Property:Comment
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Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron +
note that in ISBN10:0073040584 "Vertebrates, Kardong", the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA +
Taxon notes: Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO +
taxon notes: 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) [PMID:20959416] +
Editor notes: 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) +
Editor note: kidney terms require review for cross-vertebrate compatibility and developmental relationships. Taxon notes: 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)[GO Kidney] +
Taxon notes: A similar, but probably non-homologous, structure is found in cartilaginous fishes[WP]. Kardong has epididymis in elasmobranch.Structures notes: 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. +
Taxon notes: mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/ +
AO notes: 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. +
Terminology notes: see notes on UBERON:0000978 for possible confusion over the term 'leg'. +
Note that 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 +
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)[vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf] +
AO notes: 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 +
AO notes: FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra +
Alternate definition: Organ with cavitated organ parts, which primarily consists of compact (cortical) and cancellous bone, which surround bone marrow cavities; together with other bones, cartilages and joints, it constitutes the skeletal system. Examples: femur, sternum, maxilla, vertebra, talus[FMA] +
Editors notes: this should be reviewed for pan-vertebrate applicability. Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) +
GO says gut is region of DT, from intestines to anus. ZFA treats as synonym for alimentary canal, and treats it as the sum of DT + organs (ZF has no term from stomach). GO says intestines to anus (excludes stomach and esophagus). MA appears to agree with GO (stomach and esophagus are not parts). FMA includes stomach and esophagus as parts of gut -- the FMA divides gut into lower and upper GI tract; it's not clear if this is exhaustive (small intestine is in neither), but lower GI tract may correspond better to the GO definition. NOTE: GO now changed, see sf id in def xref. Note that FMA also has a term 'gastrointestinal tract', but this includes the liver +
AO notes: 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. Editor notes: todo - resolve discrepancies in which muscles are considered extra-ocular. Taxon notes: Mammals have 7 extra-ocular muscles, but humans lack the M. retractor bulbi. Note in ZFA this is the set of muscles. +
Editor notes: 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. +
The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. AO notes: Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA. Taxon notes: fusion of squamosal + angular (tympanic annulus) [derm] + petrosal (prootic + opisthotic)[chond] + styloid process[splanc.] +
Development notes: 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]. Composition notes: 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[WP] AO notes: It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... +
TODO: check claw vs nail. A primate's nail consists of the unguis alone; the subunguis has disappeared. +
the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures[HP] +
TODO: move ZFA:0001227 (it is the entire jaw skeleton). Editor notes: 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. Development notes: There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). +
AO notes: Note isa/partof difference MA/FMA. See notes for jaw w.r.t skeletal element vs subdivision of head +
Editor note: split out MA ter,. Note the MA term is part of the CNS. This needs to be checked w.r.t relationship between ganglia and the PNS, as the PNS and CNS are spatially disjoint. also meaning of MA term is not clear (appears to be union of nerve and ganglion, but MA 'cranial nerve' is unconnected) +
editor notes - 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. Taxon notes: 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. Development notes: 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 +
AO notes: MA and FMA differ regarding isa vs partof to vascular layer. Taxon notes: The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development - dx.doi.org/10.1006/dbio.1998.9019 +
Note that 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 +
editor note - we follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers +
Editors note: not classified as a nerve in FMA. Note the structure of EMAPA is rather odd here - EMAPA:17264 (nerve of CNS) has a single child, cranial. We make EMAPA:17264 a subclass of this structure, as this appears to be the intent +
Note that FMA distinguishes between a portion and the whole portion. We equate with whole portion here, but this is arbitrary +
Note - in many AOs these are exact synonyms, but FMA has a part of link between portion of vitreous humor and this +
Usage notes: this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former +
Arise as epithelial lined diverticula of the lining of the nasal cavity. The extent of sinus development varies with species, most of the development occurs postnatally +
Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved. +
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)" +
inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the edinburgh terms 'labyrinth' belong, we place them here for now +
Editor note: Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though [MM] +
CHECK - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM) +
CHECK - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM) +
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. ISBN10:1588900649 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 +
AO notes: MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype +
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 cerbral hemisphere +
Editors note: developmental relationships need revised. AO notes: part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships +
The telencephalon is the name for a large region within the brain that is attributed many functions. Many people refer to it as the cerebrum; however, it is technically referred to as the telencephalon. As a more technical definition, the telencephalon refers to the cerebral hemispheres and other, smaller structures within the brain, although the telencephalon is one of the larger divisions (in terms of number). It is the anterior-most embryological division of the brain that develops from the prosencephalon. The telencephalon is composed of the following sub-regions; Limbic system; Cerebral cortex or cortices of the cerebral hemispheres, Basal ganglia, Olfactory bulb. The telencephalon comprises what most people think of as the 'brain' It lies on top of the brainstem and is the largest and most well-developed of the five major divisions of the brain. The telencephalon is the newest structure in the phylogenetic sense, with mammals having the largest and most well-developed among all species. It emerges from the prosencephalon, the first of three vesicles that form from the embryonic neural tube (Christine Fennema-Notestine, NIF_GrossAnatomy:birnlex_1115). +
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]. +
AO notes: MA and ZFA think there is a distinct dorsal thalamus, but FMA says its an exact synonym. FMA has a distinct class for thalamic complex. +
Note that this class corresponds to the generic mammary gland. The human mammary gland is in the thoracic/breast region and is therefore covered by the subclass "thoracic mammary gland" // Males typically only have rudimentary mammary glands, The male Dayak fruit bat has lactating mammary glands. Male lactation occurs infrequently in some species. We make a part_of association to female organism for now as this is the canonical case +
WP: 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.[82] 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.[86] 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.[80] There is evidence that damage to the lateral pallium impairs spatial memory. +
note that FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX. Taxon notes: annelids have blood vessels, but this class is not applicable to annelids. +
The term 遯ｶ蛟ｪ�閼㌻dothelium遯ｶ蜷ｮ�� 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) +
Taxon notes: 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 [ISBN10:0073040584 "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 placenta, with reduced nutrient and oxygen exchanging capabilities. +
The white fibrocartilages admit of arrangement into four groups遯ｶ逅ｶnterarticular, connecting, circumferential, and stratiform -- WP. TODO: add mineralized +
There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. +
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 +
note that 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 +
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 +
NKT.44-NK1.1-.Th was assigned as an exact synonym based on sorting strategy displayed at immgene.org. +
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] +
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 +
Note that this class combines superficial fascia and hypodermis in FMA. Note also BTO has 'subcutis' +
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs +
Note that 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. +
Note that 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. +
Note that FMA uses 'skin' for the entire organ. XAO seems consistent. MA seems to use it analagously to zone of skin +
AO notes: note that this corresponds to FMA:'free upper limb' (a limb segment), NOT 'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Usage notes: Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm +
AO notes: 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 +
Taxon notes: 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) [PMID:20959416] +
AO notes: 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. Taxon notes: WP: 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.[7] 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. +
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) +
Taxon notes: 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[Wikipedia:Ovary#In_other_animals] +
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 +
note that BTO may contain an error here. Also note we may need to introduce taxon-specific developmental relationships: "While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke遯ｶ蜀ｱ pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head"[NBK53175] +
Editor/AO notes: 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). Taxon notes: covers the brain dorsally in chondrichthyans +
Editors note: 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 {source +
editor note: 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 +
note - 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 +
note that this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation. +
'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 (ISBN10:0471888893). 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). +
In adult humans it is present only in the mesencephalon as the inferior and the superior colliculi[WP]. +
WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. +
This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive. +
Development notes: 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 +
Editor notes: currently classified as an epithelial vesicle, consistent with EHDAA2 and UBERONREF:0000002. 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 // 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] +
Editor note: consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). Taxon notes: 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]. 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. +
Terminology notes: we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here +
Note that MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs +
Editor note: consider separate term for meninges aka collection of meninges. Note in EHDAA2 pia mater etc are part of the meninges. Also consider a new class for primary/primitive meninx. AO notes: Not consider part of the CNS/neuraxis in FMA. Taxon notes: 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). +
Editor note: 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 +
Function notes: capable of inducing chondrogenesis - requires contact with an epithelium - PMID:16496288. AO notes: in ncit this is divided into periosteal layer and meningeal layer +
Taxon notes: 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 +
check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland +
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 +
Most commonly, the term "tonsils" refers to the palatine tonsils that can be seen in the back of the throat. +
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 path is as follows: Bile canaliculi 遶� Canals of Hering 遶� interlobular bile ducts 遶� intrahepatic bile ducts 遶� left and right hepatic ducts merge to form 遶� common hepatic duct exits liver and joins 遶� cystic duct (from gall bladder) forming 遶� common bile duct 遶� joins with pancreatic duct 遶� forming ampulla of Vater 遶� enters duodenum [WP] +
Editor notes: Consider changing name to make distinction from inferred superclass 'vertebral element' clear +
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] +
Editor note: 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. +
Usage notes: 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[NIF]. 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 +
ETPs are reportedly CD1a-negative, CD4-negative, CD7-positive, CD8a-negative, CD8b-negative, CD33-low, CD34-high, CD38-low, CD45RA-positive, and CD45RO-negative. +
AO notes: NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle // Note that the formal definition is very inclusive, and includes sesamoids +
AO notes: FMA divides striatum of neuraxis into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see http://en.wikipedia.org/wiki/Striatum#History. Check caudoputamen +
