uberon.github.io

/releases/2014-06-15

This release includes some improvements to the representation of buccinator, orbicularis oris and digastric muscles, based on the Mammalian Feeding ontology FEED. A number of improvements were made to the skeletal system, continued implementation a standard pattern for endocondral bones with particular attention to the ribs and vertebrae. A number of new classes for a variety of systems have been added, including term requests for ENCODE. This release also marks the debut of the platypus bill.
/releases/2014-06-15 image

Note that the diff report for this release is large due to some systematic changes in how textual metadata about classes is stored in the ontology

  • skeletal
    • AXIAL: rib and vertebrae overhaul. Implemented endochondral pattern consistently.
    • CRANIAL: mapped ZFA orbit to orbital cavity. See issue 462
    • CRANIAL: renaming jaw joint. Issue issue 463
    • LIMB: Abstracted classes with full endochondral triad for proximal and distal mesopodials. Addresses issue 461
    • LIMB: Fixed proximal carpals to use consistent pattern
    • UPPER: reclassified some classes as being cartilage elements rather than cartilage tissue
  • muscles
    • FEED: created xrefs to MFMO (Feed ontology)
    • FEED: Buccinator improvements. Issue issue 470. FEED:rd and cw
    • FEED: Text amd logical def of orbicularis oris. Extended FEED def with surrounds relation. Issue issue 473
    • FEED: some changes to digastric based on conv with FEED:rd, added notes about Orangutans
    • LIMB: improving defs of calf muscles
    • SMOOTH: NTs for smooth muscle tissue and layer of muscle in rectum. Fixes issue issue 465
    • EAR: NTs for 3 external auriculars
  • other
    • GLANDULAR: ducts, grouping organs and
    • GLANDULAR: NT ampullary gland secretion
    • MAMMAL: NTs for platypus nill
    • RENAL: NTs for lateral renal structures: interstitium (cortex, medulla), renal pelvis. Fixes issue issue 466 Fixes issue issue 467 Fixes issue issue 468
    • EYE: eyelid def updated
  • admin/general
    • PROPERTIES: translation of comments to specific annotation assertions (editor notes, curator notes, taxon notes, etc)
    • DEFINITIONS: making WP-derived defs more concise
    • METADATA: Fixed consider link. Fixes issue issue 436
    • RELATIONS: Fixed RO ID. Fixes issue issue 447
    • METADATA: Added DOIs. Issue issue 473
    • METADATA: Fixing xref syntax in ext

Ontology Diff Report

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-05-27/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-06-15/uberon.owl

Report for classes

Class objects lost from source: 4

Class objects new in target: 38

New Class : distal mesopodial endochondral element

New Class : caudal vertebra endochondral element

New Class : anterior perforated substance

New Class : mammary lobe

New Class : transverse process of lumbar vertebra

New Class : lumbar rib

New Class : cervical rib

New Class : transverse process of cervical vertebra

New Class : ampullary gland secretion

New Class : periovarian fat pad

New Class : monotreme bill

New Class : tail fat pad

New Class : fibrocollagenous connective tissue

New Class : rugal fold of scrotum

New Class : premaxillary fenestra

New Class : maxillary fenestra

New Class : right renal medulla interstitium

New Class : right renal cortex interstitium

New Class : left renal medulla interstitium

New Class : right renal pelvis

New Class : left renal cortex interstitium

New Class : right kidney interstitium

New Class : left renal pelvis

New Class : rectum smooth muscle tissue

New Class : left kidney interstitium

New Class : posterior auricular muscle

New Class : muscle layer of rectum

New Class : posterior fascicle of palatopharyngeus

New Class : parafoveal part of retina

New Class : perifoveal part of retina

New Class : foveola of retina

New Class : superior auricular muscle

New Class : anterior auricular muscle

New Class : distal mesopodial cartilage element

New Class : distal mesopodial pre-cartilage condensation

New Class : distal mesopodial bone

New Class : proximal mesopodial endochondral element

New Class : proximal mesopodial cartilage element

Changed Class objects: 1427

Changes for: base of crypt of lieberkuhn

  • Deleted
    • - base of crypt of lieberkuhn taxon notes Clearly defined prolifieration zones found in mammals. Not observed in agnathostomes, larval amphibians. Described in advanced species of fish and adult amphibians. [ISBN:9780521617147]
  • Added
    • + base of crypt of lieberkuhn taxon notes Clearly defined prolifieration zones found in mammals. Not observed in agnathostomes, larval amphibians. Described in advanced species of fish and adult amphibians. { source=ISBN:9780521617147 }

Changes for: dartos muscle of scrotum

  • Deleted
    • - dartos muscle of scrotum external ontology notes the FMA class appears to belong here due to its synonyms. Function notes: The tunica dartos acts to regulate the temperature of the testicles, which promotes spermatogenesis. It does this by expanding or contracting to wrinkle the scrotal skin. The wrinkled (rugose) appearance of the scrotum is due to this layer of fascia[WP] { external ontology=FMA }
  • Added

Changes for: ilio-marsupialis muscle

  • Deleted
    • - ilio-marsupialis muscle comment Associated with lumbar musculature. originally postulated to be involved in mile ejection, or for mammary support and for retraction of the teats.
  • Added
    • + ilio-marsupialis muscle function notes Associated with lumbar musculature. originally postulated to be involved in mile ejection, or for mammary support and for retraction of the teats.

Changes for: body proper

Changes for: digit 3 digitopodial skeleton

  • Deleted
    • - digit 3 digitopodial skeleton comment 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.
  • Added
    • + digit 3 digitopodial skeleton curator notes 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.

Changes for: digit 4 digitopodial skeleton

  • Deleted
    • - digit 4 digitopodial skeleton comment 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.
  • Added
    • + digit 4 digitopodial skeleton curator notes 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.

Changes for: digit 5 digitopodial skeleton

  • Deleted
    • - digit 5 digitopodial skeleton comment 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.
  • Added
    • + digit 5 digitopodial skeleton curator notes 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.

Changes for: digit 2 digitopodial skeleton

  • Deleted
    • - digit 2 digitopodial skeleton comment 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.
  • Added
    • + digit 2 digitopodial skeleton curator notes 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.

Changes for: digit 1 digitopodial skeleton

  • Deleted
    • - digit 1 digitopodial skeleton comment 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.
  • Added
    • + digit 1 digitopodial skeleton curator notes 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.

Changes for: venom gland

Changes for: sphincter colli superficialis muscle

  • Added
    • + sphincter colli superficialis muscle taxon notes M. sphincter colli superficialis is present in Lagomorpha but absent in Rodentia (Meinertz, 1941, 1942; Ryan, 1989; Rinker, 1954). Some errouneous references of this muscle in rodents (e.g., Bezuidenhout and Evans, 2005) are due to decussating fibers of the deep sphincter, which creates a false superficial sphincter (Ryan, 1989)

Changes for: lenticular process of incus

  • Deleted
    • - lenticular process of incus comment the lenticular process may be homologous to the shaft of the stapes and result from fusion of the former quadrate- stapes articulation. This speculation is consistent with the observation that artiodactyls have a very short lenticular process (Thewissen & Hussain (1993)), with perhaps greater length to the corresponding process of the stapes[http://palaeos.com/vertebrates/bones/ear/incus.html]
  • Added

Changes for: platypus crural gland

Changes for: supracoracoideus muscle of wing

Changes for: stylohyoid bone

  • Deleted
    • - stylohyoid bone taxon notes The stylohyoid bone is one of the four bones ( stylohyoid, ceratohyoid, basihyoid, thyrohyoid) of the hyoid apparatus in the horse. Other species have five bones, the fifth being the epihyoid that is not present in the horse. The stylohyoid bone in the horse is significantly larger compared to other bones of the hyoid apparatus and divides the guttural pouch into two chambers, medial and lateral. The hyoid apparatus consists of a series of bony rods, jointed together and forming a means of suspending the tongue and larynx from the skull[MURDOCH]
  • Added
    • + stylohyoid bone taxon notes The stylohyoid bone is one of the four bones ( stylohyoid, ceratohyoid, basihyoid, thyrohyoid) of the hyoid apparatus in the horse. Other species have five bones, the fifth being the epihyoid that is not present in the horse. The stylohyoid bone in the horse is significantly larger compared to other bones of the hyoid apparatus and divides the guttural pouch into two chambers, medial and lateral. The hyoid apparatus consists of a series of bony rods, jointed together and forming a means of suspending the tongue and larynx from the skull { source=MURDOCH }

Changes for: pleural plate of carapace

Changes for: neural plate of carapace

Changes for: proximal tarsal bone

Changes for: trunk vertebra

Changes for: levator palatoquadrati

  • Deleted
  • Added
    • + levator palatoquadrati taxon notes In some fishes such as the chimera and in tetrapods the palatoquadrate becomes fused to the braincase and this muscle is absent. { source=ISBN10:0073040584 }

Changes for: adductor mandibulae

  • Deleted
  • Added
    • + adductor mandibulae taxon notes In teleosts, the complex is composed of several derived muscles that attach to different parts of the highly kinetic skull. { source=ISBN10:0073040584 , taxon=NCBITaxon:32443 }

Changes for: spiracularis muscle

Changes for: frontal process of maxilla

Changes for: digestive system element

Changes for: ectopterygoid bone

Changes for: surangular bone

  • Deleted
    • - surangular bone taxon notes Nevertheless, it is not completely clear that this[osteichthyans] surangular is homologous with the surangular in tetrapods[paleos]
  • Added
    • + surangular bone taxon notes Nevertheless, it is not completely clear that this[osteichthyans] surangular is homologous with the surangular in tetrapods { source=paleos }

Changes for: depressor mandibulae muscle

  • Deleted
    • - depressor mandibulae muscle taxon notes Homolog of levator operculi and epihyoidean - or in mammals, the stapedius (the digastric opens the jaws)[Kardong] The (sphenodon) m. Depressor Mandibulae originates from the posterodorsal edge of the parietal and squamosal, and from a small mid-line portion of connective tissue[http://palaeo-electronica.org/2009_2/179/other.htm]
  • Added

Changes for: levator operculi

Changes for: interclavicle

Changes for: dorsal head of rib

Changes for: diapophysis of rib

Changes for: ventral head of rib

Changes for: manual digit 5 plus metapodial segment

Changes for: manual digit 4 plus metapodial segment

Changes for: manual digit 3 plus metapodial segment

Changes for: manual digit 2 plus metapodial segment

Changes for: pedal digit 5 plus metapodial segment

Changes for: pedal digit 4 plus metapodial segment

Changes for: pedal digit 1 plus metapodial segment

Changes for: pedal digit 3 plus metapodial segment

Changes for: pedal digit 2 plus metapodial segment

Changes for: anterior prenasal cartilage

Changes for: pedal digit plus metapodial segment

Changes for: manual digit 1 plus metapodial segment

Changes for: superficial fascia

Changes for: dense irregular connective tissue

Changes for: dense connective tissue

Changes for: collection of collagen fibrils

Changes for: muscle layer of esophagus

Changes for: angular bone

  • Deleted
    • - angular bone comment The angular fuses with the articular bone in clupeocephalans forming the anguloarticular.
  • Added
    • + angular bone taxon notes The angular fuses with the articular bone in clupeocephalans forming the anguloarticular.

Changes for: mammary gland

Changes for: corpus spongiosum of penis

  • Deleted
    • - corpus spongiosum of penis function notes The function of the corpus spongiosum in erection is to prevent the urethra from pinching closed, thereby maintaining the urethra as a viable channel for ejaculation. To do this, the corpus spongiosum remains pliable during erection while the corpora cavernosum penis becomes engorged with blood.[WP]
  • Added
    • + corpus spongiosum of penis function notes The function of the corpus spongiosum in erection is to prevent the urethra from pinching closed, thereby maintaining the urethra as a viable channel for ejaculation. To do this, the corpus spongiosum remains pliable during erection while the corpora cavernosum penis becomes engorged with blood. { source=WP }

Changes for: endothelium of capillary

Changes for: lobule of mammary gland

Changes for: endothelium of venule

Changes for: endothelium of vein

Changes for: endothelium of arteriole

Changes for: endothelium of artery

Changes for: epithelium of trachea

Changes for: epithelium of small intestine

Changes for: subthalamic nucleus

Changes for: optic tract

Changes for: habenular commissure

Changes for: tuberomammillary nucleus

Changes for: lateral hypothalamic nucleus

Changes for: dorsomedial nucleus of hypothalamus

Changes for: arcuate nucleus of hypothalamus

Changes for: retrochiasmatic area

Changes for: paraventricular nucleus of hypothalamus

Changes for: lateral preoptic nucleus

Changes for: lateral mammillary nucleus

Changes for: medial mammillary nucleus

Changes for: central medial nucleus

Changes for: ventral lateral nucleus

Changes for: paraventricular nucleus of thalamus

Changes for: reuniens nucleus

Changes for: parafascicular nucleus

Changes for: preoptic area

Changes for: supraoptic nucleus

Changes for: presubiculum

Changes for: epithelium of oropharynx

  • Deleted
    • - epithelium of oropharynx comment Histology/AO notes: Composition varies with species and time. This is classified as nonkeratinizing stratified squamous in FMA, unilaminar in EHDAA2; the majority of the pharyngeal epithelium is unilaminar in zebrafish
  • Added

Changes for: epithelium of respiratory bronchiole

Changes for: submucosa of bronchus

Changes for: cartilage of bronchus

Changes for: white pulp of spleen

Changes for: epithelium of terminal bronchiole

Changes for: epithelium of nasopharynx

Changes for: jaw depressor muscle

  • Deleted
    • - jaw depressor muscle taxon notes In amphibians, ‘Muscle that pulls the hyoid apparatus forward and depresses the lower jaw.’ [AAO:0010655]. ‘The protractor hyoideus muscle in teleosts is commonly, albeit mistakenly, referred to as the geniohyoideus muscle, which is involved in the coracomandibularis coupling. According to Edgeworth (1935) and Winterbottom (1974), the protractor hyoideus is composed of a fusion of the intermandibularis posterior and the interhyoideus muscles which resulted in the protractor hyoideus which spans the hyoid and mandible. The intermandibularis spans the mandible while the closely apposed interhyoideus spans the hyoid in other fishes. Furthermore, they concluded that any muscle that is homologous to the geniohyoideus (coracomandibularis coupling) in other lower vertebrates has been lost in teleosts, as well as gars. However, the protractor hyoideus muscle is functionally analogous to the coracomandibularis coupling of other vertebrates and so we use it in our discussion to show the phylogenetically broad roles of these couplings in jaw mechanics.’[doi:10.1006/bijl.2000.0436]
  • Added
    • + jaw depressor muscle taxon notes In amphibians, ‘Muscle that pulls the hyoid apparatus forward and depresses the lower jaw.’ [AAO:0010655]. ‘The protractor hyoideus muscle in teleosts is commonly, albeit mistakenly, referred to as the geniohyoideus muscle, which is involved in the coracomandibularis coupling. According to Edgeworth (1935) and Winterbottom (1974), the protractor hyoideus is composed of a fusion of the intermandibularis posterior and the interhyoideus muscles which resulted in the protractor hyoideus which spans the hyoid and mandible. The intermandibularis spans the mandible while the closely apposed interhyoideus spans the hyoid in other fishes. Furthermore, they concluded that any muscle that is homologous to the geniohyoideus (coracomandibularis coupling) in other lower vertebrates has been lost in teleosts, as well as gars. However, the protractor hyoideus muscle is functionally analogous to the coracomandibularis coupling of other vertebrates and so we use it in our discussion to show the phylogenetically broad roles of these couplings in jaw mechanics.’ { source=http://dx.doi.org/10.1006/bijl.2000.0436 }

Changes for: medial habenular nucleus

Changes for: lateral habenular nucleus

Changes for: supramammillary nucleus

Changes for: venule

  • Deleted
    • - venule comment This class was created automatically from a combination of ontologies
  • Added
    • + venule editor note This class was created automatically from a combination of ontologies

Changes for: parenchyma of pancreas

Changes for: serosa of esophagus

Changes for: lamina propria of esophagus

Changes for: serum

  • Deleted
    • - serum comment This class was created automatically from a combination of ontologies
  • Added
    • + serum editor note This class was created automatically from a combination of ontologies

Changes for: bile

Changes for: gastric juice

Changes for: semen

  • Deleted
    • - semen taxon notes Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined a taxonomically generic way (see comments for UBERON:0006530).
  • Added
    • + semen taxon notes Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined ain taxonomically generic way (see comments for UBERON:0006530).

Changes for: reticular lamina of epithelium

  • Deleted
    • - reticular lamina of epithelium comment This class represents a continuous sheet of reticular lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class ‘lamina reticularis’ represents a portion of substance on the scale of a single cell.
  • Added
    • + reticular lamina of epithelium curator notes this class represents a continuous sheet of reticular lamina which can underlie multiple epithelial cells over large regions. In contrast, the GO class ‘lamina reticularis’ represents a portion of substance on the scale of a single cell.

Changes for: substantia nigra pars compacta

Changes for: quadrate-articular joint

  • Deleted
    • - quadrate-articular joint curator notes see comments for UBERON:0004744 articular/anguloarticular. Taxon notes: over time, the synapsids’ quadrate-articular jaw joint (which the rest of the tetrapods possess) was replaced by a dentary-squamosal joint (which all living mammals possess), while the quadrate and articular migrated, shrank, and became part of the complex of middle ear bones.[http://evolution.berkeley.edu/evolibrary/article/evograms_05]
  • Added

Changes for: joint connecting upper and lower jaws

Changes for: least splanchnic nerve

Changes for: olfactory epithelium

Changes for: iliopsoas

  • Deleted
    • - iliopsoas comment This class was created automatically from a combination of ontologies
  • Added

Changes for: cervical ganglion

Changes for: middle cervical ganglion

Changes for: superior cervical ganglion

Changes for: arteriole

  • Deleted
    • - arteriole comment This class was created automatically from a combination of ontologies
  • Added

Changes for: crypt of lieberkuhn of large intestine

Changes for: crypt of Lieberkuhn

  • Deleted
    • - crypt of Lieberkuhn taxon notes Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules[ISBN:9780521617147]
  • Added
    • + crypt of Lieberkuhn taxon notes Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules { source=ISBN:9780521617147 }

Changes for: capillary

  • Deleted
    • - capillary comment Structure notes: capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
  • Added
    • + capillary structure notes capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs

Changes for: intermetatarsal joint

  • Deleted
    • - intermetatarsal joint taxon notes 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[WP]
  • Added
    • + intermetatarsal joint taxon notes 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 { source=WP }

Changes for: root of vagus nerve

Changes for: lumbosacral nerve plexus

Changes for: autonomic nerve plexus

Changes for: brachial nerve plexus

  • Deleted
    • - brachial nerve plexus comment check superclass - nerve vs collection of fibers vs junction; note that FMA also has ‘brachial autonomic nerve plexus’
  • Added
    • + brachial nerve plexus editor note check superclass - nerve vs collection of fibers vs junction; note that FMA also has ‘brachial autonomic nerve plexus’

Changes for: paravertebral ganglion

Changes for: parasympathetic ganglion

Changes for: autonomic ganglion

Changes for: sensory ganglion

Changes for: ethmoid cartilage

Changes for: procoracoid bone

  • Deleted
    • - procoracoid bone comment In primitive synapsis 3 centers develop in the shoulder: the dorsal center gives rise to the scapula and the two ventral centers produce an anterior coracoid (procoracoid) and posterior coracoid (coracoid). Editor notes: VSAO sais that the procoracoid+coracoid are homologous to the teleost coracoid. Consider adding a separate class for posterior coracoid.
    • - procoracoid bone homology notes Kardong states that the procoracoid (or the anterior part of the procoracoid) is homologous to the coracoid, but this is controversial { is about=UBERON:0004743 , source=Kardong }
  • Added
    • + procoracoid bone editor note VSAO sais that the procoracoid+coracoid are homologous to the teleost coracoid. Consider adding a separate class for posterior coracoid.
    • + procoracoid bone homology notes Kardong states that the procoracoid (or the anterior part of the procoracoid) is homologous to the coracoid, but this is controversial { is about=UBERON:0004743 , source=ISBN10:0073040584 }
    • + procoracoid bone taxon notes In primitive synapsis 3 centers develop in the shoulder: the dorsal center gives rise to the scapula and the two ventral centers produce an anterior coracoid (procoracoid) and posterior coracoid (coracoid)

Changes for: hypothalamus

Changes for: phrenic nerve

Changes for: olfactory tubercle

Changes for: nucleus accumbens

Changes for: island of Calleja

Changes for: levator claviculae muscle

  • Deleted
    • - levator claviculae muscle taxon notes The levator claviculae is an infrequently recognized anatomical variant in humans, distinguished from, for example, cervical adenopathy or a thrombosed vein, but a normal muscle in lower mammals and anthropoids. In humans, when present, it often appears unilaterally, most commonly on the left side, or bilaterally.[WP]
  • Added
    • + levator claviculae muscle taxon notes The levator claviculae is an infrequently recognized anatomical variant in humans, distinguished from, for example, cervical adenopathy or a thrombosed vein, but a normal muscle in lower mammals and anthropoids. In humans, when present, it often appears unilaterally, most commonly on the left side, or bilaterally. { source=WP }

Changes for: lateral olfactory tract

Changes for: trunk of phrenic nerve

Changes for: internal capsule

Changes for: parietal lobe

Changes for: putamen

  • Deleted
    • - putamen comment CHECK - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)
  • Added
    • + putamen editor note check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)

Changes for: septofimbrial nucleus

Changes for: nucleus of diagonal band

Changes for: scala vestibuli

Changes for: mesethmoid bone

Changes for: cartilage of external ear

Changes for: scala tympani

Changes for: cartilaginous external acoustic tube

Changes for: skin of chest

Changes for: posterior semicircular duct

  • Deleted
    • - posterior semicircular duct comment This class was created automatically from a combination of ontologies
    • - posterior semicircular duct definition The semicircular canals are three half-circular, interconnected tubes located inside each ear. The three canals are the horizontal semicircular canal (also known as the lateral semicircular canal), superior semicircular canal (also known as the anterior semicircular canal), and the posterior semicircular canal. The canals are aligned approximately orthogonally to one another. The horizontal canal is aligned roughly horizontally in the head. The superior and anterior canals are aligned roughly at a 45 degree angle to a vertical plane drawn from the nose to the back of the skull. Thus, the horizontal canal detects horizontal head movements (such as when doing a pirouette), while the superior and posterior canals detect vertical head movements. Each canal is filled with a fluid called endolymph and contains a motion sensor with little hairs whose ends are embedded in a gelatinous structure called the cupula. As the skull twists in any direction, the endolymph is thrown into different sections of the canals. The cilia detect when the endolymph rushes past, and a signal is then sent to the brain. The semicircular canals are a component of the Labyrinth. Among species of mammals, the size of the semicircular canals is correlated with their type of locomotion. Specifically, species that are agile and have fast, jerky locomotion have larger canals relative to their body size than those that move more cautiously. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Semicircular_canal }
  • Added

Changes for: anterior semicircular duct

Changes for: lateral semicircular duct

Changes for: semicircular duct

Changes for: semicircular canal

Changes for: anterior semicircular canal

Changes for: membranous labyrinth

Changes for: auricular cartilage

Changes for: lobule of pinna

Changes for: internal ear

Changes for: cochlea

  • Deleted
    • - cochlea definition The cochlea is the auditory portion of the inner ear. 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. The name is from the Latin for snail, which is from the Greek kokhlias ‘snail, screw,’ from kokhlos ‘spiral shell,’ in reference to its coiled shape; the cochlea is coiled in most mammals, monotremes being the exceptions. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Cochlea }
  • Added

Changes for: lateral semicircular canal

Changes for: posterior semicircular canal

Changes for: saliva

  • Deleted
    • - saliva comment Taxon notes: 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[GO]
  • Added
    • + saliva taxon notes 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 { source=GO }

Changes for: sublingual duct

Changes for: carpometacarpal joint of digit 1

  • Deleted
    • - carpometacarpal joint of digit 1 taxon notes In humans it connects the trapezium to the first metacarpal bone, plays an irreplaceable role in the normal functioning of the thumb. The most important joint connecting the wrist to the metacarpus, osteoarthritis of the TMC is a severely disabling condition; up to twenty times more common among old women than in average[WP]
  • Added
    • + carpometacarpal joint of digit 1 taxon notes In humans it connects the trapezium to the first metacarpal bone, plays an irreplaceable role in the normal functioning of the thumb. The most important joint connecting the wrist to the metacarpus, osteoarthritis of the TMC is a severely disabling condition; up to twenty times more common among old women than in average { source=WP }

Changes for: femoral pore

  • Deleted
    • - femoral pore taxon notes Femoral pores are present in all genera in the families Cordylidae, Crotaphytidae, Hoplocercidae, Iguanidae, Phrynosomatidae, and Xantusiidae. They are absent in all genera in the Anguidae, Chamaeleonidae, Dibamidae, Helodermatidae, Scincidae, Xenosauridae, and Varanidae families.[1] They are present in other lizards and amphisbaenians quite variably, some geckoes, Phelsuma, for example have these pores, others in the same family do not[WP]
  • Added
    • + femoral pore taxon notes Femoral pores are present in all genera in the families Cordylidae, Crotaphytidae, Hoplocercidae, Iguanidae, Phrynosomatidae, and Xantusiidae. They are absent in all genera in the Anguidae, Chamaeleonidae, Dibamidae, Helodermatidae, Scincidae, Xenosauridae, and Varanidae families.[1] They are present in other lizards and amphisbaenians quite variably, some geckoes, Phelsuma, for example have these pores, others in the same family do not { source=WP }

Changes for: nasal cartilage

Changes for: orbital septum

Changes for: caudal-sacral region of vertebral column

Changes for: mucosa of larynx

Changes for: major salivary gland

Changes for: photoreceptor layer of retina

Changes for: outer nuclear layer of retina

Changes for: fovea centralis

  • Deleted
    • - fovea centralis comment As an anatomical term, there are several foveae around the body, including in the head of the femur.(WP)
    • - fovea centralis definition a part of the eye, located in the center of the macula region of the retina. [1] [2] The fovea is responsible for sharp central vision (also called foveal vision). The fovea is surrounded by the parafovea belt, and the perifovea outer region:[2] the parafovea is the intermediate belt where the ganglion cell layer is composed of more than five rows of cells; as well as the highest density of cones; the perifovea is the outermost region where the ganglion cell layer contains two to four rows of cells, and is where visual acuity is below the optimum. The perifovea contains an even more diminished density of cones, having 12 per 100 micrometres versus 50 per 100 micrometres in the most central fovea. This, in turn, is surrounded by a larger peripheral area that delivers highly compressed information of low resolution. Approximately 50% of the nerve fibers in the optic nerve carry information from the fovea, while the other 50% carry information from the rest of the retina. The parafovea extends to a distance of 1¼ mm from the central fovea, and the perifovea is found 2¾ mm away from the fovea centralis[WP]. { database cross reference=http://en.wikipedia.org/wiki/Fovea_centralis_in_macula }
    • - fovea centralis has exact synonym fovea
  • Added
    • + fovea centralis definition A depression in the inner retinal surface within the macula lutea, the photoreceptor layer of which is entirely cones and which is specialized for maximum visual acuity { database cross reference=http://en.wikipedia.org/wiki/Fovea , database cross reference=UBERON:cjm }
    • + fovea centralis function notes high acuity vision
    • + fovea centralis has broad synonym fovea
    • + fovea centralis taxon notes The fovea is also a pit in the surface of the retinas of many types of fish, reptiles, and birds. Among mammals, it is found only in simian primates. The retinal fovea takes slightly different forms in different types of animals. For example, in primates, cone photoreceptors line the base of the foveal pit, the cells that elsewhere in the retina form more superficial layers having been displaced away from the foveal region during late fetal and early postnatal life. Other foveae may show only a reduced thickness in the inner cell layers, rather than an almost complete absence

Changes for: spinal nerve

Changes for: vitreous chamber of eyeball

Changes for: ganglionic layer of retina

Changes for: nerve fiber layer of retina

Changes for: outer plexiform layer of retina

Changes for: inner nuclear layer of retina

Changes for: urodeum

Changes for: oral cirrus

  • Deleted
    • - oral cirrus comment This class groups a chordate and lophotrochozoan structure; these should probably be split
  • Added
    • + oral cirrus curator notes this class groups a chordate and lophotrochozoan structure; these should probably be split

Changes for: hepatic cecum

Changes for: muscularis mucosae of rectum

Changes for: mechanoreceptor

  • Deleted
    • - mechanoreceptor definition 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. { database cross reference=http://en.wikipedia.org/wiki/Mechanoreceptor }
  • Added
    • + mechanoreceptor comment 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
    • + mechanoreceptor definition a sensory receptor that responds to mechanical pressure or distortion. { database cross reference=http://en.wikipedia.org/wiki/Mechanoreceptor }

Changes for: nerve ending

Changes for: proctodeum portion of cloaca

Changes for: lumen of terminal part of digestive tract

Changes for: epiglottic cartilage

Changes for: fibrous capsule of thyroid gland

Changes for: lymphoid tissue

Changes for: parenchyma of parathyroid gland

Changes for: parenchyma of thyroid gland

Changes for: capsule of parathyroid gland

Changes for: sclera

  • Deleted
    • - sclera comment Seko et al demonstrate chondrogenic potential http://dx.doi.org/10.1371/journal.pone.0003709 and identify this as connective tissue. Disease notes: implicated in rheumatoid arthritis. Structure notes: continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. Taxon notes: in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
    • - sclera development notes 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]. Taxon notes: Multi-tissue structure that composes the opaque fibrous outer layer of the eye[ZFA]
  • Added
    • + sclera comment Disease notes: implicated in rheumatoid arthritis.
    • + sclera development notes 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].
    • + sclera development notes Seko et al demonstrate chondrogenic potential and identify this as connective tissue[doi:10.1371/journal.pone.0003709].
    • + sclera structure notes continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
    • + sclera taxon notes in fish, reptiles and monotremes the connective tissue of the sclera is skeletal

Changes for: pupil

  • Deleted
    • - pupil comment This class was created automatically from a combination of ontologies
  • Added
    • + pupil editor note This class was created automatically from a combination of ontologies

Changes for: optic choroid

  • Deleted
    • - optic choroid comment 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
  • Added
    • + optic choroid editor note 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

Changes for: substantia propria of cornea

Changes for: iris stroma

Changes for: maxillary sinus

Changes for: future foramen cecum

  • Deleted
    • - future foramen cecum definition A thickened and indented region in the midline in the floor of the rostral part of the pharyngeal region of the foregut, located between the second and third branchial arches that is the first indication of the thyroid primordium. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.132] { database cross reference=VHOG:0000826 }
  • Added
    • + future foramen cecum definition A thickened and indented region in the midline in the floor of the rostral part of the pharyngeal region of the foregut, located between the second and third branchial arches that is the first indication of the thyroid primordium. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.132] { database cross reference=ISBN10:0124020607 , database cross reference=VHOG:0000826 }

Changes for: frontal sinus

  • Deleted
    • - frontal sinus taxon notes A unique feature in the horse is that the frontal sinus communicates with the caudal maxillary sinus via the frontomaxillary opening[MURDOCh]
  • Added
    • + frontal sinus taxon notes A unique feature in the horse is that the frontal sinus communicates with the caudal maxillary sinus via the frontomaxillary opening { source=MURDOCh }

Changes for: nucleus ambiguus

Changes for: mesencephalic nucleus of trigeminal nerve

Changes for: facial modiolus

  • Deleted
    • - facial modiolus definition In facial anatomy, the modiolus is a chiasma of facial muscles held together by fibrous tissue, located lateral and slightly superior to each angle of the mouth. It is important in moving the mouth, facial expression and in dentistry. It derives its motor nerve supply from the facial nerve, and its blood supply from labial branches of the facial artery. It is contributed to by the following muscles: orbicularis oris, buccinator, levator anguli oris, depressor anguli oris, zygomaticus major, risorius quadratus labii superioris, quadratus labii inferioris. { database cross reference=http://en.wikipedia.org/wiki/Modiolus_%28face%29 }
  • Added

Changes for: eyelid

  • Deleted
    • - eyelid comment Each 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. AO notes: FMA divides this into skin, fascia, conjunctiva. Consider adding ‘eye surface’, like MA
    • - eyelid definition An eyelid is a thin fold of skin that covers and protects an eyeball. With the exception of the prepuce and the labia minora, it has the thinnest skin of the whole body. The levator palpebrae superioris muscle retracts the eyelid to ‘open’ the eye. This can be either voluntarily or involuntarily. The human eyelid features a row of eyelashes which serve to heighten the protection of the eye from dust and foreign debris, as well as from perspiration. ‘Palpebral’ (and ‘blepharo’) means relating to the eyelids. Its key function is to regularly spread the tears and other secretion on the eye surface to keep it moist, since the cornea must be continuously moist. They keep the eyes from drying out when asleep. Moreover, the blink reflex protects the eye from foreign bodies. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Eyelid }
  • Added
    • + eyelid definition A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane { database cross reference=UBERON:cjm }
    • + eyelid external ontology notes Consider adding ‘eye surface’, like MA { external ontology=MA }
    • + eyelid external ontology notes FMA divides this into skin, fascia, conjunctiva { external ontology=FMA }
    • + eyelid taxon notes 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.

Changes for: oculomotor nuclear complex

Changes for: jaw skeleton

  • Deleted
    • - jaw skeleton editor note 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
  • Added
    • + jaw skeleton editor note TODO - move ZFA:0001227 (it is the entire jaw skeleton).
    • + jaw skeleton external ontology 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 { external ontology=FMA }

Changes for: nasal cavity

  • Deleted
    • - nasal cavity comment 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]. Editor note: defne the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.
  • Added
    • + nasal cavity editor note defne the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.
    • + nasal cavity taxon notes 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 { source=HP }

Changes for: nasal septum

Changes for: obsolete viscerocranium

  • Deleted
    • - obsolete viscerocranium comment This class was made obsolete as it conflated the facial skeleton with the splanchnocranium. The facial skeleton includes: * Inferior nasal concha * Lacrimal bone * Mandible * Maxilla * Nasal bone * Palatine bone * Vomer * Zygomatic bone. The hyoid is sometimes included, and sometimes excluded (FMA includes it) (See also notes for ethmoid bone). The splanchoncranium is the endoskeleton derived from pharyngeal arches.
  • Added
    • + obsolete viscerocranium curator notes this class was made obsolete as it conflated the facial skeleton with the splanchnocranium. The facial skeleton includes: * Inferior nasal concha * Lacrimal bone * Mandible * Maxilla * Nasal bone * Palatine bone * Vomer * Zygomatic bone. The hyoid is sometimes included, and sometimes excluded (FMA includes it) (See also notes for ethmoid bone). The splanchoncranium is the endoskeleton derived from pharyngeal arches.

Changes for: neurocranium

  • Deleted
    • - neurocranium 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]
  • Added
    • + neurocranium 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]. { source=WP }
    • + neurocranium structure 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

Changes for: larynx

  • Deleted
    • - larynx comment This class was created automatically from a combination of ontologies
  • Added
    • + larynx editor note This class was created automatically from a combination of ontologies

Changes for: soft palate

  • Deleted
    • - soft palate comment This class was created automatically from a combination of ontologies

Changes for: pharyngeal tonsil

Changes for: cochlear nucleus

Changes for: sphenoidal sinus

Changes for: tongue

  • Deleted
    • - tongue editor note 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
  • Added
    • + tongue editor note 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.
    • + tongue 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

Changes for: tibialis posterior

Changes for: flexor digitorum longus

Changes for: superior cerebellar vein

Changes for: cerebellar vein

Changes for: anterior auricular vein

Changes for: cerebral vein

Changes for: triceps surae

Changes for: temporal bone

  • Deleted
    • - temporal bone comment 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.] // In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone
  • Added

Changes for: occipital bone

  • Deleted
    • - occipital bone taxon notes fusion of basi-, exo- and supra-occipitals (and maybe tabular)[Kardong]. Development notes: formed from the sclerotome of the occipital somites[PMID:11523816]. 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 an- nexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII[PMID:11523816]
  • Added
    • + occipital bone taxon notes 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 an- nexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII { source=http://www.ncbi.nlm.nih.gov/pubmed/11523816 }
    • + occipital bone taxon notes fusion of basi-, exo- and supra-occipitals (and maybe tabular) { source=Kardong }

Changes for: temporal vein

Changes for: anterior cerebral vein

Changes for: inferior cerebellar vein

Changes for: palatine bone

Changes for: mandible

  • Deleted
    • - mandible editor note consider merging with dentary - for now we make it a mammal-specific subclass. Terminology notes: ‘mandible’ also refers to either the upper OR lower part of the beak in birds
  • Added

Changes for: hyoid bone

  • Deleted
    • - hyoid bone taxon notes 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.[WP]
  • Added
    • + hyoid bone taxon notes 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. { source=WP }

Changes for: auditory ossicle

  • Deleted
    • - auditory ossicle comment Taxon and editor notes: 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. Development notes: 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.[WP]
  • Added
    • + auditory ossicle development notes 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. { source=WP }
    • + auditory ossicle editor note 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.

Changes for: stapes bone

  • Deleted
    • - stapes bone comment Taxon notes (via VHOG): “This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.” Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) 62:339-357? Development notes: As the stapes first develops embryologically from the 6th to 8th week of life, it surrounds the stapedial artery, which supplies the majority of the vasculature of the embryonic head. After that period, the external carotid artery is generated and takes over for the stapedial artery, which subsequently involutes, leaving the stapes with a windowframe-like structure[WP] The stapes develops at the cranial end of the second branchial arch through an independent anlage of the cartilage of this arch. Between the stapedial anlage and the cranial end of the Reichert’s cartilage there is a formation called the interhyale, the internal segment of which gives rise to the tendon of the stapedial muscle. The stapedial anlage is a unique formation with two distinct parts: the superior part that will comprise the base and the inferior part that will be crossed by the stapedial artery during embryonic development and will constitute the limbs and the head of the stapes. According to the results, the otic capsule is not involved in formation of the base of the stapes.[doi:10.1111/j.1469-7580.2005.00441.x]
  • Added
    • + stapes bone development notes As the stapes first develops embryologically from the 6th to 8th week of life, it surrounds the stapedial artery, which supplies the majority of the vasculature of the embryonic head. After that period, the external carotid artery is generated and takes over for the stapedial artery, which subsequently involutes, leaving the stapes with a windowframe-like structure[WP] The stapes develops at the cranial end of the second branchial arch through an independent anlage of the cartilage of this arch. Between the stapedial anlage and the cranial end of the Reichert’s cartilage there is a formation called the interhyale, the internal segment of which gives rise to the tendon of the stapedial muscle. The stapedial anlage is a unique formation with two distinct parts: the superior part that will comprise the base and the inferior part that will be crossed by the stapedial artery during embryonic development and will constitute the limbs and the head of the stapes. According to the results, the otic capsule is not involved in formation of the base of the stapes. { source=http://dx.doi.org/10.1111/j.1469-7580.2005.00441.x }
    • + stapes bone taxon notes ‘This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.’ Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) 62:339-357?[VHOG].

Changes for: sensory root of facial nerve

Changes for: petrous part of temporal bone

Changes for: external ear

Changes for: ear

  • Deleted
    • - ear comment This class was created automatically from a combination of ontologies
  • Added
    • + ear editor note This class was created automatically from a combination of ontologies

Changes for: urogenital sinus epithelium

Changes for: postnatal subventricular zone

Changes for: medial tarsal artery

Changes for: kidney arcuate artery

Changes for: digestive tract

Changes for: vein of hindlimb zeugopod

Changes for: medial marginal vein

Changes for: oblique cartilage

Changes for: popliteal vein

Changes for: inguinal lymph node

Changes for: medial plantar artery

Changes for: peroneal artery

Changes for: dorsal metatarsal vein

Changes for: small saphenous vein

Changes for: lateral marginal vein

Changes for: anterior tibial vein

Changes for: posterior tibial vein

Changes for: genioglossus muscle

Changes for: septal organ of Masera

Changes for: extrinsic muscle of tongue

  • Deleted
    • - extrinsic muscle of tongue comment The extrinsic muscles originate from bone and extend to the tongue. Their main functions are altering the tongue’s position allowing for protrusion, retraction, and side-to-side movement[WP] Innervation: 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.[WP]
  • Added
    • + extrinsic muscle of tongue function notes main functions are altering the tongue’s position allowing for protrusion, retraction, and side-to-side movement[WP]
    • + extrinsic muscle of tongue structure notes 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. { source=WP }

Changes for: facial muscle

Changes for: intrinsic muscle of tongue

  • Deleted
    • - intrinsic muscle of tongue comment 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[WP]
  • Added

Changes for: digastric muscle group

  • Deleted
    • - digastric muscle definition The digastric muscle (also digastricus) (named digastric as it has two bellies) is a small muscle located under the jaw. It lies below the body of the mandible, and extends, in a curved form, from the mastoid process to the symphysis menti. It belongs to the suprahyoid muscles group. A broad aponeurotic layer is given off from the tendon of the digastricus on either side, to be attached to the body and greater cornu of the hyoid bone; this is termed the suprahyoid aponeurosis. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Digastric_muscle }
    • - digastric muscle label digastric muscle
  • Added

Changes for: subcostal artery

Changes for: cricothyroid muscle

Changes for: geniohyoid muscle

Changes for: mylohyoid muscle

  • Deleted
    • - mylohyoid muscle comment mylohyoideus and digastricus anterior of rats derived from intermandibularis posterior, see e.g. Jarvik [53] http://www.biomedcentral.com/1471-213X/8/24/table/T3
  • Added
    • + mylohyoid muscle comment Taxon motes: mylohyoideus and digastricus anterior of rats derived from intermandibularis posterior, see e.g. Jarvik [53] http://www.biomedcentral.com/1471-213X/8/24/table/T3

Changes for: longus capitis muscle

Changes for: cheek

  • Deleted
    • - cheek definition Cheeks constitute the area of the face below the eyes and between the nose and the left or right ear. It is fleshy in humans and other mammals, the skin being suspended by the chin and the jaws, and forming the lateral wall of the human mouth, visibly touching the cheekbone below the eye. In vertebrates, markings on the cheek area (malar stripes/spots/… ), particularly immediately beneath the eye, often serve as important distinguishing features between species or individuals. ‘Buccal’ means relating to the cheek. In humans, the region is innervated by the buccal nerve. The inside of the cheek (forming part of the mouth cavity) is lined with a mucous membrane. It is the most common location from which a DNA sample can be taken (during a cheek swab). The cheeks are covered externally by hairy skin, and internally by stratified squamous epithelium. This is mostly smooth, but may have aborally directed papillae . The mucosa is supplied with secretions from the Buccal glands, which are arranged in superior and inferior groups. In carnivores, the superior buccal gland is large and discrete: the Zygomatic gland. During mastication (chewing), the cheeks and tongue between them serve to keep the food between the teeth. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Cheek }
  • Added

Changes for: muscle of larynx

Changes for: intrinsic auricular muscle

Changes for: masseter muscle

  • Deleted
    • - masseter muscle comment The division of the adductor mandibulae in the various lines of tetrapod evolution correlates with divergences in their methods of feeding. (…) As the jaws become stronger and their movements more complex in the line of evolution toward mammals, the adductor complex becomes divided into several distinct muscles (temporalis, masseter, pterygoideus, tensor tympani, tensor veli palati)[VHOG]
  • Added
    • + masseter muscle taxon notes The division of the adductor mandibulae in the various lines of tetrapod evolution correlates with divergences in their methods of feeding. (…) As the jaws become stronger and their movements more complex in the line of evolution toward mammals, the adductor complex becomes divided into several distinct muscles (temporalis, masseter, pterygoideus, tensor tympani, tensor veli palati) { source=VHOG }

Changes for: bronchial vein

Changes for: venous plexus

Changes for: auricular muscle

Changes for: pericardiacophrenic vein

Changes for: thymic vein

  • Deleted
    • - thymic vein comment This class was created automatically from a combination of ontologies
  • Added

Changes for: subclavian vein

Changes for: vertebral vein

Changes for: internal jugular vein

Changes for: extrinsic auricular muscle

Changes for: depressor labii inferioris

Changes for: buccinator muscle

Changes for: levator labii superioris

Changes for: respiratory muscle

Changes for: palmar/plantar sweat gland

Changes for: proximal mesopodial bone

Changes for: ventral part of pharyngeal pouch 2

Changes for: dorsal part of pharyngeal pouch 3

Changes for: ventral part of pharyngeal pouch 1

Changes for: mediastinum

  • Deleted
    • - mediastinum definition The mediastinum is a non-delineated group of structures in the thorax, surrounded by loose connective tissue. It is the central compartment of the thoracic cavity. It contains the heart, the great vessels of the heart, esophagus, trachea, phrenic nerve, cardiac nerve, thoracic duct, thymus, and lymph nodes of the central chest. The mediastinum lies between the right and left pleura in and near the median sagittal plane of the chest. It extends from the sternum in front to the vertebral column behind, and contains all the thoracic viscera except the lungs. It may be divided for purposes of description into two parts:an upper portion, above the upper level of the pericardium, which is named the superior mediastinum with its superior limit at the superior thoracic opening and its inferior limit at the plane from the sternal angle to the disc of T4-T5 (Plane of Ludwig at Angle of Louis); and a lower portion, below the upper level of the pericardium. This lower portion is again subdivided into three parts, viz. that in front of the pericardium, the anterior mediastinum; that containing the pericardium and its contents, the middle mediastinum; and that behind the pericardium, the posterior mediastinum. It is surrounded by the chest wall anteriorly, the lungs laterally and the spine posteriorly. It is continuous with the loose connective tissue of the neck, and extends inferiorly onto the diaphragm. { database cross reference=http://en.wikipedia.org/wiki/Mediastinum }
  • Added
    • + mediastinum definition A central thoracic cavity surrounded by loose connective tissue that contains (where present) the heart, the great vessels of the heart, esophagus, trachea, phrenic nerve, cardiac nerve, thoracic duct, thymus, and lymph nodes of the central chest. { database cross reference=http://en.wikipedia.org/wiki/Mediastinum }
    • + mediastinum taxon notes In humans, the mediastinum lies between the right and left pleura in and near the median sagittal plane of the chest. It extends from the sternum in front to the vertebral column behind, and contains all the thoracic viscera except the lungs. It may be divided for purposes of description into two parts:an upper portion, above the upper level of the pericardium, which is named the superior mediastinum with its superior limit at the superior thoracic opening and its inferior limit at the plane from the sternal angle to the disc of T4-T5 (Plane of Ludwig at Angle of Louis); and a lower portion, below the upper level of the pericardium. This lower portion is again subdivided into three parts, viz. that in front of the pericardium, the anterior mediastinum; that containing the pericardium and its contents, the middle mediastinum; and that behind the pericardium, the posterior mediastinum. It is surrounded by the chest wall anteriorly, the lungs laterally and the spine posteriorly. It is continuous with the loose connective tissue of the neck, and extends inferiorly onto the diaphragm { source=WP }

Changes for: dorsal part of pharyngeal pouch 2

  • Deleted
    • - dorsal part of pharyngeal pouch 2 development notes in humans, persists as the tonsillar fossa - the endodermal lining covers the mesodermal lymphatic tissue to form the palatine tonsil[ISBN10:1607950324]. 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[MP]
  • Added
    • + dorsal part of pharyngeal pouch 2 development notes in humans, persists as the tonsillar fossa - the endodermal lining covers the mesodermal lymphatic tissue to form the palatine tonsil[ISBN10:1607950324]. 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 { source=MP }

Changes for: dorsal part of pharyngeal pouch 1

Changes for: buccal fat pad

Changes for: ventral part of pharyngeal pouch 3

Changes for: basal nucleus of telencephalon

Changes for: spinal nerve root

Changes for: spiracle

  • Deleted
    • - spiracle taxon notes The spiracle is still found in all cartilaginous fish except chimaeras, and in bony fishes in the coelacanth, sturgeon, paddlefish and bichirs. It is also seen as an otic notch in the skull of the extinct labyrinthodonts, and is thought to be associated with the ear opening in amniotes and frogs[WP]
  • Added
    • + spiracle taxon notes The spiracle is still found in all cartilaginous fish except chimaeras, and in bony fishes in the coelacanth, sturgeon, paddlefish and bichirs. It is also seen as an otic notch in the skull of the extinct labyrinthodonts, and is thought to be associated with the ear opening in amniotes and frogs { source=WP }

Changes for: spiral valve of conus arteriosus

  • Deleted
    • - spiral valve of conus arteriosus comment Evolution notes: The spiral valve is considered to have evolved from the right member of the four embryonic endocardial ridges (Goodrich, 1930 - via Morris 1974)
  • Added

Changes for: muscle of iris

Changes for: median ovary

  • Deleted
    • - median ovary taxon notes [In other animals]](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])
  • Added

Changes for: extra-ocular muscle

Changes for: oral gland

  • Deleted
    • - oral gland comment Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
  • Added

Changes for: isthmus of thyroid gland

Changes for: spermatic artery

Changes for: auricular artery

Changes for: labial artery

Changes for: alveolar artery

Changes for: mental artery

Changes for: buccal artery

Changes for: transverse facial artery

Changes for: maxillary artery

Changes for: occipital artery

Changes for: superficial temporal artery

Changes for: copula linguae

Changes for: sublingual artery

Changes for: facial artery

Changes for: acoustico-facial VII-VIII ganglion complex

Changes for: ampullary gland

Changes for: lingual artery

Changes for: right coronary artery

Changes for: tympanic plate

  • Deleted
    • - tympanic plate comment Consider merging with tympanic ring. See discussion page on wikipedia page for ectotympanic. editor note: TODO distinguish ecto- and ento- tympanics
  • Added

Changes for: middle cerebral artery

Changes for: left coronary artery

Changes for: carotid body

Changes for: central retinal artery

Changes for: alveolar wall

Changes for: obsolete lobar bronchus bronchiole

Changes for: right lung accessory lobe

  • Deleted
    • - right lung accessory lobe comment In humans, the right lung typically has 3 lobes (superior, middle, inferior). The lobar fissures are often incomplete, making a connection between two apposed lobes. Conversely, more than the expected number of lobes may be produced by new fissures e.g. the azygous lobe of the lung. The additional lobes are termed ‘accessory lobes’ – http://www.gpnotebook.co.uk/simplepage.cfm?ID=1120927803
    • - right lung accessory lobe taxon notes In mouse this is sometimes divided into intermediate and diaphragmatic lobes[ISBN10:0123813611]
  • Added
    • + right lung accessory lobe taxon notes In mouse this is sometimes divided into intermediate and diaphragmatic lobes { source=ISBN10:0123813611 }
    • + right lung accessory lobe taxon notes in humans, the right lung typically has 3 lobes (superior, middle, inferior). The lobar fissures are often incomplete, making a connection between two apposed lobes. Conversely, more than the expected number of lobes may be produced by new fissures e.g. the azygous lobe of the lung. The additional lobes are termed ‘accessory lobes’ – http://www.gpnotebook.co.uk/simplepage.cfm?ID=1120927803

Changes for: posterior cerebral artery

Changes for: superior cerebellar artery

Changes for: basilar artery

  • Deleted
    • - basilar artery comment This class was created automatically from a combination of ontologies
    • - basilar artery definition In human anatomy, the basilar artery is one of the arteries that supplies the brain with oxygen-rich blood. The two vertebral arteries and the basilar artery are sometimes together called the vertebrobasilar system, which supplies blood to the posterior part of circle of Willis and anastomoses with blood supplied to the anterior part of the circle of Willis from the carotid arteries. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Basilar_artery }
  • Added
    • + basilar artery SubClassOf supplies some hindbrain
    • + basilar artery definition A major artery that supplues the hindbrain and runs along the ventral keel of the hindbrain. { database cross reference=BGEE:ann }
    • + basilar artery external definition Artery that runs along the ventral keel of the hindbrain. It lies between the primordial hindbrain channels(PHBC). It irrigates the hindbrain and is connected, through the hindbrain, to the PHBC by the central arteries. { source=ZFA:0005002 }
    • + basilar artery external definition The unpaired artery that is formed by the union of the two vertebral arteries, runs forward within the skull just under the pons, divides into the two posterior cerebral arteries, and supplies the pons, cerebellum, posterior part of the cerebrum, and the inner ear[MP]. { source=MP:0013186 }

Changes for: thoracic duct

Changes for: temporal artery

Changes for: glossopharyngeal nerve

Changes for: trigeminal nerve

  • Deleted
    • - trigeminal nerve taxon notes 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[ISBN10:0471888893]
  • Added
    • + trigeminal nerve taxon notes 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 { source=ISBN10:0471888893 }

Changes for: trochlear nerve

Changes for: abducens nerve

  • Deleted
    • - abducens nerve taxon notes 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[WP]
  • Added
    • + abducens nerve taxon notes 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 { source=WP }

Changes for: oculomotor nerve

Changes for: paries nasi

Changes for: transverse facial vein

Changes for: middle temporal vein

Changes for: superficial temporal vein

Changes for: retromandibular vein

Changes for: facial vein

Changes for: supra-orbital vein

Changes for: paranasal commissure

Changes for: cardiovascular system endothelium

Changes for: orbital cavity

Changes for: somatic layer of lateral plate mesoderm

Changes for: endometrium epithelium

Changes for: oronasal membrane

Changes for: accessory XI nerve cranial component

  • Deleted
    • - accessory XI nerve cranial component editor note May be obsoleted in future. WP states: Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] But because the cranial component rapidly joins the vagus nerve and serves the same function as other vagal nerve fibers, modern descriptions often consider the cranial component part of the vagus nerve and not part of the accessory nerve proper.[2]
  • Added
    • + accessory XI nerve cranial component editor note May be obsoleted in future. WP states: Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] But because the cranial component rapidly joins the vagus nerve and serves the same function as other vagal nerve fibers, modern descriptions often consider the cranial component part of the vagus nerve and not part of the accessory nerve proper.

Changes for: fibulare

  • Deleted
    • - fibulare taxon notes In salamanders this element is aproximatelly rounded, whereas in anurans it is an elongate, cylindrical bone with the proximal and distal heads fused to the heads of the tibiale[AAO]
  • Added
    • + fibulare taxon notes In salamanders this element is aproximatelly rounded, whereas in anurans it is an elongate, cylindrical bone with the proximal and distal heads fused to the heads of the tibiale { source=AAO }

Changes for: respiratory velum

Changes for: dental lamina

Changes for: centrale

Changes for: olecranon fossa

Changes for: intercuneiform joint

  • Deleted
    • - intercuneiform joint terminology notes The term ‘cuneocuboid articulation’ is sometimes used to describe the joint between the cuboid and lateral cuneiform, but this term isn’t recognized by Terminologia Anatomica[WP]
  • Added
    • + intercuneiform joint terminology notes The term ‘cuneocuboid articulation’ is sometimes used to describe the joint between the cuboid and lateral cuneiform, but this term isn’t recognized by Terminologia Anatomica { source=WP }

Changes for: cervix epithelium

  • Deleted
    • - cervix epithelium comment [Histology]](Histology notes: 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[http://en.wikipedia.org/wiki/Cervix#Histology])
  • Added
    • + cervix epithelium structure notes 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 { source=Histology }

Changes for: renal venous blood vessel

Changes for: pancreaticoduodenal lymph node

Changes for: cranial placode

  • Deleted
    • - cranial placode comment .
    • - cranial placode editor note to avoid confusion, we include neurogenic placode as a subclass. Do not merge. Terminological notes: 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. Taxon notes: 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[PMID:11523831]
  • Added

Changes for: larva

  • Deleted
    • - larva comment This class was created automatically from a combination of ontologies. EDITOR NOTE: TODO discriminate between stages and organisms
  • Added

Changes for: hatching gland

Changes for: sacral lymph node

Changes for: mediastinal lymph node

Changes for: basicranium

Changes for: corpus luteum

  • Deleted
    • - corpus luteum taxon notes maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum[PMID:20959416]
  • Added
    • + corpus luteum taxon notes maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum { source=http://www.ncbi.nlm.nih.gov/pubmed/20959416 }

Changes for: trabecula carnea

  • Deleted
    • - trabecula carnea definition The trabeculae carneae (columnae carneae, or fleshy beams), are rounded or irregular muscular columns which project from the inner surface of the right and left ventricles of the heart.[1] They should not be confused with the pectinate muscles, which are present in the right[1] and left atria only. They are of three kinds: * some are attached along their entire length on one side and merely form prominent ridges,* others are fixed at their extremities but free in the middle, * while a third set, the papillary muscles are continuous by their bases with the wall of the ventricle, while their apices give origin to the chordæ tendineæ which pass to be attached to the segments of both the mitral valve and the tricuspid valve. 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[WP]. { database cross reference=http://en.wikipedia.org/wiki/Trabeculae_carneae }
  • Added

Changes for: navicular bone of pes

  • Deleted
    • - navicular bone of pes taxon notes connections vary depending on species. AAO: Oval tarsal element that is located on the center of the mesopodium. It articulates with all other elements of the tarsus except tarsal 5. In humans: there is a cuboid instead of distal tarsal 4 and 5 - may articulate laterally with the cuboid[WP]
  • Added
    • + navicular bone of pes taxon notes connections vary depending on species. AAO: Oval tarsal element that is located on the center of the mesopodium. It articulates with all other elements of the tarsus except tarsal 5. In humans: there is a cuboid instead of distal tarsal 4 and 5 - may articulate laterally with the cuboid { source=WP }

Changes for: face

  • Deleted
    • - face development notes 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]
  • Added
    • + face development notes 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) { source=vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf }

Changes for: skin of external ear

Changes for: subdivision of head

Changes for: chest

  • Deleted
    • - chest comment editor note: FMA:24216 present in FMA1, but gone in subsequent versions
  • Added
    • + chest editor note FMA:24216 present in FMA1, but gone in subsequent versions

Changes for: tarsal bone

  • Deleted
    • - tarsal bone taxon notes 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[Wikipedia:Tarsus_(skeleton)]
  • Added
    • + tarsal bone taxon notes 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 { source=http://en.wikipedia.org/wiki/Tarsus_(skeleton) }

Changes for: distal carpal bone 3

  • Deleted
    • - distal carpal bone 3 taxon notes medially located and articulates with metacarpals 2-4, distal carpal 5 and the intermedium[VSAO] In the human hand, the capitate bone is the largest of the carpal bones, and occupies the center of the wrist - The capitate articulates with seven bones: the scaphoid and lunate proximally, the second metacarpal, third metacarpal, and fourth metacarpal distally, the lesser multangular on the radial side, and the hamate on the ulnar side[WP]
  • Added
    • + distal carpal bone 3 taxon notes medially located and articulates with metacarpals 2-4, distal carpal 5 and the intermedium[VSAO] In the human hand, the capitate bone is the largest of the carpal bones, and occupies the center of the wrist - The capitate articulates with seven bones: the scaphoid and lunate proximally, the second metacarpal, third metacarpal, and fourth metacarpal distally, the lesser multangular on the radial side, and the hamate on the ulnar side { source=WP }

Changes for: distal carpal bone 2

  • Deleted
    • - distal carpal bone 2 taxon notes located in the distal part of the carpus and articulating with the second metacarpal, the distal carpals 1 and 2 and the radiale.[VSAO] in humans - The capitate articulates with 2nd metacarpal distally, scaphoid proximally, trapezium medially, capitate medially[WP] Amphibians: Small element that articulates with the prepollex, metacarpal II(I) and metacarpal III(II). It may be fused to element Y or carpal 3(2)[AAO]
  • Added
    • + distal carpal bone 2 taxon notes located in the distal part of the carpus and articulating with the second metacarpal, the distal carpals 1 and 2 and the radiale.[VSAO] in humans - The capitate articulates with 2nd metacarpal distally, scaphoid proximally, trapezium medially, capitate medially[WP] Amphibians: Small element that articulates with the prepollex, metacarpal II(I) and metacarpal III(II). It may be fused to element Y or carpal 3(2) { source=AAO }

Changes for: distal carpal bone 4

  • Deleted
    • - distal carpal bone 4 taxon notes articulates with the lunar, distal carpal 3, the ulnare as well as metacarpals 4 and 5.[VSAO]. In the human hand the lunate proximally the fourth and fifth metacarpals distally the triangular medially the capitate laterally[WP] Amphibians: Small element that articulates anteriorly with metacarpal IV(III). It may be fused to carpal 3(2), 5(4), or other elements[AAO]
  • Added
    • + distal carpal bone 4 taxon notes articulates with the lunar, distal carpal 3, the ulnare as well as metacarpals 4 and 5.[VSAO]. In the human hand the lunate proximally the fourth and fifth metacarpals distally the triangular medially the capitate laterally[WP] Amphibians: Small element that articulates anteriorly with metacarpal IV(III). It may be fused to carpal 3(2), 5(4), or other elements { source=AAO }

Changes for: distal carpal bone 1

  • Deleted
    • - distal carpal bone 1 taxon notes located between radiale and first metacarpal[VSAO]. in humans - The capitate articulates with 1st metacarpal distally, scaphoid proximally, trapezoid medially, 2nd metacarpal medially[WP]
  • Added
    • + distal carpal bone 1 taxon notes located between radiale and first metacarpal[VSAO]. in humans - The capitate articulates with 1st metacarpal distally, scaphoid proximally, trapezoid medially, 2nd metacarpal medially { source=WP }

Changes for: metaphysis

  • Deleted
    • - metaphysis comment adjacent to or containing epiphyseal plate? Note in FMA the metaphysis is part of the diaphysis, but not in MA.
  • Added
    • + metaphysis editor note todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA.

Changes for: facial lymphatic vessel

Changes for: subscapular vein

Changes for: planum internasale

Changes for: planum conchale

Changes for: planum antorbitale

Changes for: antorbital fenestra

Changes for: lunate

  • Deleted
    • - lunate taxon notes articulating with the ulnare and the radiale[VSAO}. human articulations: radius proximally capitate and hamate distally scaphoid laterally triangular medially
  • Added
    • + lunate taxon notes articulating with the ulnare and the radiale[VSAO]. human articulations: radius proximally capitate and hamate distally scaphoid laterally triangular medially

Changes for: pisiform

Changes for: jugular lymphatic vessel

Changes for: pectoral lymphatic vessel

Changes for: radial nerve

Changes for: ulnar nerve

  • Deleted
    • - ulnar nerve comment This class was created automatically from a combination of ontologies
  • Added

Changes for: muscle of pes

Changes for: neural tissue

Changes for: distal carpal bone

Changes for: muscle of shoulder

Changes for: hip joint

  • Deleted
    • - hip joint comment Alternate def - “The articulation between the femur and the innominate bone.” [BTO:0001502]
    • - hip joint definition The hip joint is a synovial joint formed by the articulation of the rounded head of the femur and the cup-like acetabulum of the pelvis. It forms the primary connection between the bones of the lower limb and the axial skeleton of the trunk and pelvis. Both joint surfaces are covered with a strong but lubricated layer called articular hyaline cartilage. The cuplike acetabulum forms at the union of three pelvic bones — the ilium, pubis, and ischium. { database cross reference=Articulation }
  • Added

Changes for: circle of Willis

  • Deleted
    • - circle of Willis taxon notes 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[http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html]
  • Added

Changes for: infraspinatus muscle

  • Deleted
    • - infraspinatus muscle taxon notes The pectoral muscles — the pectoralis major and pectoralis minor — evolved from a primitive muscle sheet that connected the coracoid to the humerus. In late reptilians and early mammals, this muscle structure was displaced dorsally; while most of its components evolved into the pectoralis major, some fibers eventually attached to the scapula and evolved into the supraspinatus, the infraspinatus, and parts of the subscapularis.[WP]
  • Added
    • + infraspinatus muscle taxon notes The pectoral muscles — the pectoralis major and pectoralis minor — evolved from a primitive muscle sheet that connected the coracoid to the humerus. In late reptilians and early mammals, this muscle structure was displaced dorsally; while most of its components evolved into the pectoralis major, some fibers eventually attached to the scapula and evolved into the supraspinatus, the infraspinatus, and parts of the subscapularis. { source=WP }

Changes for: skin of prepuce of penis

Changes for: vaginal venous plexus

Changes for: bone element

  • Deleted
    • - bone element comment 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]

Changes for: shoulder

  • Deleted
    • - shoulder definition In human anatomy, the shoulder joint comprises the part of the body where the humerus attaches to the scapula. The shoulder refers to the group of structures in the region of the joint. It is made up of three bones: the clavicle (collarbone), the scapula (shoulder blade), and the humerus (upper arm bone) as well as associated muscles, ligaments and tendons. The articulations between the bones of the shoulder make up the shoulder joints. There are two kinds of cartilage in the joint. The first type is the white cartilage on the ends of the bones (called articular cartilage) which allows the bones to glide and move on each other. When this type of cartilage starts to wear out (a process called arthritis), the joint becomes painful and stiff. The labrum is a second kind of cartilage in the shoulder which is distinctly different from the articular cartilage. This cartilage is more fibrous or rigid than the cartilage on the ends of the ball and socket. Also, this cartilage is also found only around the socket where it is attached. The shoulder must be flexible for the wide range of motion required in the arms and hands and also strong enough to allow for actions such as lifting, pushing and pulling. The compromise between these two functions results in a large number of shoulder problems not faced by other joints such as the hip. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Shoulder }
  • Added

Changes for: arm

  • Deleted
    • - arm comment 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. Editor note: currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand
  • Added
    • + arm curator notes 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
    • + arm editor note currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand

Changes for: renal tubule

  • Added
    • + renal tubule curator notes this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules

Changes for: animal hemisphere

  • Deleted
    • - animal hemisphere comment The animal pole consists of small cells that divide rapidly, in contrast with the vegetal pole below it.[WP] Note the XAO class is specific to the zygote.
  • Added

Changes for: vegetal hemisphere

  • Deleted
    • - vegetal hemisphere comment The vegetal pole contains large yolky cells that divide very slowly, in contrast with the animal pole above it.[WP]
  • Added

Changes for: trachea cartilage

Changes for: lower respiratory tract cartilage

Changes for: neck cartilage

Changes for: blubber

  • Deleted
    • - blubber comment Lipid-rich, collagen fiber–laced blubber comprises the hypodermis and covers the whole body, except for parts of the appendages, strongly attached to the musculature and skeleton by highly organized, fan-shaped networks of tendons and ligaments. It can comprise up to 50% of the body mass of some marine mammals during some points in their lives, and can range from two inches (5 cm) thick in dolphins and smaller whales, to more than 12 inches (30 cm)thick in some bigger whales, such as right and bowhead whales
  • Added
    • + blubber location notes Lipid-rich, collagen fiber–laced blubber comprises the hypodermis and covers the whole body, except for parts of the appendages, strongly attached to the musculature and skeleton by highly organized, fan-shaped networks of tendons and ligaments. It can comprise up to 50% of the body mass of some marine mammals during some points in their lives, and can range from two inches (5 cm) thick in dolphins and smaller whales, to more than 12 inches (30 cm)thick in some bigger whales, such as right and bowhead whales

Changes for: lymph node medullary cord

Changes for: lymph node medullary sinus

Changes for: abductor pollicis longus

Changes for: dorsalis pedis artery

Changes for: posterior tibial artery

Changes for: anterior tibial artery

Changes for: vertebral artery

Changes for: lumbrical muscle of manus

Changes for: brachialis muscle

Changes for: coracobrachialis muscle

Changes for: cupular organ

  • Deleted
    • - cupular organ comment Homology: possible homologues of neuromasts in the inner ear (Bone & Ryan, 1978; Wada et al 1998). In the tunicate cupular organ, the sensory cell is a primary neuron sending an axon to the CNS. The sensory cilium is within a deep indentation of the cell and is surrounded by a collar of short microvilli.
  • Added
    • + cupular organ taxon notes possible homologues of neuromasts in the inner ear (Bone & Ryan, 1978; Wada et al 1998). In the tunicate cupular organ, the sensory cell is a primary neuron sending an axon to the CNS. The sensory cilium is within a deep indentation of the cell and is surrounded by a collar of short microvilli.

Changes for: eyelid tarsus

  • Deleted
    • - eyelid tarsus taxon notes 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). [PMID:16496288]
  • Added
    • + eyelid tarsus taxon notes 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). { source=http://www.ncbi.nlm.nih.gov/pubmed/16496288 }

Changes for: posterior nasal aperture

Changes for: muscle of manus

Changes for: skin of pes

  • Deleted
    • - skin of pes comment This class was created automatically from a combination of ontologies
  • Added

Changes for: skin of manus

Changes for: skin of wrist

Changes for: skin of elbow

Changes for: ventral pancreas

Changes for: dorsal pancreas

Changes for: molar tooth

  • Deleted
    • - molar tooth comment Adult humans have twelve molars, in four groups of three at the back of the mouth. The third, rearmost molar in each group is called a wisdom tooth. It is the last tooth to appear, breaking through the surface of the gum at about the age of twenty, although this varies from individual to individual. Ethnicity can also have an impact on the age at which this occurs, with statistical variations between groups. The human mouth contains upper (maxillary) and lower (mandibular) molars. They are: maxillary first molar, maxillary second molar, maxillary third molar, mandibular first molar, mandibular second molar, and mandibular third molar.
  • Added
    • + molar tooth comment Human variation notes: Adult humans have twelve molars, in four groups of three at the back of the mouth. The third, rearmost molar in each group is called a wisdom tooth. It is the last tooth to appear, breaking through the surface of the gum at about the age of twenty, although this varies from individual to individual. Ethnicity can also have an impact on the age at which this occurs, with statistical variations between groups. The human mouth contains upper (maxillary) and lower (mandibular) molars. They are: maxillary first molar, maxillary second molar, maxillary third molar, mandibular first molar, mandibular second molar, and mandibular third molar.

Changes for: skin of knee

Changes for: skin of leg

  • Deleted
    • - skin of leg comment This class was created automatically from a combination of ontologies
  • Added

Changes for: cochlear nuclear complex

  • Deleted
    • - cochlear nuclear complex comment Location notes: 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
  • Added
    • + cochlear nuclear complex location notes 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

Changes for: endochondral bone tissue

  • Deleted
    • - endochondral bone tissue comment The text and logical definition of this term was modified from the definition of ‘endochondral bone’ in ZFA. AO notes: note 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
  • Added

Changes for: intramembranous bone tissue

  • Deleted
    • - intramembranous bone tissue comment 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)
  • Added
    • + intramembranous bone tissue external ontology notes 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) { external ontology=MA }

Changes for: masticatory muscle

  • Deleted
    • - masticatory muscle curator notes we use this specifically for a jaw muscle that is innervates by the mandibular nerve. Development notes: Masticatory muscles (MM) originate from the somitomeres. These muscles develop late and are not complete even at birth. Tongue muscles develop before masticatory muscles and complete by birth [http://php.med.unsw.edu.au/embryology]
  • Added

Changes for: pronephric glomerulus

  • Deleted
    • - pronephric glomerulus comment a glomus differs from a glomerulus in that each vascular glomus services several tubules. ISBN10:0073040584 “Vertebrates, Kardong”. AO notes: GO treats glomus and pronephric glomerulus differently
  • Added

Changes for: archenteron

  • Deleted
    • - archenteron definition The cavity of a gastrula forming a primitive gut[BTO]. The primitive gut that forms during gastrulation in the developing blastula. It develops into the digestive tract of an animal. As primary mesenchyme cells detach from the vegetal pole in the blastula and enter the fluid filled cavity in the center (the blastocoel), the remaining cells at the vegetal pole flatten to form a vegetal plate. This buckles inwards towards the blastocoel in a process called invagination. The cells continue to be rearranged until the shallow dip formed by invagination transforms into a deeper, narrower pouch formed by the gastrula’s endoderm. This narrowing and lengthening of the archenteron is driven by convergent extension. The open end of the archenteron is called the blastopore. The filopodia–thin fibers formed by the mesenchyme cells–found in a late gastrula contract to drag the tip of the archenteron across the blastocoel. The endoderm of the archenteron will fuse with the ectoderm of the blastocoel wall. At this point gastrulation is complete, and the gastrula has a functional digestive tube. The indentation that is actually formed is called the lip of the blastopore in amphibians and fish, and the primitive streak in birds and mammals. Each is controlled by the dorsal blastopore, and primitive node (also known as Hensen’s node), respectively. { database cross reference=http://en.wikipedia.org/wiki/Archenteron }
  • Added
    • + archenteron definition The cavity of a gastrula forming a primitive gut. { database cross reference=BTO:0001696 }
    • + archenteron development notes The primitive gut that forms during gastrulation in the developing blastula. It develops into the digestive tract of an animal. As primary mesenchyme cells detach from the vegetal pole in the blastula and enter the fluid filled cavity in the center (the blastocoel), the remaining cells at the vegetal pole flatten to form a vegetal plate. This buckles inwards towards the blastocoel in a process called invagination. The cells continue to be rearranged until the shallow dip formed by invagination transforms into a deeper, narrower pouch formed by the gastrula’s endoderm. This narrowing and lengthening of the archenteron is driven by convergent extension. The open end of the archenteron is called the blastopore. The filopodia–thin fibers formed by the mesenchyme cells–found in a late gastrula contract to drag the tip of the archenteron across the blastocoel. The endoderm of the archenteron will fuse with the ectoderm of the blastocoel wall. At this point gastrulation is complete, and the gastrula has a functional digestive tube. The indentation that is actually formed is called the lip of the blastopore in amphibians and fish, and the primitive streak in birds and mammals. Each is controlled by the dorsal blastopore, and primitive node (also known as Hensen’s node), respectively { source=WP }

Changes for: coracoid bone

  • Deleted
    • - coracoid bone editor note check developmental relationships. Taxon notes: In Theria, coracoid bones non-existent or fused with the shoulder blades to form coracoid processes[WP]. Procoracoid+coracoid are homologuous with coracoid of teleostomi. The coracoid is a triangular shaped-bone that usually has an anteriorly directed long process that may joins its counterpart in some fish groups. It may be perforated by the coracoid foramen or it may be notched dorsally and forms the scapulo-coracoid foramen together with a similar notch of the ventral margin of the scapula[VSAO]
  • Added
    • + coracoid bone editor note check developmental relationships.
    • + coracoid bone taxon notes In Theria, coracoid bones non-existent or fused with the shoulder blades to form coracoid processes[WP]. Procoracoid+coracoid are homologuous with coracoid of teleostomi. The coracoid is a triangular shaped-bone that usually has an anteriorly directed long process that may joins its counterpart in some fish groups. It may be perforated by the coracoid foramen or it may be notched dorsally and forms the scapulo-coracoid foramen together with a similar notch of the ventral margin of the scapula { source=VSAO , source=WP }

Changes for: liver stroma

Changes for: cleithrum

  • Deleted
    • - cleithrum taxon notes Found in some early members of Chelonia (e.g. Triassochelys), but missing in all later forms.[VSAO]
  • Added
    • + cleithrum taxon notes Found in some early members of Chelonia (e.g. Triassochelys), but missing in all later forms. { source=VSAO }

Changes for: fused sacrum

Changes for: supraoccipital bone

  • Deleted
    • - supraoccipital bone comment Taxon notes (via VHOG): See Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution, Fourth Edition (2006) McGraw-Hill, p.237 Table 7.1; usually forming a part of the occipital in the adult, but distinct in the young [PMID:10742104]
  • Added

Changes for: cerebellar vermis

  • Added
    • + cerebellar vermis taxon notes In bony fish, or teleosts, it has been proposed that the cerebellar auricles, which receive a large amount of input from the vestibulolateral line system, constitute the vestibulocerebellum and are homologues of the flocculonodular lobe of higher vertebrates along with the corpus cerebelli, which receives spinocerebellar and tectocerebellar fibers. The labyrinth and the lateral line organs of lampreys have structural and functional similarity. An important difference between the two structures is that the arrangement of the lateral line organs are such that they are sensitive to relative motion of the fluid surrounding the animal, whereas the labyrinths, having very similar sensing mechanisms, are sensitive to endolymph, providing information concerning the animal’s own equilibrium of the body and orientation in space { source=WP }

Changes for: piriform cortex

  • Deleted
    • - piriform cortex definition In anatomy of animals, the piriform cortex, or pyriform cortex is a region in the brain. The piriform cortex is part of the rhinencephalon situated in the telencephalon. The function of the piriform cortex relates to olfaction, which is the perception of smells. Sometimes called the olfactory cortex, olfactory lobe or paleopallium, 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. It is Brodmann area 27. { database cross reference=http://en.wikipedia.org/wiki/Piriform_cortex }
  • Added
    • + piriform cortex definition A part of the rhinencephalon situated in the telencephalon, the function of which relates to olfaction. { database cross reference=http://en.wikipedia.org/wiki/Piriform_cortex }
    • + piriform cortex taxon notes 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 { source=WP }

Changes for: cervix glandular epithelium

  • Deleted
    • - cervix glandular epithelium comment Histology notes: 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.[http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx]
  • Added
    • + cervix glandular epithelium structure notes 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. { source=http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx }

Changes for: digestive syncytial vacuole

  • Deleted
    • - digestive syncytial vacuole taxon notes in Aceola, Digestion is accomplished by means of a syncytium that forms a vacuole around ingested food. There are no epithelial cells lining the digestive vacuole, although there is sometimes a short pharynx leading from the mouth to the vacuole[WP]
  • Added
    • + digestive syncytial vacuole taxon notes in Aceola, Digestion is accomplished by means of a syncytium that forms a vacuole around ingested food. There are no epithelial cells lining the digestive vacuole, although there is sometimes a short pharynx leading from the mouth to the vacuole { source=WP }

Changes for: paired limb/fin

Changes for: secondary olfactory cortex

Changes for: olfactory cortex

Changes for: popliteus muscle

Changes for: deep brachial artery

Changes for: brachial artery

Changes for: subscapular artery

Changes for: lateral thoracic artery

Changes for: thoraco-acromial artery

Changes for: semimembranosus muscle

Changes for: gastrocnemius

Changes for: fibularis longus

Changes for: frontal lobe

  • Deleted
    • - frontal lobe editor note Many species don’t have lobes but they do have frontal cortex. Lobe isn’t a really well defined term though [MM]
  • Added
    • + frontal lobe editor note Many species don’t have lobes but they do have frontal cortex. Lobe isn’t a really well defined term though { source=MM }

Changes for: soleus muscle

Changes for: primary motor cortex

  • Deleted
    • - primary motor cortex editor note TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 {source=’MA-modified’} ! parietal lobe
  • Added
    • + primary motor cortex editor note TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 parietal lobe

Changes for: tibialis anterior

Changes for: perineal artery

Changes for: inferior epigastric artery

Changes for: deep femoral artery

Changes for: medial circumflex femoral artery

Changes for: inferior rectal artery

Changes for: coccyx

Changes for: lacrimal sac

Changes for: external acoustic meatus

Changes for: brown adipose tissue

Changes for: white adipose tissue

Changes for: obsolete fornix

Changes for: epithelium of vagina

  • Deleted
    • - epithelium of vagina comment AO notes: FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)
  • Added

Changes for: semitendinosus

Changes for: gluteus maximus

Changes for: gluteus medius

Changes for: nigrostriatal tract

Changes for: iliacus muscle

Changes for: great saphenous vein

Changes for: femoral vein

Changes for: perineal vein

Changes for: external anal sphincter

Changes for: deep circumflex iliac vein

Changes for: inferior vesical vein

Changes for: vaginal vein

Changes for: obturator artery

Changes for: superior gluteal artery

Changes for: external iliac vein

Changes for: internal iliac vein

Changes for: inferior vesical artery

Changes for: iliolumbar artery

Changes for: superior vesical artery

Changes for: internal iliac artery

Changes for: capsule of ovary

Changes for: external iliac artery

Changes for: ovarian follicle

Changes for: cumulus oophorus

Changes for: left uterine tube

Changes for: right uterine tube

Changes for: epididymis

  • Deleted
    • - epididymis comment 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.
    • - epididymis taxon notes A similar, but probably non-homologous, structure is found in cartilaginous fishes[WP]
  • Added
    • + epididymis structure 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.
    • + epididymis taxon notes A similar, but probably non-homologous, structure is found in cartilaginous fishes { source=WP }

Changes for: scrotum

  • Deleted
    • - scrotum definition In some male mammals the scrotum (also referred to as the cod) is a protuberance of skin and muscle containing the testicles. It is an extension of the abdomen, and is located between the penis and anus. In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty. In common speech, the scrotum is often improperly referred to as the testicles, which actually refer to organs encased inside the scrotum. The scrotum is homologous to the labia majora in females. It becomes tight when sexually aroused. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Scrotum }
  • Added

Changes for: spongiose part of urethra

Changes for: lumbar vertebra endochondral element

Changes for: superior prenasal cartilage

Changes for: skin of penis

Changes for: pampiniform plexus

Changes for: thoracic vertebra endochondral element

Changes for: cervical vertebra endochondral element

Changes for: prostatic urethra

Changes for: coccygeus muscle

Changes for: lobe of prostate

  • Deleted
    • - lobe of prostate SubClassOf organ part
    • - lobe of prostate comment 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 [PMID:15163300]
  • Added
    • + lobe of prostate EquivalentTo anatomical lobe and part of some prostate gland
    • + lobe of prostate SubClassOf anatomical lobe
    • + lobe of prostate definition A portion of a prostate that forms a lobe.
    • + lobe of prostate taxon notes 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 { source=http://www.ncbi.nlm.nih.gov/pubmed/15163300 }

Changes for: prostate gland anterior lobe

Changes for: sacral vertebra endochondral element

Changes for: iliolumbar vein

Changes for: tibial nerve

Changes for: rib endochondral element

  • Added
    • + rib endochondral element taxon notes 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.

Changes for: obturator vein

Changes for: dorsolateral prefrontal cortex

Changes for: semispinalis thoracis

Changes for: ulnar artery

Changes for: semispinalis capitis

Changes for: semispinalis cervicis

Changes for: spinalis thoracis muscle

Changes for: radial artery

Changes for: basilic vein

  • Deleted
    • - basilic vein SubClassOf arm blood vessel
    • - basilic vein SubClassOf part of some arm
    • - basilic vein comment This class was created automatically from a combination of ontologies
    • - basilic vein definition In human anatomy, the basilic vein is a large superficial vein of the upper limb that helps drain parts of manus and forearm. It originates on the medial (ulnar) side of the dorsal venous network of the manus, and it travels up the base of the forearm and arm. Most of its course is superficial; it generally travels in the subcutaneous fat and other fasciae that lie superficial to the muscles of the upper extremity. Because of this, it is usually visible through the skin. Near the region anterior to the cubital fossa, in the bend of the elbow joint, the basilic vein usually connects with the other large superficial vein of the upper extremity, the cephalic vein, via the median cubital vein. The layout of superficial veins in the forearm is highly variable from person to person, and there are generally a variety of other unnamed superficial veins that the basilic vein communicates with. About halfway up the arm proper (the part between the shoulder and elbow), the basilic vein goes deep, travelling under the muscles. There, around the lower border of the teres major muscle, the anterior and posterior circumflex humeral veins feed into it, just before it joins the brachial veins to form the axillary vein. Along with other superficial veins in the forearm, the basilic vein is a possible site for venipuncture. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Basilic_vein }
  • Added
    • + basilic vein SubClassOf drains some forelimb
    • + basilic vein SubClassOf forelimb blood vessel
    • + basilic vein SubClassOf part of some forelimb
    • + basilic vein definition A superficial vein of the upper limb that drain parts of manus and forearm. { database cross reference=http://en.wikipedia.org/wiki/Basilic_vein }
    • + basilic vein editor note This class was created automatically from a combination of ontologies
    • + basilic vein taxon notes It originates on the medial (ulnar) side of the dorsal venous network of the manus, and it travels up the base of the forearm and arm. Most of its course is superficial; it generally travels in the subcutaneous fat and other fasciae that lie superficial to the muscles of the upper extremity. Because of this, it is usually visible through the skin. Near the region anterior to the cubital fossa, in the bend of the elbow joint, the basilic vein usually connects with the other large superficial vein of the upper extremity, the cephalic vein, via the median cubital vein. The layout of superficial veins in the forearm is highly variable from person to person, and there are generally a variety of other unnamed superficial veins that the basilic vein communicates with. About halfway up the arm proper (the part between the shoulder and elbow), the basilic vein goes deep, travelling under the muscles. There, around the lower border of the teres major muscle, the anterior and posterior circumflex humeral veins feed into it, just before it joins the brachial veins to form the axillary vein. Along with other superficial veins in the forearm, the basilic vein is a possible site for venipuncture. { source=WP,unvetted }

Changes for: common palmar digital artery

Changes for: urogenital sinus mesenchyme

  • Deleted
    • - urogenital sinus mesenchyme comment 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
  • Added
    • + urogenital sinus mesenchyme development notes 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

Changes for: skin of limb

Changes for: skin of thorax

Changes for: skin of neck

Changes for: skin of abdomen

Changes for: skin of pelvis

Changes for: median cubital vein

Changes for: brachial vein

Changes for: tarsal skeleton

  • Deleted
    • - tarsal skeleton taxon notes 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]
  • Added
    • + tarsal skeleton taxon notes Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present { source=PHENOSCAPE:ad }

Changes for: proximal carpal cartilage

Changes for: proximal carpal endochondral element

Changes for: distal carpal endochondral element

Changes for: distal carpal cartilage element

Changes for: distal tarsal endochondral element

Changes for: proximal tarsal cartilage

Changes for: secondary heart field

  • Deleted
    • - secondary heart field taxon notes 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 [PMID:17276708]
  • Added
    • + secondary heart field taxon notes 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 { source=http://www.ncbi.nlm.nih.gov/pubmed/17276708 }

Changes for: proximal tarsal endochondral element

Changes for: interlobar vein

Changes for: proximal tarsal bone pre-cartilage condensation

Changes for: ciliary stroma

Changes for: interlobar artery

Changes for: medullary ray

Changes for: carpal skeleton

  • Deleted
    • - carpal skeleton taxon notes [Evolutionary variations]](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]. AO notes: 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. Taxon notes: 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[14] [Wikipedia:Carpus#Evolutionary_variations])
  • Added
    • + carpal skeleton external ontology notes 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. { external ontology=MA }
    • + carpal skeleton taxon notes 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]. { source=Evolutionary variations }
    • + carpal skeleton taxon notes 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

Changes for: centrale (fore)

Changes for: centrale 1

Changes for: centrale 2

Changes for: vein of abdomen

  • Deleted
    • - vein of abdomen comment 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. EDITOR NOTE: TODO mirror representation of abdominal aorta
  • Added
    • + vein of abdomen curator notes 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
    • + vein of abdomen editor note TODO mirror representation of abdominal aorta

Changes for: interdental plate

  • Deleted
    • - interdental plate taxon notes In paleobiology, the presence or absence of the interdental plate can determine the place of an animal in the evolutionary scale, and paleontologists use the interdental plate when trying to classify a new specimen. Thecodont reptiles and theropod dinosaur fossils have an interdental plate, whereas acrodont reptiles such as Sphenodontia do not.[3] Its presence in Archaeopteryx, an extinct avian, resulted in the proposal of the dinosaur-bird connection[WP]
  • Added
    • + interdental plate taxon notes In paleobiology, the presence or absence of the interdental plate can determine the place of an animal in the evolutionary scale, and paleontologists use the interdental plate when trying to classify a new specimen. Thecodont reptiles and theropod dinosaur fossils have an interdental plate, whereas acrodont reptiles such as Sphenodontia do not.[3] Its presence in Archaeopteryx, an extinct avian, resulted in the proposal of the dinosaur-bird connection { source=WP }

Changes for: psoas major muscle

Changes for: inner medulla of kidney

Changes for: distal convoluted tubule

Changes for: junk chamber

Changes for: blowhole ligament

Changes for: nephron

  • Deleted
    • - nephron 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]
  • Added
    • + nephron editor note kidney terms require review for cross-vertebrate compatibility and developmental relationships.
    • + nephron 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) { source=GO }

Changes for: hepatic sinusoid

Changes for: liver parenchyma

Changes for: bile canaliculus

Changes for: entotympanic bone

Changes for: ovarian medulla

Changes for: epithelium of large intestine

Changes for: ilium

Changes for: innominate bone

  • Deleted
    • - innominate bone external ontology notes 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. Taxon notes: 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[WP] { external ontology=FMA }
  • Added
    • + innominate bone external ontology notes 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. { external ontology=FMA }
    • + innominate bone taxon notes 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 { source=WP }

Changes for: femoral nerve

Changes for: acetabular part of hip bone

Changes for: pancreatic acinus

Changes for: trabecula of spleen

Changes for: pancreas

  • Deleted
    • - pancreas SubClassOf part of some endocrine system
    • - pancreas 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]
  • Added
    • + pancreas SubClassOf has part some endocrine pancreas
    • + pancreas SubClassOf located in some coelemic cavity lumen
    • + pancreas 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) { source=http://www.ncbi.nlm.nih.gov/pubmed/20959416 }

Changes for: lamina propria of urinary bladder

Changes for: posterior dorsal bursa

Changes for: nasal air sac

Changes for: mucosa of urinary bladder

Changes for: adventitia of ureter

Changes for: closed circulatory system

  • Deleted
    • - closed circulatory system editor note consider merging with cardiovascular system? Taxon notes: The circulatory systems of all vertebrates, as well as of annelids (for example, earthworms) and cephalopods (squid and octopus) are closed, just as in humans. Still, the systems of fish, amphibians, reptiles, and birds show various stages of the evolution of the circulatory system
  • Added
    • + closed circulatory system editor note consider merging with cardiovascular system?
    • + closed circulatory system taxon notes The circulatory systems of all vertebrates, as well as of annelids (for example, earthworms) and cephalopods (squid and octopus) are closed, just as in humans. Still, the systems of fish, amphibians, reptiles, and birds show various stages of the evolution of the circulatory system

Changes for: wall of urinary bladder

Changes for: trigone of urinary bladder

  • Deleted
    • - trigone of urinary bladder development notes Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present[WP]
  • Added
    • + trigone of urinary bladder development notes Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present { source=WP }

Changes for: neck of urinary bladder

Changes for: hilum of spleen

Changes for: muscularis mucosae of intestine

Changes for: crypt of Lieberkuhn of small intestine

Changes for: interlobular bile duct

Changes for: internal anal sphincter

Changes for: paraaortic body

Changes for: muscularis mucosae of large intestine

Changes for: right adrenal gland

Changes for: left adrenal gland

Changes for: right ureter

Changes for: left ureter

  • Deleted
    • - left ureter comment This class was created automatically from a combination of ontologies
  • Added

Changes for: quadratus lumborum

Changes for: inferior mesenteric vein

Changes for: jejunal vein

Changes for: middle colic vein

Changes for: ileocolic vein

Changes for: muscularis mucosae of small intestine

Changes for: duodenal gland

  • Deleted
    • - duodenal gland editor note currently defined as equivalent to any submucosal gland in the duodenum. Taxon notes: Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds [ISBN:9780521617147]
  • Added
    • + duodenal gland editor note currently defined as equivalent to any submucosal gland in the duodenum.
    • + duodenal gland taxon notes Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds { source=ISBN:9780521617147 }

Changes for: Peyer’s patch

  • Deleted
    • - Peyer’s patch comment 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. Taxon notes: Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer’s patches (Zapata and Solas).
  • Added

Changes for: serosa of small intestine

Changes for: inner medulla vasa recta ascending limb

  • Deleted
    • - inner medulla vasa recta ascending limb comment This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb
  • Added
    • + inner medulla vasa recta ascending limb external ontology notes This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb { external ontology=CL }

Changes for: mucosa of large intestine

Changes for: vasa recta ascending limb

  • Deleted
    • - vasa recta ascending limb comment This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb
  • Added
    • + vasa recta ascending limb external ontology notes This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb { external ontology=CL }

Changes for: mucosa of small intestine

Changes for: outer medulla vasa recta descending limb

  • Deleted
    • - outer medulla vasa recta descending limb comment This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb
  • Added
    • + outer medulla vasa recta descending limb external ontology notes This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb { external ontology=CL }

Changes for: submucosa of small intestine

Changes for: submucosa of large intestine

Changes for: outer medulla vasa recta ascending limb

  • Deleted
    • - outer medulla vasa recta ascending limb comment This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb
  • Added
    • + outer medulla vasa recta ascending limb external ontology notes This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb { external ontology=CL }

Changes for: inner medulla vasa recta descending limb

  • Deleted
    • - inner medulla vasa recta descending limb comment This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb
  • Added
    • + inner medulla vasa recta descending limb external ontology notes This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb { external ontology=CL }

Changes for: muscularis mucosae of stomach

Changes for: submucosa of stomach

Changes for: haemal node

Changes for: distal tarsal bone pre-cartilage condensation

Changes for: pessulus

Changes for: distal tarsal cartilage

Changes for: wall of ureter

Changes for: renal lobe

  • Deleted
    • - renal lobe editor note todo - add has_part relationships. Taxon notes: human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys[MP]
  • Added

Changes for: lobule

  • Added
    • + lobule editor note todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland)

Changes for: hypothalamo-hypophyseal system

  • Deleted
    • - hypothalamo-hypophyseal system taxon notes in lampreys and teleost hormones enter the adenohypophysis by diffusion. Editor notes: we represent this structure strictly as a system of blood vessels (presumably in line with the FMA). It could also be extended to include neurons and fiber tracts, as per the MESH definition. Function notes: One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis). The hypothalamus is responsible for certain metabolic processes and other activities of the autonomic nervous system. It synthesizes and secretes certain neurohormones, often called hypothalamic-releasing hormones, and these in turn stimulate or inhibit the secretion of pituitary hormones. The hypothalamus controls body temperature, hunger, thirst, fatigue, sleep, and circadian cycles[WP]
  • Added
    • + hypothalamo-hypophyseal system editor note we represent this structure strictly as a system of blood vessels (presumably in line with the FMA). It could also be extended to include neurons and fiber tracts, as per the MESH definition
    • + hypothalamo-hypophyseal system function notes One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis). The hypothalamus is responsible for certain metabolic processes and other activities of the autonomic nervous system. It synthesizes and secretes certain neurohormones, often called hypothalamic-releasing hormones, and these in turn stimulate or inhibit the secretion of pituitary hormones. The hypothalamus controls body temperature, hunger, thirst, fatigue, sleep, and circadian cycles
    • + hypothalamo-hypophyseal system taxon notes in lampreys and teleost hormones enter the adenohypophysis by diffusion. . { source=WP }

Changes for: epithelium of pancreatic duct

Changes for: internodal tract

  • Deleted
    • - internodal tract comment evidence is sparse [http://www.gpnotebook.co.uk/simplepage.cfm?ID=-483065798] There is some functional evidence for the existence of specialized conducting pathways within the atria (termed internodal tracts), although this is controversial[http://www.cvphysiology.com/Arrhythmias/A003.htm]. Editor note: include 3 subtypes?
  • Added

Changes for: neurogenic placode

  • Deleted
    • - neurogenic placode comment Includes: trigeminal, otic, lateral line and epibranchial placodes. Taxon notes: 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)[NBK53171]
  • Added

Changes for: olfactory bulb plexiform layer

Changes for: cartilage of nasal septum

Changes for: patella cartilage element

Changes for: replacement bone

  • Deleted
    • - replacement bone comment 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.
  • Added

Changes for: geniculate placode

Changes for: petrosal placode

Changes for: nodosal placode

Changes for: adenohypophyseal placode

  • Deleted
    • - adenohypophyseal placode comment Addtional notes: 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)
  • Added
    • + adenohypophyseal placode development notes 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)

Changes for: cranial sensory ganglion

  • Deleted
    • - cranial sensory ganglion editor note check this - merge into cranial ganglion? WP: the geniculate, petrosal and nodose ganglia, appended respectively to cranial nerves VII, IX and X. Other ontology notes: has no subtypes in FMA
  • Added

Changes for: branchial basket

  • Deleted
    • - branchial basket comment May also be present in amphioxus. Editor notes: developmental relationship needs to be changed if the scope is broadened, as NC is vertebrate-specific
  • Added

Changes for: vestibulocochlear ganglion

  • Deleted
    • - vestibulocochlear ganglion comment 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[Wikipedia:Cochlear_nerve]
  • Added
    • + vestibulocochlear ganglion terminology notes 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 { source=http://en.wikipedia.org/wiki/Cochlear_nerve }

Changes for: macula lutea proper

Changes for: mammary gland sebaceous gland

Changes for: periventricular zone of hypothalamus

Changes for: hyaloid artery

  • Deleted
    • - hyaloid artery comment Taxon notes: In humans, Usually fully regressed before birth, its purpose is to supply nutrient to the developing lens in the growing fetus. During the tenth week of development the lens grows independent of a blood supply and the hyaloid artery usually regresses. Its proximal portion remains as the central artery of the retina. Regression of the hyaloid artery leaves a clear central zone through the vitreous called the hyaloid canal or Cloquet’s canal. Occasionally the artery may not fully regress, resulting in the condition persistent hyaloid artery. More commonly, small remnants of the artery may remain. Free remnants can sometimes be seen as ‘floaters’. An anterior remnant of the hyaloid artery can be seen in some people as Mittendorf’s dot, a small pinpoint-like scar on the posterior surface of the lens. A posterior remnant may be seen where the artery left the optic disc, and is known as Bergmeister’s papilla
  • Added
    • + hyaloid artery taxon notes In humans, Usually fully regressed before birth, its purpose is to supply nutrient to the developing lens in the growing fetus. During the tenth week of development the lens grows independent of a blood supply and the hyaloid artery usually regresses. Its proximal portion remains as the central artery of the retina. Regression of the hyaloid artery leaves a clear central zone through the vitreous called the hyaloid canal or Cloquet’s canal. Occasionally the artery may not fully regress, resulting in the condition persistent hyaloid artery. More commonly, small remnants of the artery may remain. Free remnants can sometimes be seen as ‘floaters’. An anterior remnant of the hyaloid artery can be seen in some people as Mittendorf’s dot, a small pinpoint-like scar on the posterior surface of the lens. A posterior remnant may be seen where the artery left the optic disc, and is known as Bergmeister’s papilla

Changes for: lateral zone of hypothalamus

Changes for: medial zone of hypothalamus

Changes for: udder

Changes for: vestibular aqueduct

Changes for: reticular formation

  • Deleted
    • - reticular formation comment Usage notes: this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
  • Added

Changes for: perifornical nucleus

Changes for: lamina of spiral limbus

Changes for: hyponychium

Changes for: vestibular membrane of cochlear duct

Changes for: Grueneberg ganglion

Changes for: choroid plexus of third ventricle

Changes for: choroid plexus of fourth ventricle

Changes for: biliary system

Changes for: supraorbital gland

  • Deleted
    • - supraorbital gland comment Function notes: The gland’s function is similar to that of the kidneys, though it is much more efficient at removing salt, allowing Penguins to survive without access to fresh water. Contrary to popular belief, the gland does not directly convert saltwater to freshwater. The term supraorbital refers to the area just above the eye socket (which is known as the orbit of the eye. ) Living in saltwater environments would naturally pose a large problem for penguins because the ingestion of saltwater would be detrimental to a penguin’s health. Although penguins do not directly drink water, it is taken in when they engulf prey. As a result, saltwater enters their system and must be effectively excreted. The supraorbital gland has thus enabled the penguins’ survival in such environments due to its water-filtering capability. The gland is located just above the eyes and surrounds a capillary in the head. This capillary constantly strains out the salt in the saltwater that a penguin takes in. Since the byproduct of the gland has roughly five times as much salt as would normally be found in the animal’s fluids, the supraorbital gland is highly efficient. The penguin excretes the salt byproduct as a brine through its bill. Often, the fluid drips out, and this gives the appearance of a runny nose. However, the fluid may also be sneezed out. In the absence of saltwater, caused by captivity, the supraorbital gland will lie dormant as it has no other purpose. Having a dormant supraorbital gland does not negatively affect the health of a penguin
  • Added
    • + supraorbital gland function notes The gland’s function is similar to that of the kidneys, though it is much more efficient at removing salt, allowing Penguins to survive without access to fresh water. Contrary to popular belief, the gland does not directly convert saltwater to freshwater. The term supraorbital refers to the area just above the eye socket (which is known as the orbit of the eye. ) Living in saltwater environments would naturally pose a large problem for penguins because the ingestion of saltwater would be detrimental to a penguin’s health. Although penguins do not directly drink water, it is taken in when they engulf prey. As a result, saltwater enters their system and must be effectively excreted. The supraorbital gland has thus enabled the penguins’ survival in such environments due to its water-filtering capability. The gland is located just above the eyes and surrounds a capillary in the head. This capillary constantly strains out the salt in the saltwater that a penguin takes in. Since the byproduct of the gland has roughly five times as much salt as would normally be found in the animal’s fluids, the supraorbital gland is highly efficient. The penguin excretes the salt byproduct as a brine through its bill. Often, the fluid drips out, and this gives the appearance of a runny nose. However, the fluid may also be sneezed out. In the absence of saltwater, caused by captivity, the supraorbital gland will lie dormant as it has no other purpose. Having a dormant supraorbital gland does not negatively affect the health of a penguin

Changes for: caudofemoralis

  • Deleted
    • - caudofemoralis comment Action: The Caudofemoralis acts to flex the tail laterally to its respective side when the pelvic limb is bearing weight. When the pelvic limb is lifted off the ground, contraction of the Caudofemoralis causes the limb to abduct and the shank to extend by extending the hip joint (acetabulofemoral or coxofemoral joint)
  • Added
    • + caudofemoralis actions notes The Caudofemoralis acts to flex the tail laterally to its respective side when the pelvic limb is bearing weight. When the pelvic limb is lifted off the ground, contraction of the Caudofemoralis causes the limb to abduct and the shank to extend by extending the hip joint (acetabulofemoral or coxofemoral joint)

Changes for: anterior jugular vein

Changes for: cartilage of main bronchus

Changes for: costal cartilage

Changes for: external jugular vein

Changes for: head of rib

  • Deleted
    • - head of rib comment This class was created automatically from a combination of ontologies
  • Added

Changes for: body of rib

  • Deleted
    • - body of rib comment This class was created automatically from a combination of ontologies
  • Added

Changes for: entire embryonic mesenchyme

Changes for: sternothyroid muscle

Changes for: sternohyoid muscle

  • Deleted
    • - sternohyoid muscle comment Action: draws hyoid posteriorly . AO notes: Note that as defined here, this structure attaches to the sternum, which is a tetrapod structure. TAO has class ‘sternohyoid’ as part of mandibular muscle, but no sternum, so excluded here. The TAO/ZFA class has no definition, but the dictionary of icthyology states: “a large muscle originating on the ventral spine of the postcleithrum and inserting on the sides of the urohyal. It functions in rapid opening of the jaw and expanding the buccal cavity” - a generic way of grouping these is via a hyoid - girdle connection
  • Added
    • + sternohyoid muscle actions notes draws hyoid posteriorly .
    • + sternohyoid muscle external ontology notes Note that as defined here, this structure attaches to the sternum, which is a tetrapod structure. TAO has class ‘sternohyoid’ as part of mandibular muscle, but no sternum, so excluded here. The TAO/ZFA class has no definition, but the dictionary of icthyology states: ‘a large muscle originating on the ventral spine of the postcleithrum and inserting on the sides of the urohyal. It functions in rapid opening of the jaw and expanding the buccal cavity’ - a generic way of grouping these is via a hyoid - girdle connection { external ontology=TAO }

Changes for: clavicle

  • Deleted
    • - clavicle taxon notes 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] AO Notes: FMA and MA differ in whether they consider this part of the shoulder. Development notes: 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.[ISBN:978-0-12-319060-4]
  • Added
    • + clavicle development notes 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. { source=ISBN:978-0-12-319060-4 }
    • + clavicle external ontology notes FMA and MA differ in whether they consider this part of the shoulder { external ontology=FMA }
    • + clavicle taxon notes 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].

Changes for: cephalic vein

Changes for: left lobe of liver

Changes for: right lobe of liver

Changes for: dorsal thoracic nucleus

Changes for: intercostal muscle

Changes for: quadrate lobe of liver

Changes for: median artery

Changes for: scalenus medius

Changes for: splenius

Changes for: thyroglossal duct

Changes for: dorsal horn of spinal cord

Changes for: serratus ventralis

Changes for: ventral horn of spinal cord

Changes for: scalenus posterior

Changes for: popliteal artery

Changes for: vertebral foramen

Changes for: anterior olfactory nucleus

Changes for: cardiac muscle tissue

  • Deleted
    • - cardiac muscle tissue comment check relationship with myocardium. part_of in MA - but we also have a more specific class ‘cardiac muscle tissue of myocardium’. Check ncit
  • Added
    • + cardiac muscle tissue editor note check relationship with myocardium. part_of in MA - but we also have a more specific class ‘cardiac muscle tissue of myocardium’. Check ncit

Changes for: parathyroid gland

  • Deleted
    • - parathyroid gland development notes table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. Additional notes: 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]. The parathryoid gland is not formed in fish, but is only found in tetrapods. In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch[PMID:16313389]
  • Added
    • + parathyroid gland comment Additional notes: 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]. The parathryoid gland is not formed in fish, but is only found in tetrapods. In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch
    • + parathyroid gland development notes table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. { source=http://www.ncbi.nlm.nih.gov/pubmed/16313389 }

Changes for: olfactory bulb

  • Deleted
    • - olfactory bulb comment 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). Development notes: 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).
  • Added
    • + olfactory bulb development notes 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).
    • + olfactory bulb taxon notes 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)

Changes for: pupillary membrane

Changes for: laterodorsal tegmental nucleus

Changes for: mesothelium

  • Deleted
    • - mesothelium comment This class was created automatically from a combination of ontologies
  • Added

Changes for: dorsal root of spinal cord

Changes for: celiac ganglion

Changes for: ventral root of spinal cord

Changes for: superior mesenteric vein

Changes for: common iliac vein

Changes for: ovarian vein

Changes for: suprarenal vein

Changes for: trunk of peripheral nerve

Changes for: median nerve

Changes for: testicular vein

  • Deleted
    • - testicular vein EquivalentTo vein and connected to some testis
    • - testicular vein SubClassOf connected to some testis
    • - testicular vein comment comment: editor note: TODO - check testicular vs spermatic vein (MA:0002218)
    • - testicular vein definition The testicular vein (or spermatic vein), the male gonadal vein, carries deoxygenated blood from its corresponding testis to the inferior vena cava or one of its tributaries. 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: 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. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Testicular_vein , database cross reference=https://sourceforge.net/tracker/?func=detail&aid=3220553&group_id=76834&atid=1205376 }
  • Added
    • + testicular vein EquivalentTo vein and drains some testis
    • + testicular vein SubClassOf drains some testis
    • + testicular vein definition 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. { database cross reference=http://en.wikipedia.org/wiki/Testicular_vein , database cross reference=https://sourceforge.net/tracker/?func=detail&aid=3220553&group_id=76834&atid=1205376 , database cross reference=UBERON:cjm }
    • + testicular vein editor note TODO - check testicular vs spermatic vein (MA:0002218)
    • + testicular vein taxon notes 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

Changes for: fibrous joint

Changes for: xiphoid process

  • Deleted
    • - xiphoid process comment this class may represent a mixed bony-cartilage element, or it may be the superclass of either purely cartilage or purely ossified elements. Taxon notes: usually ossified in the adult human. By age 15 to 29, the xiphoid usually fuses to the body of the sternum with a fibrous joint. Unlike the synovial articulation of major joints, this is non-movable. Much the way the first seven ribs articulate with the sternum, the cartilage in the celiac plexus joins on the xiphoid process, reinforcing it, and indirectly attaches the costal cartilage to the sternum. [WP,unvetted]
  • Added
    • + xiphoid process curator notes this class may represent a mixed bony-cartilage element, or it may be the superclass of either purely cartilage or purely ossified elements { source=WP,unvetted }
    • + xiphoid process taxon notes usually ossified in the adult human. By age 15 to 29, the xiphoid usually fuses to the body of the sternum with a fibrous joint. Unlike the synovial articulation of major joints, this is non-movable. Much the way the first seven ribs articulate with the sternum, the cartilage in the celiac plexus joins on the xiphoid process, reinforcing it, and indirectly attaches the costal cartilage to the sternum.

Changes for: body of pancreas

Changes for: tail of pancreas

Changes for: paleocortex

  • Deleted
    • - paleocortex comment Location notes: Paleocortex is present in the parahippocampal gyrus,[1] olfactory bulb, accessory olfactory bulb, olfactory tubercle, piriform cortex, periamygdalar area,[2] anterior olfactory nucleus, anterior perforated substance, and prepyriform area[WP]
  • Added
    • + paleocortex location notes Paleocortex is present in the parahippocampal gyrus,[1] olfactory bulb, accessory olfactory bulb, olfactory tubercle, piriform cortex, periamygdalar area,[2] anterior olfactory nucleus, anterior perforated substance, and prepyriform area { source=WP }

Changes for: descending colon

Changes for: submucosa of trachea

Changes for: sigmoid colon

Changes for: vasculature of trunk

Changes for: transverse colon

Changes for: vasculature of head

Changes for: caecum

  • Deleted
    • - caecum taxon notes 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.[WP]
  • Added
    • + caecum taxon notes 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. { source=WP }

Changes for: lesser curvature of stomach

Changes for: greater curvature of stomach

Changes for: wall of stomach

Changes for: synchondrosis

Changes for: wall of small intestine

Changes for: macula of utricle of membranous labyrinth

Changes for: wall of large intestine

Changes for: cartilaginous joint

Changes for: macula of saccule of membranous labyrinth

Changes for: rib

  • Deleted
    • - rib comment 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.[1]

Changes for: interparietal bone

Changes for: manual minor digit (Aves) digitopodial skeleton

  • Deleted
    • - manual minor digit (Aves) digitopodial skeleton comment 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.
  • Added
    • + manual minor digit (Aves) digitopodial skeleton curator notes 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.

Changes for: manual major digit (Aves) digitopodial skeleton

  • Deleted
    • - manual major digit (Aves) digitopodial skeleton comment 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.
  • Added
    • + manual major digit (Aves) digitopodial skeleton curator notes 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.

Changes for: alular digit digitopodial skeleton

  • Deleted
    • - alular digit digitopodial skeleton comment 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.
  • Added
    • + alular digit digitopodial skeleton curator notes 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.

Changes for: hepatic acinus

Changes for: portal lobule

Changes for: right hepatic duct

Changes for: thoracic cavity

Changes for: visceral peritoneum

Changes for: basilar membrane of cochlea

Changes for: peritoneal cavity

Changes for: testicular artery

Changes for: embryonic urethral groove

  • Deleted
    • - embryonic urethral groove comment Taxon notes: 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[Wikipedia:Urethral_groove]
  • Added

Changes for: superior suprarenal artery

Changes for: ileocolic artery

Changes for: middle colic artery

Changes for: inferior pancreaticoduodenal artery

Changes for: splenic artery

Changes for: left gastric artery

Changes for: cell group

Changes for: pharyngeal membrane of 1st arch

  • Deleted
    • - pharyngeal membrane of 1st arch comment 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
  • Added

Changes for: nephric duct

Changes for: vasa recta descending limb

  • Deleted
    • - vasa recta descending limb comment This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb
  • Added
    • + vasa recta descending limb external ontology notes This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb { external ontology=CL }

Changes for: lateral cervical nucleus

Changes for: lateral funiculus of spinal cord

Changes for: outer cortex of kidney

Changes for: respiratory bronchiole

  • Deleted
    • - respiratory bronchiole taxon notes mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts[ISBN10:0123813611]
  • Added

Changes for: bronchiole

  • Deleted
    • - bronchiole comment Structure notes: lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer[ISBN10:0123813611]
  • Added
    • + bronchiole structure notes lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer { source=ISBN10:0123813611 }

Changes for: ventral funiculus of spinal cord

Changes for: lobar bronchus

  • Deleted
    • - lobar bronchus comment Structure notes: 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.
  • Added
    • + lobar bronchus structure notes 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.

Changes for: primary nodular lymphoid tissue

Changes for: principal inferior olivary nucleus

Changes for: nucleus raphe pallidus

Changes for: medial accessory inferior olivary nucleus

Changes for: oropharyngeal choana

Changes for: fastigial nucleus

Changes for: nucleus raphe magnus

Changes for: gigantocellular nucleus

Changes for: middle cerebellar peduncle

Changes for: pontine nuclear group

Changes for: left lung

  • Deleted
    • - left lung comment This class was created automatically from a combination of ontologies
  • Added

Changes for: right lung

  • Deleted
    • - right lung comment This class was created automatically from a combination of ontologies
  • Added

Changes for: endocardium of atrium

Changes for: tectobulbar tract

Changes for: inferior cerebellar peduncle

Changes for: area postrema

Changes for: gracile nucleus

Changes for: nucleus prepositus

Changes for: cerebellar nuclear complex

Changes for: anterior lobe of cerebellum

Changes for: vas deferens

  • Deleted
    • - vas deferens taxon notes 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.[WP]
  • Added
    • + vas deferens taxon notes 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. { source=WP }

Changes for: dentate nucleus

Changes for: skin epidermis

  • Deleted
    • - skin epidermis comment 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).
  • Added
    • + skin epidermis taxon notes 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).

Changes for: habenulo-interpeduncular tract

Changes for: digestive system

Changes for: embryonic nasal process

Changes for: parvocellular oculomotor nucleus

Changes for: interpeduncular nucleus

Changes for: pedunculopontine tegmental nucleus

Changes for: dorsal tegmental nucleus

Changes for: adipose tissue

Changes for: superior salivatory nucleus

Changes for: pulmonary valve

Changes for: reticulotegmental nucleus

Changes for: artery smooth muscle tissue

Changes for: smooth muscle of esophagus

Changes for: right ovary

  • Deleted
    • - right ovary comment This class was created automatically from a combination of ontologies
  • Added

Changes for: left ovary

  • Deleted
    • - left ovary taxon notes [In other animals]](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])
  • Added
    • + left ovary 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 { source=In other animals }

Changes for: solitary tract nuclear complex

Changes for: inferior olivary complex

Changes for: medulla of thymus

Changes for: lobule of thymus