic and thalamic territories of the future mid-diencephalon.
Modeling this as a line may not be correct - see http://code.google.com/p/caro2/issues/detail?id=17
The border between the dorsal and ventral thalamus.[TAO]
A multicellular organism that existence_starts_and_ends_during a nematode larval stage.
Branch or outpocketing of the digestive tract.
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach
Outer portion of the renal cortex. Site of formation of medullary and cortical elements.
see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish.
Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region.
The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton.
Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad].
Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO]
The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]
Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present
we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad].
Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO]
Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad].
The structure of the carpus varies widely between different groups of tetrapods, even among those that retain the full set of five digits. In primitive fossil amphibians, such as Eryops, the carpus consists of three rows of bones; a proximal row of three carpals, a second row of four bones, and a distal row of five bones. The proximal carpals are referred to as the radiale, intermediale, and ulnare, after their proximal articulations, and are homologous with the scaphoid, lunate, and triquetal bones respectively. The remaining bones are simply numbered, as the first to fourth centralia (singular: centrale), and the first to fifth distal carpals. Primitively, each of the distal bones appears to have articulated with a single metacarpal. However, the vast majority of later vertebrates, including modern amphibians, have undergone varying degrees of loss and fusion of these primitive bones, resulting in a smaller number of carpals. Almost all mammals and reptiles, for example, have lost the fifth distal carpal, and have only a single centrale - and even this is missing in humans. The pisiform bone is somewhat unusual, in that it first appears in primitive reptiles, and is never found in amphibians. Because many tetrapods have less than five digits on the forelimb, even greater degrees of fusion are common, and a huge array of different possible combinations are found. The wing of a modern bird, for example, has only two remaining carpals; the radiale (the scaphoid of mammals) and a bone formed from the fusion of four of the distal carpals. In some macropods, the scaphoid and lunar bones are fused into the scaphollunar bone
we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla.
Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla
The interlobar veins are veins of the renal circulation which drain the renal lobes.
A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract).
extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708].
In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested
in mouse has left ventricular identity[PMID:22855565]
Mesenchyme that is part of a developing face.
A nerve root that extends_fibers_into a nerve connecting eye with brain.
TODO - check. See comments for optic tract. FMA also has medial root.
todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland)
A portion of an organ, such as the liver, lung, breast, or brain.
The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP].
human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys
The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys.
Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis
An anatomical wall that is part of a ureter.
The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary.
The loose collection of neurons that reside in the rostral medulla close to the medullary surface, ventral and immediately caudal of nVII, that are crucial for CO2 sensing in the brain.
The smooth muscle tissue surrounding the epithelium of the ureter.
A multicellular organism that existence_starts_with a post-embryonic stage.
Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.
Includes: trigeminal, otic, lateral line and epibranchial placodes.
While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)
An anatomical space that is enclosed by a urinary bladder.
An epithelium that is part of a pancreatic duct.
in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this
The junction between the ureter and the renal pelvis of the kidney.
The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney.
An anatomical cavity that surrounded_by a Rathke's pouch.
An anatomical structure that has more than one cell as a part.
A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF].
Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum.
it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity.
The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG]
Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III)
dorsal 3rd arch pharyngeal pouch endoderm
cranial dorsal aspect of third dorsal pharyngeal pouch
The ventral wings fuse to form the cytoreticular cells of the thymus[WP] the caudal ventral part of the pouch gives rise to the thymus epithelium
ventral 3rd arch pharyngeal pouch endoderm
caudal ventral aspect of third dorsal pharyngeal pouch
Mesenchyme that is part of a pharyngeal arch 6.
The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch.
The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue
An organ of the digestive tract that is capable of retaining and storing food.
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
Mesenchyme that is part of a pharyngeal arch 1.
Mesenchyme that is part of a 1st arch maxillary component.
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
entire pharyngeal arch associated mesenchyme
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
A mucosa that is part of a dorsum of tongue.
develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324
Any organ that plays a role in the process of echolocation.
A compound organ that has the potential to develop into a tongue.
An anatomical space with at least one opening to another space or the exterior.
A portion of the external acoustic meatus epithelium which makes up the outer (cuticular) layer of the tympanic membrane.
outer cuticular layer of tympanic membrane
tympanic membrane external acoustic meatus epithelial component
outer epithelial layer of tympanic membrane
The intermediate fibrous layer of the tympanic membrane.
connective tissue layer of tympanic membrane
intermediate fibrous layer of tympanic membrane
In mammals, this class groups together the two epithelial layers plus the intermediate fibrous layer
Organ system subdivision that consists primarily of chromaffin cells and their supporting structures.
in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies
One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia.
Tissue cavity consisting of intercommunicating trabecular spaces in the cancellous bone.
network of trabecular spaces in bone tissue
An epithelium consisting of cuboidal epithelial cells.
TODO - coordinate with CL, add cuboidal cell
An extrahepatic bile duct that has the potential to develop into a common hepatic duct.
Mesenchyme that has the potential to develop into a dermis.
A structure that will develop into a diaphragm.
A multi-tissue structure that has the potential to develop into a meninx of hindbrain.
A developing anatomical structure that has the potential to develop into a metencephalon.
A developing anatomical structure that has the potential to develop into a myelencephalon.
A gray matter that has the potential to develop into a facial nucleus.
A gray matter that has the potential to develop into a inferior salivatory nucleus.
A gray matter that has the potential to develop into a superior salivatory nucleus.
A gray matter that has the potential to develop into a nucleus ambiguus.
A gray matter that has the potential to develop into a dorsal motor nucleus of vagus nerve.
A femur endochondral element that is composed primarily of cartilage tissue.
The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw).
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
Any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli.
A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid.
A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid.
An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
A sex cord that is part of a indifferent gonad.
note that this represents the indifferent structure.
A bodily secretion that is produced by a seminal vesicle.
constitutes 60-70 % of the ejaculate in humans[MP]
important for semen coagulation, sperm motility, and stability of sperm chromatin and suppression of the immune activity in the female reproductive tract[MP]
in ncit, seminal fluid is a subtype of seminal vesicle secretion
Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
A mucous secretion that is produced by glands in the epidermis.
The Sphenofrontal suture is the cranial suture between the sphenoid bone and the frontal bone.
The Sphenoparietal suture is the cranial suture between the sphenoid bone and the parietal bone.
An anatomical cavity that surrounded_by a lymphatic vessel.
An anatomical cavity that surrounded_by a blood vessel.
An anatomical cluster that composed_primarily_of a strand of hair.
A collection of hairs that is part of a face.
A strand of hair that is part of a face.
The portion of the left ventricular outflow tract delineated by the sinotubular ridge superiorly and the bases of the valve leaflets inferiorly; it comprises the aortic sinuses, the aortic valve leaflets, the commissures, and the interleaflet triangles.
The dilated first part of the aorta containing the aortic semilunar valves and the aortic sinuses.
Any of the numerous small mucous-secreting glands located in the wall of the penile urethra.
glandulae urethrales urethrae masculinae
An urethral gland that is part of a female urethra.
One of the laterally paired arteries that supply the gonads.
A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver.
Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO]
An anatomical boundary that corresponds to some physical discontinuity.
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
The lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line develops from cranial ectodermal placodes situated behind the ear and between the eye and ear.
A vasculature that is part of a post-anal tail.
A fold of the mucous membrane of the conjunctiva in many animals. At rest, it is hidden in the medial canthus. It can extend to cover part or all of the cornea to help clean the cornea.
We exclude the shark structure for this via a taxon constraint.
In most primate species, a plica semilunaris is present, although fully developed nictitating membranes can be found in lemurs and lorisoid primates[Wikipedia:Nictitating_membrane]
Some reptiles, birds, and sharks have full nictitating membranes; in many mammals, a small, vestigial portion of the membrane remains in the corner of the eye. Some mammals, such as camels, polar bears, seals, and aardvarks, have full nictitating membranes. fully developed nictitating membranes can be found in lemurs and lorisoid primates.
The Calabar angwantibo (Arctocebus calabarensis, a lorisoid) is the only primate to have a functioning nictitating membrane[Wikipedia:Calabar_angwantibo]
in mice, the nictitating membrane is very small and composed of a very thin core of cartilage covered by loose connective tissue
A semisolid gelatinous mass of coagulated blood that consists of red blood cells, white blood cells, and platelets entrapped in a fibrin network.
Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring.
check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton
Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6?
A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified].
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
The core globe-shaped component of the camera-type eye.
The connective tissue that supports the lobules and follicles of the thyroid gland.
An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged.
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme.
1st arch maxillary mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme.
pharyngeal arch 2 mesenchyme from neural crest
branchial arch 2 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme.
3rd pharyngeal arch mesenchyme derived from neural crest
mesenchyme derived from neural crest of mesenchyme of 3rd arch
pharyngeal arch 3 mesenchyme from neural crest
branchial arch 3 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme.
4th pharyngeal arch mesenchyme derived from neural crest
mesenchyme derived from neural crest of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from neural crest
branchial arch 4 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
pharyngeal arch 6 mesenchyme from neural crest
branchial arch 6 mesenchyme from neural crest
Mesenchyme that develops_from a rhombencephalon neural crest.
mesenchyme from rhombencephalic neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
mesenchyme derived from neural crest of mesenchyme of 1st arch
pharyngeal arch 1 mesenchyme from neural crest
branchial arch 1 mesenchyme from neural crest
One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta.
A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage.
Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO]
relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO]
In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process).
A zone of bone organ that is part of a hyoid bone.
Any anatomical space that is part of a vertebral column.
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
Portion of neural tube that gives rise to the midbrain.
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
An endothelium that is part of a sclera.
Mesenchyme surrounding the developing optic cup which develops into the sclera.
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
A single extraembryonic epithelium, which closes the germband dorsally.
May be obsoleted once added to insect ontology. Coordinate with cell type in CL
An epithelium that is part of a extraembryonic structure.
Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus.
epithelium stratificatum squamosum noncornificatum
nonkeratinizing stratified squamous epithelium
stratified squamous non-keratinized epithelium
stratified squamous nonkeratinizing epithelium
non-keratinized stratified squamous epithelium
One of the three major regions of the conjunctiva.
Thin cartilage element that stiffens the nictitating membrane.
these laminae may consist of purely hyaline cartilage (cats and horses) or may be heavily invested with elastic fibers (dogs, pigs, and cows; Schlegel et al., 2001)
Morphology notes: Generally, the cartilage consists of a long narrow appendix which is followed by a variable crossbar[PMID:11325064]
Developing anatomical structure that develops into the eyeball and associated structures.
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
A skeletal element that is part of a orbital region.
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
Mesenchyme that is part of a limb/fin bud.
Mesenchyme that is part of a developing eyelid.
An epithelium that is part of a handplate.
Mesenchyme that is part of a extraembryonic membrane.
Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme.
maxillary process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme.
maxillary process mesenchyme from head mesenchyme
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme.
1st arch maxillary mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
1st arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme.
head mesenchyme derived arch 2 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 2nd arch
pharyngeal arch 2 mesenchyme from head mesenchyme
branchial arch 2 mesenchyme from head mesenchyme
2nd arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme.
head mesenchyme derived arch 3 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 3rd arch
pharyngeal arch 3 mesenchyme from head mesenchyme
branchial arch 3 mesenchyme from head mesenchyme
3rd arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme.
head mesenchyme derived arch 4 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from head mesenchyme
branchial arch 4 mesenchyme from head mesenchyme
4th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
head mesenchyme derived arch 6 mesenchyme
pharyngeal arch 6 mesenchyme from head mesenchyme
branchial arch 6 mesenchyme from head mesenchyme
6th arch mesenchyme from head mesenchyme
An otic capsule endochondral element that is composed primarily of a pre-cartilage condensation.
The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&.
currently classified as a zone of a bone organ, but exists prior to bone ossifying
An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum.
Note that humans do not have hemal arches, so VA=NA for FMA
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from neural crest
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from head mesenchyme
pharyngeal arch mesenchyme from head mesenchyme
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla.
in many vertebrates, odontoid tissue is not restricted to the teeth
Classified as a portion of organism substance in FMA
A vasculature that is part of a conjunctiva.
The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa.
A unit of lung supplied by three to five terminal bronchioles and contained by fibrous septa.
a pyramidal mass of lung tissue with sides that are bounded by the incomplete interlobular connective tissue septa and with a base, which is 1-2 cm in diameter, which usually faces the pleural surface of the lung; lobules that occupy a more central position in the lung are not well defined and are considered to consist of three to five pulmonary acini with proximate terminal bronchioles.
One of the veins of the lower leg; empty into the popliteal vein.
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen')
Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')
Mesenchyme that develops_from a somatopleure.
the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
Mesenchyme that develops_from a splanchnopleure.
The neurons that innervate the esophagus, stomach, small and large bowel.
A lymphoid follicle that is part of a Peyer's patch.
The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID].
The proximal rib derives from the caudal half of somite[PMID:15906248]
A bone which corresponds to the inner plate of the pterygoid process of the human skull, but which, in all vertebrates below mammals, is not connected with the posterior nares, but serves to connect the palatine bones with the point of suspension of the lower jaw.
In tetrapods, the pterygoid is a complex, but relatively stable, paired palatal bone with a number of parts. For the following discussion, it may be best to refer to the images of tetrapod palates at, for example Ornithosuchus, Therapsida, or Palatines. In many tetrapods, it is the largest palatal bone and serves as the main structural support. Most typically, the pterygoids meet extensively on the mid-line of the palate and jointly send a process, the palatal ramus, anteriorly, which may cover the parasphenoid more or less completely. Sometimes this term is used to include the main body of the pterygoid as well. More variably, there are one or two anterolateral processes which go by various names, such as ectopterygoid ramus. In many amniotes, the pterygoid develops a strong transverse process or transverse flange which forms a bar running laterally across the palate. The pterygoid also articulates with (where present) the dorsoventral supports for the palate: the epipterygoid (dorsal) and the basipterygoid process of the braincase. Finally, the pterygoid sends a long, robust quadrate ramus with complex curvature down (posteroventrally) to grasp the quadrate and support the jaw articulation. Basally, in fishes, the terminology tends to be a little different. Refer to the image of the Frasnian actinistian Diplocercides. The pterygoid bone of tetrapods is, roughly speaking, derived from the middle, entopterygoid (see also entry at entopterygoid for alternative definitions) portion of the palatoquadrate complex. The entopterygoid is not actually a part of the palatoquadrate. It is a dermal bone which has replaced the middle section of the primitively continuous endochondral bone of the palatoquadrate, the original upper jaw. In tetrapods, the pterygoid advances further, and also replaces the central part of the posterior, pterygoquadrate unit. This becomes the quadrate ramus. The upper part of this unit, the portion involved in the dorsal and basipterygoid articulations between jaw and braincase, is referred to as the metapterygoid. In tetrapods, most of this region is incorporated into the pterygoid as well, with the exception of the ascending process of the palatoquadrate, which becomes the epipterygoid. Since the anterior braincase articulation is lost in tetrapods, the only remaining sections of the palatoquadrate are the epipterygoid and the quadrate (or, in mammals, the incus). Everything else is either lost or is replaced by the pterygoid[Palaeos]
Palatal bones of intramembranous origin that lie anterior to the otic capsules, lateral to the orbits, and medial to the maxillae.[AAO]
lamina lateralis (processus pterygoideus)
lamina lateralis processi pterygoideus ossis sphenoidalis
Sources vary as to whether the pterygoid corresponds to the pterygoid processes in general, or the latter/inner plate.
An organ cavity that is part of a urethra.
An unstimulated network of follicular dendritic cells and small resting B cells in the lymph node cortex.
One of the branches of the splenic artery[MP].
When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia]
One of the veins that feed the splenic vein.
The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia]
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
Encapsulated adipose tissue found on the dorsal side of the peritoneum.
Encapsulated adipose tissue associated with the epididymis.
An orifice that is part of a lower urinary tract.
A part of the secondary follicle in which naive B cells reside along with some helper T cells, macrophages and follicular dendritic cells; these are displaced by the expanding germinal centre and form a 'mantle' around it.
mantle zone of lymph node germinal center
The area of the (spleen) secondary B follicle that surrounds the germinal center and harbors the small recirculating B lymphocytes.
A lymphoid follicle containing naive B cells.
The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles
A naris that is located inside the nasal cavity and connects to the pharynx.
In humans the only internal naris is the posterior nasal aperture, which connects to the nasopharynx
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow.
In an adult mammal, most red blood cells are formed in flat bones
Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment
Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.
glandular in NCIT; we consider the two NCIT terms synonymous
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
pseudostratified ciliated columnar epithelium
An organ that is capable of detecting electrical stimulus.
Skeletal element that forms as a replacement or substitution of another element or tissue.
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
An organ cavity that surrounded_by a bone.
different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic.
nephrogenic interstitium of nephrogenic zone
cap mesenchyme of metanephros of urinary system
An epithelial tube that is fated to become a nephron.
EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells
The metanephric cortex is the outer region of the metanephros[GO].
Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons.
A primitive nephron that is part of a metanephros.
Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells.
An appendage segment that is part of a limb/fin.
A pre-cartilage condensation that has the potential to develop into a tarsal bone.
A cartilaginous condensation that has the potential to develop into a tarsal bone.
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified].
The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted].
Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]
Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus.
Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]
Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton.
Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
A pre-cartilage condensation that is part of a pedal digit mesenchyme.
hind limb digit phalanx pre-cartilage condensation
hindlimb phalanx pre-cartilage condensation
foot digit phalanx pre-cartilage condensation
pedal digit phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a manual digit mesenchyme.
fore limb digit phalanx pre-cartilage condensation
forelimb phalanx pre-cartilage condensation
manus phalanx pre-cartilage condensation
hand digit phalanx pre-cartilage condensation
manual digit phalanx pre-cartilage condensation
A cartilage element that is part of a pedal digit mesenchyme.
hind limb digit phalanx cartilage condensation
A cartilage element that is part of a manual digit mesenchyme.
fore limb digit phalanx cartilage condensation
hand digit phalanx cartilage condensation
hind limb digit metatarsal pre-cartilage condensation
metatarsal bone pre-cartilage condensation
foot digit metatarsal pre-cartilage condensation
pedal digit metatarsal pre-cartilage condensation
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the manual autopodium - i.e. the bones of the hands or their cartilaginous precursors[VSAO,modified].
Mesenchyme of the carpal region that contributes to the tarsal skeleton.
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm].
EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton
hind limb digit metatarsal cartilage condensation
foot digit metatarsal cartilage condensation
pedal digit metatarsal cartilage element
fore limb digit metacarpus pre-cartilage condensation
metacarpal bone pre-cartilage condensation
hand digit metacarpus pre-cartilage condensation
manual digit metacarpus pre-cartilage condensation
fore limb digit metacarpus cartilage element
manual digit metacarpus cartilage element
The collection of all skeletal elements in an forelimb zeugopod region.
adding proxinally_connected_to humerus causes inconsistencies - requires investigation
Segment of the forearm corresponding to the radius and ulna.[AAO]
An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle.
Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)
pectoral girdle plus anterior limb or fin
pectoral girdle plus pectoral limb or fin
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here
pelvic girdle plus posterior limb or fin
Paired fin skeleton that consists of the supporting endochondral proximal and distal radials and the dermal fins rays or lepidotrichia. The pectoral fin skeleton is located in the thoracic region of the body and articulates with the scapula and coracoid.
Paired fin skeleton located in the abdominal position that consists of supporting endochondral radialsB and dermal fin rays or lepidotrichia.
the girdle is part of the pelvic fin skeleton in ZFA - needs resolved
Skeletal subdivision that is a segment of the limb skeleton.
note the distinction between this and skeleton of limb
The collection of all skeletal elements in a single paired fin.
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[VSAO]
The subdivision of the skeleton of either the pectoral or pelvic girdle.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula.
Segment of the leg corresponding to the tibia and fibula.[AAO]
An orbitosphenoid endochondral element that is composed primarily of a pre-cartilage condensation.
sphenoid lesser wing pre-cartilage condensation
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin.
considering adding pectoral and pelvic complex skeleton classes
note that the MA class includes girdle parts so it belongs here;
bone of forelimb or pectoral fin or pectoral girdle
A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle
The collection of all meningeal layers that line a central nervous system.
In some primitive organisms, the meningeal cluster includes only the primitive meninx
A lymphoid follicle that is part of a lymph node.
A secondary follicle that is located in a lymph node.
A collection of activated B cells at the center of a secondary follicle, formed after B cells become activated and migrate to the center.
A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation.[GO]
The part of the secondary follicle that surrounds the germinal center.
consider making terminology consistent amongst subclasses - see https://github.com/obophenotype/uberon/issues/7
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
subdivision of organism along appendicular axis
A cartilaginous condensation that has the potential to develop into a clavicle.
A pre-cartilage condensation that has the potential to develop into a clavicle.
A cartilaginous condensation that has the potential to develop into a tibia.
A pre-cartilage condensation that has the potential to develop into a tibia.
A cartilaginous condensation that has the potential to develop into a fibula.
A pre-cartilage condensation that has the potential to develop into a fibula.
A zone of skin that is part of a forelimb wing.
A skeletal element that is part of a limb and composed of cartilage tissue.
A skeletal element that is part of a limb and composed of pre-cartilage tissue.
A cartilaginous condensation that has the potential to develop into a forelimb bone.
forelimb wing cartilaginous condensation
A pre-cartilage condensation that has the potential to develop into a forelimb bone.
forelimb bone pre-cartilage condensation
A cartilaginous condensation that has the potential to develop into a hindlimb bone.
A pre-cartilage condensation that has the potential to develop into a hindlimb bone.
Muscles of the pelvic girdle, hindlimb or pelvic fin.
Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]
A muscle of a pectoral girdle, pectoral fin or anterior limb.
the MA class belongs here, based on its current child classes
Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]
Am unpaired external naris that lies in the midline of the head.
The hagfish's jawless mouth contains two parallel rows of pointed keratinous teeth
Hermaphroditic organism that produces both male and female gametes at the same time.
A primordium that develops into a clavicle bone.
lateral part derives from a fish dermal bone while the medial part comes from a spur off the manubrium endochondral bone[JB]
Skeletal element that is often isolated, small, and variable in composition.
Ossicles are composed of a combination skeletal tissues, including bone, calcified cartilage, hyaline cartilage, etc, and exhibit variable development across species. Ossicles are not necessarily jointed, and examples include the menisci of synovial joints, 'Panda's thumb' (radial sesamoid), cardiac skeletal elements, sclerotic bones, middle ear ossicles, and sesamoids.
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Skeletal element that forms around the notochord and is part of the vertebral column.
we include a distinct subclass for bony vertebra
In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG]
Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage
DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011)
A muscle organ that attaches_to a clavicle and attaches_to a occipital bone.
Some studies have indicated a supernumerary cleido-occipital muscle more or less separate from the sterno-cleido-mastoid muscle; The frequency of cleido-occipital muscle occurrence has been reported up to 33%
A muscle organ that has_muscle_insertion a occipital bone and has_muscle_origin a sternum.
Any muscle organ that is part of either the head or the neck.
A cartilage element that is part of a splanchnocranium.
The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG].
A ligament that is part of a knee joint.
A skeleton of pelvic girdle that is part of a right pelvic girdle region.
A skeleton of pelvic girdle that is part of a left pelvic girdle region.
A pelvic girdle region that is in the right side of a multicellular organism.
A pelvic girdle region that is in the left side of a multicellular organism.
The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups
vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist
The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve.
A synovial joint that is part of a pelvic girdle region.
A synovial joint that is part of a pectoral girdle region.
in FMA, these are part of the bony pectoral girdle
A joint that connects the tibia and the fibula.
we include location as part of the logical definition to prevent accidental classification of ankle joints as tibiofibular joints
The tarsometatarsal articulations are arthrodial joints in the pes.
The carpometacarpal joints (CMC) are joints in the wrist that articulates the distal row of carpal bones and the proximal bases of the metacarpal bones.
A skeletal joint that connects a laryngeal cartilage.
A skeletal joint that connects two adjacent metacarpals[FMA,modified].
A skeletal joint that connects two carpal bones.
A joint that connects two adjacent metatarsals.
In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
Any synovial joint that is part of a (free) limb.
Ossicle that is part of the appendicular skeleton.
Examples of appendicular ossicles include the patella and meniscus of the knee joint.
Ossicle that is part of the axial skeleton.
Examples of axial ossicles include the ossified tendons adjacent to the neural spines of the vertebral column.
Subdivision of urinary system which consists of the kidney and the ureters.
Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue.
Subdivision of skull that consists of the facial bones.
The skull can be divided into two: the neurocranium and the facial skeleton.
primary subdivision of cranial skeletal system
A suture joining a nasal bone to another bone.
A bone that is part of a neurocranium [Automatically generated definition].
Synovial joint that articulates bones of upper and lower jaw.
Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long
A sphincter muscle that is part of the gastrointestinal system.
A lamina propria that is part of a large intestine.
lamina propria of mucosa of large intestine
Ophthalmic veins are veins which drain the eye. More specifically, they can refer to: Superior ophthalmic vein Inferior ophthalmic vein.
The superior ophthalmic vein begins at the inner angle of the orbit in a vein named the nasofrontal which communicates anteriorly with the angular vein; it pursues the same course as the ophthalmic artery, and receives tributaries corresponding to the branches of that vessel. Forming a short single trunk, it passes between the two heads of the Rectus lateralis and through the medial part of the superior orbital fissure, and ends in the cavernous sinus. The ethmoidal veins drain into the superior ophthalmic vein. Vorticose veins also drain into the superior ophthalmic vein.
An epithelium that is part of a parathyroid gland.
A muscle layer that is part of a large intestine.
A muscle layer that is part of a small intestine.
A root of cranial nerve that is part of a vagus nerve.
FMA distinguishes between roots and rootlets - we mix the two here
A neural nucleus that is part of a midbrain tectum.
A multi cell part structure that is part of a central nervous system.
central nervous system cell part cluster
Muscles within the eye (bulbus oculi).[AAO]
Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa.
Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]
synovial membrane of synovial tendon sheath
fibrous membrane of synovial tendon sheath
The most anterior region of the braincase. Provides structural support for peripheral olfactory organ.
currently this is not restricted to skeletal elements, unlike UBERONREF:0000007
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones.
The part of the trunk that is in the dorsum[cjm].
In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
The submucous layer of the wall of the uterine tube.
A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum.
CNS white matter that is part of the telencephalon[ZFA:0000597].
predominantly white regional part of telencephalon
A portion of gray matter that is part of a telencephalon.
predominantly gray regional part of telencephalon
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
A lymph vasculature that is part of a head.
A transverse process of vertebra that is part of a vertebral bone 1.
An evagination of the cloaca. In Testudines these are hypothesized to function in different physiological roles, primarily in respiration.
Taxon notes: in cryptodires, bursae apparently function primarily in buoyancy control and secondarily in ion transport and nesting, but several pleurodires have been shown recently to use them in aquatic respiration.[PMID:11479904]
An anatomical cavity that is part of a esophagus.
A tube lumen that is part of a mesonephric duct.
The collection of all skeletal elements in an individual limb or fin.
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]
Section of the forelimb skeleton located between the stylopodium and the autopodium.
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix.
Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix.
Cartilage tissue that is not mineralized.
add developmental relationships; add disjointness axiom
A commissure that is part of a diencephalon.
An axon tract that is part of a diencephalon.
A tooth that is attached to a maxilla[TAO,modified].
this ontology also contains a class for 'tooth of upper jaw'. This is not equivalent to 'maxillary tooth' in a multi-species context, because many vertebrates have other tooth-bearing bones in the upper jaw[http://orcid.org/0000-0002-6601-2165]
Tooth that is attached to the maxilla.[TAO]
Tooth that is attached to a dentary/mandible[TAO,modified].
Note that we treat dentary tooth and mandibular tooth as equivalent
Tooth that is attached to the dentary.[TAO]
relationship loss: part_of dentary tooth row (TAO:0001952)[TAO]
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species).
A gingiva that is part of a upper jaw region.
A gingiva that is part of a lower jaw region.
A palatal bone which -- like many palatal bones -- may originally have developed as a dermal bone replacing part of the palatoquadrate, the primitive upper jaw. Like the palatine (also called dermopalatine), the ectopterygoid replaces the middle part of the autopalatine. It may be serially homologous with the palatine(s), but is somewhat specialized, being the last (most posterior in palatal view) of the series and bordering the fossa for the jaw muscles. In a typical tetrapod it abuts the palatine anteriorly, the maxilla laterally, the pterygoid or the fossa mandubuaris medially, and the fossa posteriorly.
Dermal bone that forms the lateral border of the palate and articulates with the quadrate posteriorly, the entopterygoid medially and the dermopalatine and/or autopalatine antero-laterally. The ectopterygoid is a paired bone.[TAO]
The ectopterygoid is often toothed.[TAO]
taken from TAO but is present in tetrapods
may be serially homologous with the palatines
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly.
A tarsal bone that connected_to a hindlimb zeugopod skeleton.
extraembryonic portion of umbilical artery
A cardiovascular system that is part of a conceptus.
A cardiac valve leaflet that is part of a aortic valve.
Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[uncertain][VHOG]
A cardiac valve leaflet that is part of a pulmonary valve.
The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP]
vagus X nerve left recurrent laryngeal branch
vagus X nerve right recurrent laryngeal branch
Anatomical projection that is composed of cartilage tissue.
An anatomical space that is part of a bone of lower jaw.
An anatomical space that is part of a bone of upper jaw.
A cranial nerve nucleus that is associated with a vagus nerve.
A neural nucleus that is part of the spinal cord.
in ZFA this is the superclass of dorsolateral and medial (which have not been generalized above ZFA). In this ontology it is a broad grouping class covering these zebrafish structures as well as the generalized dorsal motor nucleus
Ectodermal placode that does not develop into a component of the nervous system.
An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales).
A tube lumen that is part of a atrioventricular canal.
An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets.
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
A duct that is part of a sebaceous gland.
An acinus that is part of a sebaceous gland.
An acinus that is part of a salivary gland.
An acinus that is part of a mammary gland.
An acinus that is part of a lacrimal gland.
An acinus that is part of a exocrine gland.
the FMA class specifically refers to ureter
The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity.
A cranial suture that connects a nasal bone and connects a maxilla.
articulation of the nasal bone with maxilla
A skeletal ligament that is part of a sternoclavicular joint.
A muscle layer that is part of a wall of esophagus.
In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
An organ cavity that is part of a vagina.
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
The Epimysium also protects muscles from friction against other muscles and bones
Masses of developing blood cells attached to endothelium in the yolk sac.
in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels
Nerve fibers which project from cell bodies of autonomic ganglia to synapses on target organs.
Nerve fibers which project from the central nervous system to autonomic ganglia. In the sympathetic division most preganglionic fibers originate with neurons in the intermediolateral column of the spinal cord, exit via ventral roots from upper thoracic through lower lumbar segments, and project to the paravertebral ganglia; there they either terminate in synapses or continue through the splanchnic nerves to the prevertebral ganglia. In the parasympathetic division the fibers originate in neurons of the brain stem and sacral spinal cord. In both divisions the principal transmitter is acetylcholine but peptide cotransmitters may also be released.
A noradrenergic or adrenergic axonal fiber projecting from a sympathetic ganglion to an effector organ.
A cholinergic axonal fiber projecting from the CNS to a sympathetic ganglion.
A cholinergic axonal fiber projecting from a parasympathetic ganglion to an effector organ.
A cholinergic axonal fibers projecting from the CNS to a parasympathetic ganglion.
An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle.
A region of the stomach that is lined with glandular epithelium.
as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus
A hepatic vein that is part of a left lobe of liver.
A hepatic vein that is part of a right lobe of liver.
An articular capsule that is part of the glenohumeral joint.
In a saddle joint (sellar joint, articulation by reciprocal reception) the opposing surfaces are reciprocally concave-convex.
A skeletal ligament that connects a tibia and connects a tarsal skeleton.
deltoid collateral ligament of ankle joint
ligamentum collaterale mediale (articulatio talocruralis)
ligamentum collaterale mediale articulationis talocruralis
ligamentum deltoideum (articulatio talocruralis)
medial collateral ligament of ankle joint
An epiphysis that is part of a phalanx of a pes [Automatically generated definition].
An epiphysis that is part of a proximal phalanx of pes.
An epiphysis that is part of a middle phalanx of pes.
An epiphysis that is part of a distal phalanx of pes.
An epiphysis that is part of a proximal phalanx of manus.
An epiphysis that is part of a middle phalanx of manus.
An epiphysis that is part of a distal phalanx of manus.
A joint that connects the bones of the crus to the proximal tarsal bones.
an ankle joint that passes between the astragalus and calcaneum[Palaeos].
line of flexion between calcaneus and astragalus
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6
A tooth that is on the roof of the mouth.
this is distinct (but not disjoint) from palatine bone
A tooth that is attached to a palatine bone.
Teeth present in some fishes on the palatine bones, bones that lie inside the upper jaw bones (sometimes maxillaries, sometimes premaxillaries) usually behind the vomerine tooth patch.
A subdivision of skeletal system that subdivision_of a hard palate.
Bone that forms as a replacement of another structural tissue.
Bone that forms as a replacement of another structural tissue.[TAO]
This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
A cartilaginous condensation that has the potential to develop into a patella.
Note some sources have this as intramembranous
A pre-cartilage condensation that has the potential to develop into a patella.
An anatomical cavity that is part of a bronchus.
An anatomical cavity that is part of a lobar bronchus.
An anatomical cavity that is part of a segmental bronchus.
A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region.
some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod
A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region.
A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region.
A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton.
A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton.
A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton.
Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]
A primordium that has the potential to develop into a stomach.
facio-acoustic ganglion complex VII-VIII
facio-acoustic VII-VIII ganglion complex
acoustico-facial VII-VIII ganglion complex
An apocrine gland that is part of a skin of body.
Note that 'skin apocrine gland' does not cover 'apocrine sweat gland': in the former, "apocrine" refers to the type of secretion mechanism, while in the latter it refers to a structural feature.
A zone of skin that is part of a craniocervical region.
The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins.
Network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP].
External opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP].
A urethral meatus that is part of a male urethra[Automatically generated definition].
The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis.
ostium urethrae externum (urethra masculina)
The usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone.
internal urethral orifice of urinary bladder
Mucus-secreting glands in the mucosa of the uterine cervix.
Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing.
The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium.
distinction between two FMA classes not clear - we merge them here
A glandular epithelium that is part of a uterine cervix.
The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium.
An epithelium that is part of a ectocervix.
The glandular epithelium that lines the endocervix.
Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet.
squamo-columnar junction of uterine cervix
squamocolumnar junction of uterine cervix
Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia.
An artery that originates from the abdominal aorta.
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].
Epithelium that derives from the mesoderm. [Automatically generated definition].
The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands.
Encapsulated adipose tissue associated with the mammary gland.
Encapsulated adipose tissue associated with the femur.
An epithelial sac that is part of a Rathke's pouch.
One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly.
We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts
One of five swellings formed during the development of the face.
Roof of the buccal cavity, formed from the fusion of vomer, pterygoid, parasphenoid, palatine, ectopterygoid.
Anatomical cluster that is the upper roof of the mouth that is underlain by bones such as the parasphenoid, vomer, metapterygoid, orbitosphenoid.[TAO]
Roof of the mouth lined with ciliated epithelium.[AAO]
The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice.
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery.
Unclear if MA class belongs here or in parent
descending branch of the transverse cervical
Keratinized stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesize and accumulate keratin.
epithelium stratificatum squamosum cornificatum
keratinized stratified squamous epithelium
The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals.
A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis.
Any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen.
Skeletal subdivision consisting of all the skeletal elements in a single fin.
The segment of the autopod that is distal to the metapodial region and consists of the digits.
class refers to an entire limb segment, not just the bones
The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers).
The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes).
A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton.
A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton.
A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton.
A bone element that is part of a jaw region.
A muscle layer that is part of an intestine.
A nerve plexus that is part of a sympathetic nervous system.
A layer of tissue between the muscularis and serosa.
Contains nerves, blood vessels, lymphatics and lymph nodes
A muscular coat that is part of a urinary bladder.
respiratory system arterial smooth muscle
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified].
a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction
increases the surface area of a cell lining whilst minimizing increase in volume
FMA class represents an individual microvillus.
A microvillus layer that is striated and found in the intestine.
Blood-forming tissue, consisting of reticular fibers and cells.
Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue
The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.
A sensory receptor that responds to mechanical pressure or distortion.
Normally there are four main types in glabrous skin: Pacinian corpuscles, Meissner's corpuscles, Merkel's discs, and Ruffini endings. There are also mechanoreceptors in hairy skin, and the hair cells in the cochlea are the most sensitive mechanoreceptors, transducing air pressure waves into nerve signals sent to the brain. In the periodontal ligament, there are some mechanoreceptors, which allow the jaw to relax when biting down on hard objects; the mesencephalic nucleus is responsible for this reflex
A sensory nerve ending that responds to a stimulus in the internal or external environment of an organism. In response to stimuli the sensory receptor initiates sensory transduction by creating graded potentials or action potentials in the same cell or in an adjacent one.
Specialized terminations of peripheral neurons. Nerve endings include NEUROEFFECTOR JUNCTION(s) by which neurons activate target organs and sensory receptors (see RECEPTORS, SENSORY) which transduce information from the various sensory modalities and send it centrally in the nervous system. Presynaptic nerve endings are PRESYNAPTIC TERMINALS.
this class and subclasses may be ceded to GO
An anatomical space that is enclosed by a cloaca.
the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/
The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives.
An anatomical space that is enclosed by a terminal part of digestive tract.
includes the cloacal lumen, in species where this is present
lumen of terminal part of digestive tract
An anatomical space with no opening to another space or to the exterior.
Triangular calcified papillae (often five) placed radially around the anus of some Holothuriidae.
The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle.
skeleton of anterior limb/fin and girdle
The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
skeleton of posterior limb/fin and girdle
The posterior region of the neck, including the suboccipital region.
A mucosa that is part of a cloaca [Automatically generated definition].
cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium.
A submucosa that is part of a cloaca [Automatically generated definition].
A serous membrane that is part of a cloaca [Automatically generated definition].
A muscular coat that is part of a cloaca.
A sphincter muscle that is part of a vagina.
A muscular coat that is part of a duodenum.
A muscular coat that is part of a colon.
A muscular coat that is part of a anal canal.
A serous membrane that is part of a fallopian tube.
An adventitia that is part of a esophagus.
A smooth muscle tissue that is part of a umbilical cord.
An anatomical junction that connects a stomach and connects a duodenum.
A mucosa that is part of a gastroduodenal junction.
A depression on the ventral side of the femur, at the knee joint, between the condyles.
A depression or fissure in the surface of the brain. It surrounds the gyri, creating the characteristic appearance of the brain in humans and other large mammals.
sulci are considered absent from lissencephalic mammals such as mice, but they may possess fissures. For example, the Allen mouse brain Atlas includes hippocampal, rhinal and choroid fissure. For this reason we do not place a taxon constraint on this class
Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)
TODO mirror representation of abdominal aorta
this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein
The part of the venous system that drains the lungs[Kardong].
Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung.
A nonskeletal ligament that is part of a liver.
Any vein within the general circulation that transports blood back to the right atrium of the heart.
consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html).
Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle'
One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions.
A gland that is part of a foregut-midgut junction.
A telencephalic ventricle that is in_the_left_side_of a telencephalon.
A telencephalic ventricle that is in_the_right_side_of a telencephalon.
The layer of the ovary lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles.
Highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles.
composed of loose connective tissue that contains blood vessels, lymph vessels and nerves
A bodily secretion that is produced by a gland of anal sac.
the anal gland secretions of species such as civet and beavers are used perfumery
A rete mirabile (Latin for 'wonderful net'; plural retia mirabilia) is a complex of arteries and veins lying very close to each other, found in some vertebrates. The rete mirabile utilizes countercurrent blood flow within the net (blood flowing in opposite directions. ) It exchanges heat, ions, or gases between vessel walls so that the two bloodstreams within the rete maintain a gradient with respect to temperature, or concentration of gases or solutes.
Glands of Moll, also known as ciliary glands, are modified apocrine sweat glands that are found on the margin of the eyelid. They are next to the base of the eyelashes, and anterior to the Meibomian glands within the distal eyelid margin. These glands are relatively large and tubular-shaped. The glands of Moll are named after Dutch oculist Jacob Anton Moll (1832-1914). Glands of Moll empty into the adjacent lashes. Glands of Moll and Zeis secrete lipid that adds to the superficial layer of the tear film, retarding evaporation. The glands of Moll are prone to infection and blockage of its duct with sebum and cell debris. Blockage of the gland's duct causes swelling which can manifest itself as a stye.
Any gland that is part of an eyelid. This includes sebaceous glands (Zeis gland, tarsal gland) and sweat glands (Moll's gland).
A gland producing tears in a third eyelid in the corner of each eye.
This gland is distinct from the other medial ocular gland, the Harderian gland, and is typified by clusters of glandular tissue within the nictitating membrane
superficial gland of the nictitating membrane
Disease notes: Prolapse of the Nicititans Gland is also known as Cherry Eye
Any of the sebaceous glands that are in the eyelid. Examples: gland of Zeis (services eyelashes), gland of Meibom (tarsal gland - unconnected to eyelids).
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
A major organism subdivisionthat is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane.
A future glans that is part of a male genital tubercle.
A future glans that is part of a female genital tubercle.
In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week
An epithelial tube that develops from a Mullerian duct in a male. Later degenerates.
consider separating the duct from the degenerating portion, as in EMAPA
degenerating mesonephric portion of male paramesonephric duct
A diaphysis that is part of a fibula[Automatically generated definition].
The body of fibula presents four borders - the antero-lateral, the antero-medial, the postero-lateral, and the postero-medial; and four surfaces - anterior, posterior, medial, and lateral[Wikipedia:Body_of_fibula].
The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia].
Anatomical cavity that is the lumen of the skull and contains the brain.
A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus.
In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil
A blood vessel endothelium that is part of a lung [Automatically generated definition].
vestibulo-cochlear VIII ganglion complex
A sphincter muscle that is part of a cloaca.
the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938).
A mesenchyme that is part of a pharyngeal arch 5.
A caudal vertebra endochondral element that is composed primarily of cartilage tissue.
coccygeal vertebral cartilage condensation group
A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
coccygeal vertebra pre-cartilage condensation
tail vertebral pre-cartilage condensation
caudal vertebra pre-cartilage condensation
A cervical vertebra endochondral element that is composed primarily of cartilage tissue.
cervical vertebral cartilage condensation group
A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
cervical vertebra pre-cartilage condensation
A thoracic vertebra endochondral element that is composed primarily of cartilage tissue.
thoracic vertebral cartilage condensation group
A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation.
thoracic vertebra pre-cartilage condensation
A section through the tube or network of tubes that connects the ovaries to the outside of the body.
FMA class may only represent the uterine portion
The anatomical space that is enclosed by a stomach.
Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585].
An anatomical cavity that is part of a ear vesicle.
Short bones are designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement. They are one of five types of bones: long, short, flat, irregular and sesamoid. Examples of these bones include the tarsals in the foot and the carpals in the hand.
Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation.
Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage.
A sesamoid element that is composed primarily of cartilage tissue.
sesamoid cartilage of cricopharyngeal ligament
An epithelium that is part of a intestinal villus.
The prostate gland lobe that is located on the lateral side of the organ.
A dorsal thalamus that is in_the_left_side_of a diencephalon.
A dorsal thalamus that is in_the_right_side_of a diencephalon.
Anatomical space that is an opening in a bone of the skull.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
Vascular endothelium found in blood vessels of the blood-brain-barrier.
Vascular endothelium found in colon blood vessels.
Epithelium lining the exocrine pancreas.
A strand of hair that is part of a axilla.
Musculature of the head and neck, spine, and ribs.
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
Anatomical projection that is part of the integumentl system.
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
Fluid contained within the notochordal canal.
A metaphysis that is part of a metaphysis.
A diaphysis that is part of a metacarpal bone.
An organ component layer that is part of a integumental system.
One of two openings in the uterine cervix.
Opening of uterine cervix into the vagina.
The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus].
The cavity formed by the walls of the cervix.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
An organ cavity that is part of a uterus.
A nipple that is in_the_left_side_of a body proper.
A nipple that is in_the_right_side_of a body proper.
A diaphysis that is part of a metatarsal bone.
Deepest of 3 cytoarchitecturally defined layers of the piriform cortex characterized by a moderately high density of pyramidal cells and large numbers of basal dendrites descending from pyramidal cells in layer 2.
Embryonic structure that gives rise to the telencephalon.
paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP]
A collection of hairs that is part of a craniocervical region.
Mesenchyme that develops_from the neural crest[Automatically generated definition].
The simple cuboidal epithelium lining the lumen of kidney collecting ducts.
In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis
collecting duct of renal tubule epithelium
epithelium of collecting duct of renal tubule
A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae.
Sweat that is produced by the glands of the axilla.
Encapsulated adipose tissue associated with the uterus.
A proximal mesopodial endochondral element that is composed primarily of a bone tissue.
Muscle that is part of the respiratory system.
this class may be merged with 'respiratory system muscle'; check intercostals
An anatomical space that is enclosed by a sinusoid.
A sinusoidal space that is part of a hepatic sinusoid.
Any member of the network of tubes that return blood from the renal tissues to the systemic circulation.
we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta
A part of the body present only in a specific gender.
A part of the body present only in males.
A part of the body present only in females.
A neural nucleus of the pretectal area (between dorsal thalamus and optic tectum) that receives afferents primarily from the retina and the optic tectum and are involved in modulating motor behavior in response to visual input.
Any of the groups of neurons located between the thalamus and midbrain that receive binocular sensory input from retinal ganglion cells of the eyes and are responsible for maintaining the pupillary light reflex
in hagfishes, there are two: the pretectal nucleus and the nucleus of the posterior commissure[ISBN:0471888893]
see notes for pretectal region. Note this is midbrain in FMA, midbrain (mesencephalon) in HBA, midbrain in DHBA
A taste bud that is located on the tongue, situated on a gustatory papilla.
A gustatory epithelium that is part of a tongue.
A gustatory epithelium that is part of a roof of mouth.
Subcutaneous adipose tissue that is located in the peritoneal cavity.
Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041].
Subcutaneous adipose tissue that is located in the abdominal region.
Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery.
Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery[http://medical-dictionary.thefreedictionary.com/cardiac+ganglion].
Encapsulated adipose tissue associated with the kidney.
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
Subdivision of skeletal system that consists of all ribs and rib joints in an organism. In many vertebrates this consists of the combination of the rib cage and all rib joints, but some vertebrates have ribs outside the thoracic rib cage.
white matter lamina of cerebral hemisphere
A subdivision of the central canal of the spinal cord along its anterior-posterior axis. This is typically subdivided into cervical, thoracic, lumbar and sacral segments.
regional part of spinal cord central canal
subdivision of spinal cord central canal
The white laminae of cerebellum is subdivision of the cerebellar cortex comprised of myelinated axons lying deep to the granule cell layer of the cerebellar cortex.
Part of spinal cord central canal contained in the thoracic spinal cord. It is continuous rostrally with the cervical spinal cord central canal and caudally with the lumbar spinal cord central canal.
thoracic division of spinal cord central canal
Part of central canal contained within the cervical spinal cord. It is continuous caudally with the thoracic spinal cord central canal and rostrally with the fourth ventricle of the brain via the obex.
cervical division of cord spinal central canal
A dorsal horn of spinal cord that is part of a thoracic spinal cord.
A ventral horn of spinal cord that is part of a thoracic spinal cord.
A gray matter of spinal cord that is part of a cervical spinal cord.
A white matter of spinal cord that is part of a cervical spinal cord.
A nerve root that is part of a accessory XI nerve.
accessory portion of spinal accessory nerve
cranial portion of eleventh cranial nerve
A dorsal horn of spinal cord that is part of a cervical spinal cord.
A ventral horn of spinal cord that is part of a cervical spinal cord.
A dorsal root of spinal cord that overlaps a cervical spinal cord.
dorsal nerve root of cervical spinal cord
posterior nerve root of cervical spinal cord
A gray matter of spinal cord that is part of a thoracic spinal cord.
A white matter of spinal cord that is part of a thoracic spinal cord.
A sulcus of brain that is part of a frontal cortex.
A white matter that is part of a medulla oblongata.
The angular vein formed by the junction of the frontal vein and supraorbital vein, runs obliquely downward, on the side of the root of the nose, to the level of the lower margin of the orbit, where it becomes the anterior facial vein. It receives the external nasal veins of the ala nasi, and communicates with the superior ophthalmic vein through the nasofrontal vein, thus establishing an important anastomosis between the anterior facial vein and the cavernous sinus.
Any of three grooves in the temporal lobe including the inferior, middle, and superior temporal sulci.
The deep auricular artery often arises in common with the anterior tympanic artery. It ascends in the substance of the parotid gland, behind the temporomandibular articulation, pierces the cartilaginous or bony wall of the external acoustic meatus, and supplies its cuticular lining and the outer surface of the tympanic membrane. It gives a branch to the temporomandibular joint.
A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component.
A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component.
An epithelium that is part of a frontonasal prominence.
A unilaminar epithelium that develops_from a ectoderm and is part of a anal region.
An anatomical space that is enclosed by a pleuroperitoneal canal.
An epithelium that is part of a median lingual swelling.
A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory.
The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells.
A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular.
A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory.
A blood vessel that drains from from an eyelid.
An artery that supplies blood to an eyelid.
In humans, the eyelids are supplied with blood by two arches on each upper and lower lid. The arches are formed by anastamoses of the lateral palpebral arteries and medial palpebral arteries, branching off from the lacrimal artery and ophthalmic artery, respectively. In amphibians, the eyelids may be supplied by branches of the lateral pretrosal arteries.[cjm]
A neuromere that is part of the presumptive forebrain.
A neuromere that is part of the presumptive midbrain.
A neuromere that is part of the presumptive spinal cord.
Any muscle organ that is part of a cloaca.
The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ.
Any collection of muscles that is part of the forelimb stylopod region [Automatically generated definition].
Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin.
Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin.
Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin).
Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin).
A ring of fibrous tissue surrounding the optic nerve at its entrance at the apex of the orbit.
Chorda tendinea which is attached to the leaflet of mitral valve and is continuous with the endocardium of papillary muscle of left ventricle.
Chorda tendinea which is attached to the leaflet of tricuspid valve and is continuous with the endocardium of papillary muscle of right ventricle.
White matter that is part of a brainstem [Automatically generated definition].
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
A muscle structure of invertebrates whose origin and insertion sites are in basal side of the epidermis or structures derived from it. The simplest somatic muscles consist of a single cell and associated extracellular structures.
The muscle that is attached at either end to the cuticle[HAO].
A somatic muscle that consists of one or more somatic muscle myotubes and any associated extracellular structures.
A portion of tissue that will develop into vasculature.
One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites.
Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4].
The space between a blood vessel and the pia mater.
VRS belonging to the subarachnoid space are continuous with VRS of the subpial space. The direct communication between VRS of the subarachnoid space and the subpial space is unique to the brain's arteries, as no leptomeningeal layers surround the brain's veins[WP]
these layers primarily refer to the mammalian future neocortex
The major preaxial endochondral element in the posterior zeugopod[Phenoscape].
A vertebral endochondral element in the cervical region of the vertebral column.
A vertebral endochondral element in the thoracic region of the vertebral column.
The major postaxial endochondral element in the posterior zeugopod[Phenoscape].
A rib bone or its cartilage or pre-cartilage precursor.
Humans have 24 ribs (12 pairs). The first seven sets of ribs, known as 'true ribs', are directly attached to the sternum through the costal cartilage. The following five sets are known as 'false ribs', three of these sharing a common cartilaginous connection to the sternum, while the last two (eleventh and twelfth ribs) are termed floating ribs (costae fluitantes) or vertebral ribs. They are attached to the vertebrae only, and not to the sternum or cartilage coming off of the sternum. Some people are missing one of the two pairs of floating ribs, while others have a third pair. Rib removal is the surgical excision of ribs for therapeutic or cosmetic reasons. In fish, there are often two sets of ribs attached to the vertebral column. One set, the dorsal ribs, are found in the dividing septum between the upper and lower parts of the main muscle segments, projecting roughly sideways from the vertebral column. The second set, of ventral ribs arise from the vertebral column just below the dorsal ribs, and enclose the lower body, often joining at the tips. Not all species possess both types of rib, with the dorsal ribs being most commonly absent. Sharks, for example, have no dorsal ribs, and only very short ventral ribs, while lampreys have no ribs at all. In some teleosts, there may be additional rib-like bones within the muscle mass. Tetrapods, however, only ever have a single set of ribs which are probably homologous with the dorsal ribs of fishes. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. The sacral ribs were stout and short, since they formed part of the pelvis, connecting the backbone to the hip bones.[1] In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis.[1]. In birds, ribs are present as distinct bones only on the thoracic region, although small fused ribs are present on the cervical vertebrae. The thoracic ribs of birds possess a wide projection to the rear; this uncinate process is an attachment for the shoulder muscles.[1]. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals.
A forelimb bone or its cartilage or pre-cartilage precursor.
A hindlimb bone or its cartilage or pre-cartilage precursor.
A phalanx bone or its cartilage or pre-cartilage precursor.
A manual digit phalanx bone or its cartilage or pre-cartilage precursor.
manual digit phalanx endochondral element
A pedal digit phalanx bone or its cartilage or pre-cartilage precursor.
pedal digit phalanx endochondral element
A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor.
pedal digit metatarsal endochondral element
A manual digit metacarpus bone or its cartilage or pre-cartilage precursor.
manual digit metacarpus skeletal element
manual digit metacarpus endochondral element
A carpus bone or its cartilage or pre-cartilage precursor.
A tarsus bone or its cartilage or pre-cartilage precursor.
A femur bone or its cartilage or pre-cartilage precursor.
A humerus bone or its cartilage or pre-cartilage precursor.
A scapula bone or its cartilage or pre-cartilage precursor.
An orbitosphenoid bone or its cartilage or pre-cartilage precursor.
A sphenoid bone or its cartilage or pre-cartilage precursor.
A limb bone or its cartilage or pre-cartilage precursor.
An endochondral element that is part of a autopod region.
An autopod endochondral element that is composed primarily of cartilage tissue.
A proximal mesopodial endochondral element that is part of a forelimb.
A proximal carpal endochondral element that is composed primarily of cartilage tissue.
A proximal carpal endochondral element that is composed primarily of a pre-cartilage condensation.
proximal carpal bone pre-cartilage condensation
A proximal mesopodial endochondral element that is part of a hindlimb.
A proximal tarsal endochondral element that is composed primarily of cartilage tissue.
A proximal tarsal endochondral element that is composed primarily of a pre-cartilage condensation.
proximal tarsal bone pre-cartilage condensation
consider merging into myocardial compact layer
perimysial connective tissue of subepicardium
Visceral intrapericardial fat contiguous with the myocardial surface.
A portion of connective tissue that is part of a prostate gland.
A large fat pad that is located at the base of the abdominal wall, in the falciform ligament of the liver.
Encapsulated adipose tissue associated with the mesentery.
A strand of hair that is part of a autopod region.
A strand of hair that is part of a manus.
A strand of hair that is part of a pinna.
A strand of hair that is part of a tail.
A strand of hair that is part of a ventrum.
A strand of hair that is part of a dorsum.
A duct that is part of a Harderian gland. opens into the conjunctival sac at the base of the nictitating membrane.
Typically a single duct per gland, but Harderian glands can have more than 1 duct, e.g. in lizards, amphisbaenids and primitive snakes (Bellairs & Boyd, 1947) and possibly some avian species (Burns, 1992)
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
A gland that is located in the ocular region, nearer the inner canthi. Typically associated with or part of the nictitating membrane, when present.
Rabbits, pigs and Mongolian gerbils have both a Harderian and a nictitans gland[ISBN:1118473523]
the distinction between Harderian and nictitans gland is only valid in mammals - the medial ocular glands in other terapods are called Harderian glands regardless of their secretion[DOI:10.1007/978-3-642-76685-5_2]
A gland that is located in or around the ocular region, nearer the outer canthi.
The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104
An anatomical space that is enclosed by a conjunctiva.
The inferior branch of the oculomotor nerve or the inferior division, the larger, divides into three branches. One passes beneath the optic nerve to the medial rectus. Another, to the inferior rectus. The third and longest runs forward between the inferior recti and lateralis to the inferior oblique. From the last a short thick branch is given off to the lower part of the ciliary ganglion, and forms its short root. All these branches enter the muscles on their ocular surfaces, with the exception of the nerve to the inferior oblique, which enters the muscle at its posterior border.
ramus inferior (nervus oculomotorius [III])
An eye consisting of multiple light-sensing organs.
present on mantle edge in arcacean Bivalvia
The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species
A blood vessel that is part of a endometrium.
A region of somite adjacent to presomitic mesoderm.
Epithelium located in the intersomitic region.
The slightly constricted part of a tooth, between the crown and the root.
An anatomical group whose component structures share a common function.
A non-connected functional system that is composed primarily of a gland.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
An anatomical conduit that is part of a ventricular septum intermedium.
An anatomical conduit that is part of a atrial septum intermedium.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
The feeding organ, a neuro-muscular pump in the head of the animal, used to ingest food, bacteria suspended in liquid, filter them out, grind them up and transport posteriorly into the instestine.
A nucleus of brain that is part of a dorsal thalamus.
Hagfish possess a habenular complex and separate nuclei in the dorsal thalamus
A nucleus of brain that is part of a ventral thalamus.
A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals.
A zone of skin that is part of a digit [Automatically generated definition].
A pancreatic lobule that is in_the_left_side_of a exocrine pancreas.
A pancreatic lobule that is in_the_right_side_of a exocrine pancreas.
A basement membrane of epithelium that is part of a respiratory system.
A lymph node that is part of a hypodermis.
A fat pad that is part of a mediastinum.
A zone of skin that is part of a axilla.
A zone of skin that is part of a external nose.
The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery.
A hepatic artery that is part of a left lobe of liver.
ramus sinister (arteria hepatica propria)
A hepatic artery that is part of a right lobe of liver.
Hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla.
A gyrus that is part of a frontal cortex.
An epithelium that is part of a anal canal.
A smooth muscle tissue that is part of a ejaculatory duct.
smooth muscle tissue layer of ejaculatory duct
An epithelium that is part of a duct of salivary gland.
A smooth muscle tissue that is part of a hypodermis.
muscle layer in fatty layer of subcutaneous tissue
stratum musculosum panniculi adiposi telae subcutaneae
smooth muscle layer in fatty layer of subcutaneous tissue
Any anatomical conduit which is part of the upper respiratory tract.
Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132].
An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper
A zone of skin that is part of a autopod region.
A portion of connective tissue that is part of a digit.
An epithelium that is part of a lobar bronchus of left lung.
An epithelium that is part of a lobar bronchus of right lung.
An epithelium that is part of a camera-type eye.
An epithelium that is part of a middle ear.
An epithelium that is part of a external ear.
An epithelium that is part of a foregut.
A lamina propria that is part of a duodenum.
Any of the lymph nodes that are part of a face.
In humans, these comprise three groups: (a) infraorbital or maxillary, scattered over the infraorbital region from the groove between the nose and cheek to the zygomatic arch; (b) buccinator, one or more placed on the Buccinator opposite the angle of the mouth; (c) supramandibular, on the outer surface of the mandible, in front of the Masseter and in contact with the external maxillary artery and anterior facial vein.
A lymph node that is located close to the surface.
A lymph node that is located deeper within the organism, further from the surface.
A lymph node that is part of a hindlimb.
A lymph node that is part of a forelimb.
The infrapatellar fat pad, also known as Hoffa's fat pad, is a cylindrical piece of fat that is situated under and behind the patella bone within the knee.
A breast that is part of a male organism.
Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall.
The line of junction between the horizontal parts of the palatine bones that extends from both sides of the skull to form the posterior part of the hard palate.
A strand of hair that is part of a head.
A strand of hair that is part of a trunk.
A hole in the diaphragm through which the esophagus passes.
A collagenous capsule covering the external surface of the liver.
It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells.
A lymph node that is part of a bronchus.
Is the sensory system for the sense of hearing.
Auditory system is general anatomical term in FMA
Luminal space of the right ventricle of the heart.
An epithelium that is part of a male urethra.
An anatomical space that is part of a duodenum.
Luminal space of the left atrium of the heart.
Luminal space of the left ventricle of the heart.
An epithelium that is part of a female urethra.
Luminal space of the right atrium of the heart.
Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border.
Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though
Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified].
We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts.
A white matter of cerebral lobe that is part of a frontal lobe.
Grey matter neocortex region of a lobe of the cerebral hemisphere.
gray matter of lobe of cerebral hemisphere
Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border.
A white matter of cerebral lobe that is part of a parietal lobe.
A white matter of cerebral lobe that is part of a temporal lobe.
A white matter of cerebral lobe that is part of a limbic lobe.
Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals.
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
A layer of of the central nervous system that is part of gray matter.
central nervous system gray matter layer
A layer of of the central nervous system that is composed of white matter.
central nervous system white matter layer
Mucus produced in the respiratory tract.
Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm).
A white matter that is part of the midbrain.
A blood vessel that is part of a cerebellum.
An roughly circular indentation in a surface.
An acellular membrane in the vestibular labyrinth that is composed of the otoconial layer, gelatinous layer, and a subcupular meshwork.
See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/132/
An acellular membrane in the inner ear that is part of the statoconial membrane and consists of long branching filaments cross-bridged to one another. The filaments are continuous with those of the otolithic membrane on one side and with the surface of the epithelium on the other.
subcupular meshwork of statoconial membrane
A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix.
auditory hillocks, pharyngeal arch 1 derived
A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus.
auditory hillocks, pharyngeal arch 2 derived
The dorsal region of the optic cup that gives rise to the dorsal part of the retina.
The ventral region of the optic cup that gives rise to the ventral part of the retina.
Primordium that develops into the central nervous system.
Primordium that develops into the nervous system.
The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints.
Epithelium lining the distalmost portion of the digestive tract.
epithelium of terminal part of digestive tract
Any muscle tissue of the distalmost portion of the digestive tract.
muscle tissue of terminal part of digestive tract
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A bony structure embedded in skin, roughly equivalent to osteoderms.
A sesamoid element that is part of a tarsal skeleton.
A set of teeth in which each tooth that attaches to a vomer.
A structure with numerous blood vessels (retia mirabilia) in the gas bladder that secretes gases from the blood.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
A primordium that has the potential to develop into a saliva-secreting gland.
A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton.
awaiting approval by phenoscape curators
proximal mesopodial endochondral element
A proximal mesopodial endochondral element that is composed primarily of cartilage tissue.
A muscle layer that is part of the rectum.
Any portion of smooth muscle tissue that is part of the rectum.
A kidney interstitium that is part of a left kidney.
A kidney interstitium that is part of a right kidney.
A renal pelvis that is part of a left ureter.
A renal pelvis that is part of a right ureter.
A renal cortex interstitium that is part of a left kidney.
cortical interstitial tissue of left kidney
A renal cortex interstitium that is part of a right kidney.
cortical interstitial tissue of right kidney
A renal medulla interstitium that is part of a left kidney.
medullary interstitial tissue of left kidney
A renal medulla interstitium that is part of a right kidney.
medullary interstitial tissue of right kidney
Encapsulated adipose tissue that is part of a tail.
The platypus uses its tail for storage of fat reserves (an adaptation also found in animals such as the Tasmanian devil and fat-tailed sheep)
Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx).
A transverse process that is part of a cervical vertebra.
May be homologous with the cervical ribs of some vertebrates
A rib that is attached to a cervical vertebra.
Trunk, presacral and sacral ribs do not have a 'part of some region' asserted for them, we should add it to them[PHENOSCAPE:ad]
May be homologous with the transverse processes of cervical vertebra
should be all Theria, see https://github.com/obophenotype/mouse-anatomy-ontology/issues/116
A zone of skin that is part of a lower lip.
A zone of skin that is part of a upper lip.
A ligament that is part of a middle ear.
An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels.
A lymphatic vessel that is part of a lung.
A capsule that divides the parenchyma of the pancreas into lobes and lobules.
A sensory tract originating in the spinal cord responsible for transmitting fine touch, vibration and conscious proprioceptive information from the body to the cerebral cortex. The components include the fasciculus gracilis and fasciculus cuneatus.
posterior column-medial leminscus pathway
posterior column-medial lemniscus system
posterior column/medial leminscus pathway
A nucleus that contain secondary neurons of the dorsal column-medial lemniscus pathway, which carries fine touch and proprioceptive information from the body to the brain. Examples: gracile nucleus, cuneat nucleus, nucleus of Bishoff.
A vein that supplies blood to the thymus.
thymic branch of internal thoracic artery
The arteries supplying the thymus are derived from the internal thoracic artery, and from the superior thyroid artery and inferior thyroids.[WP]
An artery that supplies a cervical thymus.
In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault.
Accompanying vein of internal pudendal artery.
In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
Any portion of submucosa that lines the digestive tract.
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
A muscular coat that is part of a digestive tract.
responsible for gut movement, such as peristalsis
A protuberence or true tooth that is used during hatching to break the eggshell.
Epidermal outgrowth that facilitates breaking of the eggshell in archosaurs and monotremes.
Tissue that is part of some adrenal gland.
TODO - describe typology of adrenal gland tissue used in this ontology
Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX).
A sensory receptor that detects stimulus within the body. Examples of stimuli that would be detected by interoceptors include blood pressure and blood oxygen level.
A sensory receptor that detects chemical stimulus within the body.
Cells specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.
A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment .
There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)]
Taxon nodes: In humans, refers to anterior or posterior ethmoid foramina
A vascular foramen opening on the outer surface of a nasal bone.
The anatomical space within the intestine.
see notes in inclusivity in class 'intestine'
Muscle innervated by the trigeminal nerve (Cranial Nerve V).
muscle innervated by the trigeminal nerve
muscles innervated by the trigeminal nerve
Any acellular shell or covering that surrounds the pupal form of an insect.
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
Any region of epithelium that is part of a skin region.
The part of the eye that consists of both the retina and the optic choroid.
A white matter that is part of the hindbrain.
A white matter that is part of the forebrain.
A white matter that is part of the myelencephalon.
predominantly white regional part of pontine tegmentum
Epithelial layer that is part of the external part of the nose.
The initial segment of an olfactory nerve, leaving the central nervous system.
An oily substance that prevents evaporation of the eye's tear film.
provides barrier to prevent dessication of cornea[ISBN:0123813611]
part of surface lipid layer of tear film
An exocrine gland that is part of a integumental system.
The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals.
accessory nucleus of anterior column of spinal cord
nucleus accessorius columnae anterioris medullae spinalis
See also: Wikipedia:Spinal_accessory_nucleus
A blood vessel that supplies or drains an ear.
The thalamic fasciculus is a component of the subthalamus. It is sometimes considered synonymous with 'field H1 of Forel'. Nerve fibres forming a composite bundle containing cerebellothalamic (crossed) and pallidothalamic (uncrossed) fibres that is insinuated between the thalamus and zona incerta. The thalamic fasciculus consists of the joint fibers of the ansa lenticularis and the lenticular fasciculus, coming from different portions of the medial globus pallidus, before they jointly enter the ventral lateral nucleus of the thalamus.
area subthalamica tegmentalis, pars dorsomedialis
A merocrine secretion that is produced by a Harderian gland, containing lipids.
in amphibians, chiefly seromucoid with some lipids[PMID:7559104]
in birds, mucoid and lipid[PMID:7559104]
in mammals, predominantly lipid; mucoid secretion restricted to extraglandular duct tissue[PMID:7559104]
in the armadillo and opossum, mucous or serous acini may be present[PMID:7559104]
The single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland).
in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe
A secretion that is produced by a nictitans gland, containing glycoprotein.
seromucuous in cattle, cat and dog, elephant [ISBN:1118473523]
An aqueous substance that covers the anterior surface of the eyeball, keeping the cornea wet.
the thin acellular fluid layer that adheres to the most superficial layer of the corneal epithelium and lubricates and protects the ocular surface; the film is generally composed of three layers: (i) an inner mucous layer, secreted largely by the conjunctival goblet cells with contributions from the lacrimal glands, which coats the cornea, provides a hydrophobic layer, and allows for even distribution of the tear film; (ii) a middle aqueous layer, secreted by the lacrimal glands, which keeps the corneal surface moist, and provides a mechanism for oxygenation and nutrient exchange with the avascular anterior corneal tissue; and (iii) an outer lipid layer, secreted principally by the Meibomian (tarsal) glands although lipid tear elements also are contributed by the Harderian glands; tear film lipids form a monolayer on the tear surface, and function by enhancing the surface tension which supports the integrity of the tear film against collapse due to gravity and also slows down the loss of the tear film by evaporation; in addition , the lipid layer provides a glassy, smooth interface between the air and the transparent cornea
maintenance of the avascular transparent corneal epithelium
The tear film is structurally complex with three distinct layers: a surface lipid layer, a middle aqueous layer, and an inner mucus layer[http://physiologyonline.physiology.org/content/13/2/97]
A portion of organism substance that is secreted by a reproductive gland.
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
Surface layer of the olfactory cortex that contains dendrites, fiber systems and a small number of neurons. It has been divided into a superficial part and a deep part.
Middle layer of olfactory cortex lying deep to layer 1 and superficial to layer 3, characterized by a compact layer of cell bodies. It can be divided into a superficial part and a deep part.
dorsal cochlear nucleus pyramidal cell layer
Serous membrane layer that is adjacent to and lines an organ.
Serous membrane layer that lines to a body cavity.
The layer of endometrial epithelium adjacent to the uterine cavity.
A mammary gland duct that is part of a male organism. This structure typically regresses.
A specific region of the foregut into the area in which the lung will develop.
A set of neural structures that subserve a specific function, e.g., visual system.
this class was inherited from NIFSTD as part of the replacement of NIFSTD with Uberon. It may be obsoleted in the future
White matter that lies deep to the granular cell layer of the cerebellar cortex. It contains afferents to the cerebellar cortex and axons that run between the cerebellar cortex and the deep cerebellar nuclei.
The part of the central nervous system that is involved with movement.
It consists of the pyramidal and extrapyramidal system
The sensory system for the sense of proprioception.
A taste bud that is located on the soft palate, in the roof of the mouth.
Any organ that is the primary organ of vocalization behavior. Examples: The laryngeal vocal cord (humans), the syrinx (birds).
An embryonic or larval epithelium that is committed to form part of the nervous system.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047]
spinal cord lateral wall ventricular layer
The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate.
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.
A cranial nerve fiber tract that innervates the parietal eye.
This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN:0471888893]
A cranial nerve fiber tract that innervates the pineal body.
A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish.
A taste bud that is located on the skin of the head.
A taste bud that is located in the pharynx.
A taste bud that is located on the roof of the mouth.
A taste bud that is located in the esophagus.
A taste bud that is located on the skin of the trunk.
The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa.
Telencephalic white matter which extends between the olfactory bulb and the ipsilateral dorsal telencephalon and carries secondary olfactory fibers. From Neuroanatomy of the Zebrafish Brain.
olfactory tract linking bulb to ipsilateral dorsal telencephalon
A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
Any substance in the body or expelled from the body that is in a gaseous state.
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
The outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland.
The area of axial mesoderm that develops into the prechordal plate.
The thickened ridge of bone that contains the tooth sockets on the premaxilla.
Endocardium that is part of the left atrium.
Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein.
Parenchymal tissue that forms the pineal gland.
Any of the muscles that are responsible for moving the scapula. In humans these are the levator scapulae, the infraspinatus muscle, the teres major, the teres minor, and the supraspinatus muscle.
A cranial suture in the midline of the skull that connects the left and right maxilla bones.
in humans, the upper maxillae (the upper jaw) is composed of the right and left maxilla bones, which are fused in the midline at the intermaxillary suture to form the upper jaw.[https://orcid.org/0000-0001-5889-4463]
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
An anatomical collection that is arranged in a line.
resolve if this should be a subclass of or merged with aligned anatomical group.
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts.
Any organ component layer that consists of smooth muscle tissue.
An enlarged chamber in the blood sinus capable of accumulating a large volume of blood.
organ region with floating fiat boundary
Any gaseous product of an excretory process.
Any excreted gas that is produced by the digestive tract.
In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum
Any portion of gas located in a part of the respiratory system.
Any portion of gas located in a part of the respiratory system that is composed primarily of carbon dioxide.
A population of lymphatic endothelial cell precursors that will form the lymph vessels.
Mesenchyme that is part of a developing jaw [Automatically generated definition].
A peripheral terminal of a peripheral, afferent sensory pain receptor cell that is sensitive to injury or pain, usually caused by extreme thermal exposures, mechanical forces, or other noxious stimuli. The nociceptor nerve ending innervates target tissue and transduces noxious stimuli to the central nervous system via some axon(s).
Cellular receptors which mediate the sense of temperature. Thermoreceptors in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and NOCICEPTORS which detect cold or heat extreme enough to cause pain.
An epithelium that is part of an eyelid [Automatically generated definition].
An epithelium that is part of a naris [Automatically generated definition].
Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized].
A vertebra that has a transverse process.
A post-anal tail that attaches outside the tail.
A transverse process that is part of a caudal vertebra.
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
The flattened aspect of the prostate with a slight furrow facing the rectum and anus.
The organ of hearing located on the right side of the head.
The tubules that carry lymph throughout the body that are just beneath the surface of the skin.
The narrowest portion of the gallbladder and distal to the cystic duct.
The organ of hearing located on the left side of the head[ncit,modified].
The membrane the surrounds the prostate gland.
trunk of right common iliac arterial tree
A lymph node located in the retroperitoneal space.
An artery that supplies the pituitary gland.
The parietal pleura that lines the mediastinum.
A vein that drains blood from the right adrenal gland into the inferior vena cava.
The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces.
A vein that drains blood from the left adrenal gland into the left renal artery.
The aspect of the prostate facing the pubic symphysis.
trunk of left common iliac arterial tree
Any of several arteries that arise from the aorta and supply blood to the esophagus.
The tubules that carry lymph throughout the body that are in the interior of the body or limbs.
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
Any chamber of the left side of the heart.
Any chamber of the right side of the heart.
An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.
ophthalmic lobe of trigeminal placode complex
Any lymph vessel that is located in the dura mater of the brain.
while Louveau et al (DOI:10.1038/nature14432) state this is within the CNS (thus overturning dogma about the presence of lymphatics in the CNS), in this ontology the dura
Louveau et al (DOI:10.1038/nature14432) claim the discovery of lymphatics in the cerebral dura mater, but this is disputed by Bucchieri et al (DOI:10.1111/joa.12381)
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.
A portion of semen in a coagulated state.
The primordial mouth region of the developing head.
A muscle layer that is part of the sigmoid colon.
The sum of epicardial and paracardial fat deposits.
Fat deposits in the mediastinum outside the parietal pericardium .
Any fat deposit surrounding a visceral organ.
The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity.
A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity.
The thick outer layer of the adrenal gland that is in the left side of the abdomen.
The adrenal gland medulla that is in the left side of the abdomen.
The thick outer layer of the adrenal gland that is in the right side of the abdomen.
The adrenal gland medulla that is in the right side of the abdomen.
A suture between the orbital surface of the body of the maxilla with the orbital plate of the ethmoid bone.
An inconstant suture between the pterygoid process of the sphenoid bone and the body of the maxilla.
A suture between the maxilla and premaxilla.
The endocardial cushion that forms on the ventral surface of the AV canal.
The endocardial cushion that forms on the dorsal surface of the AV canal.
One of two longitudinal ridges that develop caudal to the pharynx and fuses to give rise to the tracheoesophageal septum.
The tracheoesophageal septum is formed from the tracheoesophageal folds which fuse in the midline to form a structure called tracheoesophageal septum. It divides the esophagus from the trachea. It divides the foregut tube into the laryngotracheal tube ventrally and esophagus dorsally. Developmental abnormalities can lead to a tracheoesophageal fistula.
respiratory primordium associated mesenchyme
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
An organ subunit in the skin that gives rise to cutaneous appendage.
An anatomical junction that is between the sigmoid colon and rectum.
Material anatomical entity that forms the outermost boundary of an anatomical structure.
A bodily fluid that is located in the coelom.
he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]
The corticobulbar and corticospinal tracts combined.
Any gland that is part os the respiratory system.
A notochord that has persisted beyond the embryonic stage.
Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands.
Parenchymal tissue that consists of the alveoli, grape-like clusters where milk is stored, and branching ducts, which are tubular canals carrying gladular secretions.
Any synovial joint that connects auditory ossicles.
The system that is responsible for sensing the internal state of the body.
Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments.
The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit.
ramus zygomaticotemporalis (Nervus zygomaticus)
ramus zygomaticotemporalis nervus zygomatici
zygomaticotemporal branch of zygomatic nerve
Wall of ventricle which is continuous with the wall of aorta.
Wall of ventricle which is continuous with the wall of pulmonary trunk.
Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle.
myocardium of anterior wall of left ventricle
myocardium of anterior wall of right ventricle
A mucosa that is part of a lip region [Automatically generated definition].
The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra.
vasculature of central nervous system plus retina
An anatomical structure that is located along the line dividing two regions of an anatomical structure.
Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees.
An artery that supplies oxygenated blood to the cystic duct.
Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament.
Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament.
A collection of hairs that grows on the external ear.
A zone of skin that is part of the face.
The parenchyma of the spleen, consisting of lymphocytes and macrophages. It lies between the splenic trabecula. Red pulp is the part suffused with blood and white pulp consists of areas of lymphatic tissue where there are sleeves of lymphocytes and macrophages.
An anatomical junction between two parts of the digestive tract.
A sinus located in a lymph node. Lymph nodes have subcapsular, cortical (trabecular) and medullary sinuses.
Small but distinctive epithelial sac containing fluid, located midventrally posterior to the yolk cell or its extension, and transiently present during most of the segmentation period. Kimmel et al, 1995. Kupffer's vesicle has been compared to the mouse embryonic node. Drummond et al, 2005.
This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Ganglion that develops from a cranial ectodermal placode and contains sensory neurons that innervate a lateral line.
Cranial nerve which enters the brain between cranial nerves VIII and IX; contains afferents and sensory efferents to the posterior lateral line ganglion and middle ganglion. Fibers from the posterior lateral line ganglion innervate the occipital dorsal lateral line and trunk lateral lines.
olfactory tract linking bulb to ipsilateral ventral telencephalon
Cranial nerve which enters the brain between cranial nerves VI and VII; contains afferents and sensory efferents to the anterior lateral line ganglia.
Musculature that is part of the dorsal fin.
Neuromast that is part of the posterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.).
A migrating group of cells originating from the posterior lateral line placode. The primordium deposits seven to nine neuromasts and interneuromasts between them during its posterior migration to the tail. Gompel et al, 2001.
Fin or limb undergoing the process of regeneration.
The posterior lateral line ganglion develops from a cranial ectodermal placode and contains sensory neurons that innervate the posterior lateral line system.
Dorsolateral placode that gives rise to the anterior lateral line.
Lateral line placode that gives rise to the anterior lateral line nerve[XAO:0004221, XAO:EJS].
An epithelium that is part of a regenerating fin/limb.
The anteror lateral line ganglia develops from cranial ectodermal placodes and contain sensory neurons that innervate the anterior lateral line system.
Cartilage which is part of the axial skeleton.
The anterior lateral line system develops from cranial ectodermal placodes, situated between the eye and the ear, that give rise to both the neuromasts and the anterior lateral line sensory nerves that innervate the neuromasts. The anterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians and are innervated by several lateral line nerves, which project to the hindbrain. The anterior lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.
The anterior lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The anterior lateral line develops from cranial ectodermal placodes situated between the eye and ear.
The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance.
Neuromast that is part of the anterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.).
Tooth that is attached to the premaxilla.
Tooth that is attached to the ectopterygoid bone.
Joint that articulates the left and right premaxillary bones. Inter-premaxillary joint is unpaired.
Joint that articulates the premaxilla and maxilla. Premaxillary-maxillary joint is paired.
A migrating group of cells originating from an anterior lateral line placode. The primordium deposits neuromasts and interneuromasts between them during its migration.
Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse.
the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences
Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA].
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
Dermal, epidermal, glandular and pigment structures of the external head integument.
Dermal, epidermal, glandular and pigment structures of the body integument.
Dermal, epidermal, glandular and pigment structures of the limb integument.
Dermal, epidermal, glandular and pigment structures of the tail integument.
Extracellular matrix that is mineralized.
This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Bone tissue mineralized with hydroxyapatite.
Fin that is an unpaired fin located in the sagittal plane of the organism.
Median fin that is located posterior to the anus.
The caudal fin is the most posterior median fin. It is composed of a complex of modified centra and modified neural and hemal arches and spines.
Median fin skeleton that is located posterior to the anus.
Median fin skeleton supporting the caudal fin.
Median fin skeleton located on the dorsal surface of the organism.
Postcranial axial skeleton that is unpaired and located on the sagittal plane of the organism.
Anatomical projection that is composed of bone or cartilage tissue.
An anatomical surface that is part of a bone.
A paired fin bud that develops into a pectoral fin.
A paired fin bud that develops into a pelvic fin.
Mesenchyme that is part of a forelimb bud.
Mesenchyme that is part of a hindlimb bud.
Mesechyme that is part of a pectoral fin bud.
Mesechyme that is part of a pelvic fin bud.
Mesenchyme that is part of a forelimb wing bud.
A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit.
pedal digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
manual digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element.
this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials.
A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element.
A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element.
individual digit of digitopodial skeleton
One of the main divisions of the whole organism of arthropods formed from groups of segments.
Strictly speaking the term "tagma" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods.
Any segment that is part of some insect head.
The main middle section of the insect body comprising three thoracic rings: the pro-, the meso- and the metathoraces which are more or less well fused and cask-like sometimes having on the upper lateral part one of two pairs of wings, while on the ventrolateral part each thoracic ring bears a pair of legs.
Any segment (UBERON:6000003) that is part of some thorax (UBERON:6000015).
The region of the ectoderm anterior to the cephalic furrow.
Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052).
Any insect segment that is part of some embryo.
Any segment that is part of some insect embryonic head.
Any thorax (UBERON:6000015) that is part of some embryo (UBERON:6000052).
Any segment (UBERON:6000003) that is part of some embryonic thorax (UBERON:6000166).
Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727).
Any segment that is part of some larval head.
Any thorax (UBERON:6000015) that is part of some larva (UBERON:6001727).
Any segment (UBERON:6000003) that is part of some larval thorax (UBERON:6001741).
Any sense organ that is part of some larva.
Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004).
Any segment (UBERON:6000003) that is part of some adult thorax (UBERON:6003018).
Section of the insect foregut anterior to the esophagus.
Any appendage segment that is part of some antenna.
Any appendage segment that is part of some leg.
Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727).
Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730).
Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730).
insect embryonic/larval head sense organ
An insect embryonic structure that develops from the anterior ectoderm.
The tibial tuberosity is on the anterior side of a tibia and is where a patella ligament attaches.
Nasal bone on the left side of an organism when in anatomical position.
Nasal bone on the right side of an organism when in anatomical position.
Part of the orbital plate formed by the jugal (part of the zygomatic), lacrimal (which is sometimes fused), sometimes nasal (typically in species with elongated rostra), and maxilla bones anterior to the orbit.
A hollow (fossa) in the preorbital region, typically lying on the maxillary bone, although sometimes can touch nasal bones (e.g., modern Equus).
A suture joining a sphenoid bone with the alae of a vomer to form a schindylesis type of joint.
An epithelial layer that lines the ascending colon.
An epithelial layer that lines the transverse colon.
An epithelial layer that lines the descending colon.
An epithelial layer that lines the sigmoid colon.
Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles.
A forelimb that is on the right side of a pectoral complex.
A forelimb that is on the left side of a pectoral complex.
A hindlimb that is on the right side of a pelvic complex.
A hindlimb that is on the left side of a pelvic complex.
Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact.
Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson.
Region of liver parenchyma immediately below the capsule. This region is frequently specified in pathology diagnoses.
A lymphatic vessel that supplies the small intestine.
A venule that is located in the anorectum.
An arteriole that is located in the anorectum.
The anatomical junction between the descending colon and the sigmoid colon.
A portal vein that drains the descending colon. It is a tributary of the inferior mesenteric vein, and follows the path of its corresponding artery, the left colic artery.
A portal vein that drains the ascending colon. It is a tributary of the superior mesenteric vein, and travels with its corresponding artery, the right colic artery.
An anatomical junction between two parts of the intestine.
The trabecular sinus is the lymph-filled space outside the trabeculae between lobules of the lymph node. This is a continuation of the subcapsular sinus which receives the afferent vessels and is present beneath the capsule. This space is traversed by both reticular fibers and cells in the lymph.
A vein where lymph node venules condense and which exits at the lymph node hilum. It is also called hilar vein.
An artery that enters the lymph node at the hilum and branches into smaller arterioles.
An arteriole that arises from the hilar artery of a lymph node and radiates centrifugally, branching in the medulla.
Medullary venules are a continuation of high endothelial venules which condense repeatedly in the interfollicular cortex and peripheral deep cortical unit and then transition to medullary venules at the corticomedullary junction. The medullary venules condense and return centripetally to the hilar vein.
An arteriole that is part of a lymph node.
A submucosal gland located in a bronchus.
A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus.
The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum.
A lymphatic vessel located in the colon.
A capillary that is part of the anorectum.
A capillary that is part of a small intestine.
blood vessel capillary of small intestine
A submucosal gland found in a respiratory tract.
Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.
One or a subset of adjacent layers of the neocortex.
Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin).
An individual reproductive unit containing a single oocyte and one or several layers of support cells (Armstrong et al., 2020).
An anatomical system that eliminates waste products that arise as a result of metabolic activity.
A craniocervical region that is part of an embryo.
A portion of smooth muscle tissue that is part of an iliac vein.
A portion of smooth muscle tissue that is part of the thoracic aorta.
A portion of smooth muscle tissue that is part of an iliac artery.
An endothelium that is part of an iliac vein.
An endothelium that is part of the placental artery.
Lymphatic vessel that is part of the mesentery.
A zone of skin that is above the clavicle zone in the pectoral girdle region.
A zone of skin that is above the iliac crest in the pelvic girdle bone/zone.
A zone of skin that is part of the external genitalia.
A zone of skin that is part of the breast.
Subserosa that is part of the uterine tube. It contains loose connective tissue, blood vessels and lymphatic tissue.
A portion of smooth muscle tissue that is part of a saphenous vein.
The facial tuberosity (tuber faciale) is a prominence located on the facial surface of the maxilla; it finishes the facial crest and varies much according to the species.
it is well developed in equids; it is above the first molar tooth in ruminants; it is above the second molar tooth in sheep
A muscle tissue that is associated with soft internal organs (viscera).
It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated.
A striated muscle tissue that is associated with soft internal organs (viscera).
A spherical or tubular structure in a submucosal gland that produces and secretes mucus and other substances into the ducts leading to the surface epithelium.
A discrete anatomical unit of the lung that is composed of a segmental bronchus and the lung tissue supplied by that bronchus. A bronchopulmonary segment exhibits a pyramidal shape, with its apex pointing towards the center of the lung and its base toward the pleural surface.
A bronchopulmonary segment is surrounded by connective tissue septa, which are continuous with the pleural surface and prevent air collateralization between segments somewhat. In humans, the right lung has ten bronchopulmonary segments and eight or nine bronchopulmonary segments in the left lung.
A regulatory system of the body that integrates the nervous system and the endocrine system. This system is formed by specialized neuroendocrine cells located mainly in the nervous system and neuroendocrine glands. However, they can also be found as either single cells or small clusters of cells dispersed throughout the surface epithelium of different tissues. The neuroendocrine system functions through the release of neurotransmitters and neurohormones, enabling communication between the endocrine and nervous systems to govern vitally important processes that include growth, reproduction, metabolism and energy homeostasis, electrolyte and water balance, and responses to stress.
In vertebrates, the hypothalamic-pituitary-target organ axis (H-P axis), the autonomic nervous system (ANS) and the diffuse neuroendocrine or APUD system contribute to the neuroendocrine system.
A blood vessel that is part of the chorionic plate.
A stroma that is part of a chorionic villus (placental villus). A placental villous stroma supports the fetal capillaries and villous trophoblast.
A venule that is part of a lung and drains oxygenated blood from pulmonary capillaries. A pulmonary venule merges into a pulmonary vein branch that runs in the pulmonary interlobular septa.
A disc-shaped structure that is part of the placenta. A placental disc supports fetal development through the exchange of nutrients between maternal and fetal bloodstreams. The placental disc is structured to keep the blood streams separate, while maximizing surface area for the transport of nutrients between them, to maintain an immunological barrier.
A mesenchyme that is part of a chorionic villus.
A lymphatic vessel that is part of an endometrium.
A ganglion that is part of the atrial region of the heart. The activation of efferent neurons in this ganglion results in the modulation of heart rate, atrio-ventricular node conduction, and inotropism of atria and ventricles.
A parasympathetic ganglion that is located within the airway walls of the lower respiratory tract. This ganglion is responsible for controlling the constriction of the airway by stimulating smooth muscle contraction in the lower respiratory tract to regulate airflow.
A simple columnar epithelium that is part of the fallopian tube.
The lamina propria that underlies the epithelial lining of the ascending colon.
The lamina propria that underlies the epithelial lining of the descending colon.
The lamina propria that underlies the epithelial lining of the sigmoid colon.
The lamina propria that underlies the epithelial lining of the transverse colon.
The lamina propria that underlies the epithelial lining of the stomach.
The lamina propria that underlies the epithelial lining of the caecum.
The lamina propria that underlies the epithelial lining of the rectum.
A surface structure that is part of a calcareous tooth.
An anatomical cavity that is part of the alveolus of the lung
The epithelium that lines the anorectum.
midface division only makes sense for gnathostomes
myelin not present in all taxa that have a commissure
may be present in other parts in other species
conservatively place at deuterostome, excluding acoelomates