2014-05-24 release

Reproductive system improvements - more terms for unusual cartilaginous fish and reptile intromittent organs, mammary glands now consistent with GO. Various new terms added for character matrix annotation in phenoscape
2014-05-24 release image

Ontology Diff Report

  • reproductive system
    • NTs for clasper related terms
    • NTs: hemipenal sheath, lumen, glands
    • mammary glands: now in sync with GO, latest MP
  • phenoscape-requested terms
    • NT: exoccipital-atlas joint
    • NT: extensor pollicis brevis
    • NTs: retractor lateralis - anterior, posterior
    • flexor cruris
    • cephalic spine
    • added specific cingulae
  • admin
    • many comments translated to more specific annotations properties
  • ext
    • massive tidy up of terms inherited from AAO
    • many equivalence axioms added to tooth and skeletal series terms, inherited from TAO
    • fixed interepipodial space. Fixes issue #460
  • other
    • NTs: transverse folds of rectum, rectal valve
    • NTs: gas gland, mormyromast
    • improvements in early aortic arch arteries
    • NTs: pineal corpora arenacea, choroid plexus corpora arenacea

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-05-22/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-05-24/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 37

New Class : retractor lateralis posterior muscle

New Class : retractor lateralis anterior muscle

New Class : exoccipital-atlas joint

New Class : flexor cruris lateralis muscle

New Class : flexor cruris lateralis pars accessoria muscle

New Class : hemipenis keratinized epithelium

New Class : hemipenial mucuous gland

New Class : lumen of hemipenial sheath

New Class : hemipenial holocrine gland

New Class : retractor lateralis muscle

New Class : cingulum of tooth

New Class : cingulum of incisor tooth

New Class : cingulum of canine tooth

New Class : cingulum of upper incisor tooth

New Class : cingulum of lower incisor tooth

New Class : cingulum of upper canine tooth

New Class : cingulum of lower canine tooth

New Class : cingulum of upper jaw molar

New Class : cingulum of lower jaw molar

New Class : vomerine dentition

New Class : cingulum of molar tooth

New Class : afferent spiracular artery

New Class : efferent spiracular artery

New Class : extensor pollicis brevis muscle

New Class : cephalic spine

New Class : spine appendage of head

New Class : transverse folds of rectum

New Class : pterygopodial gland

New Class : pseudoclasper

New Class : prepelvic clasper

New Class : mormyromast organ

New Class : rectal valve

New Class : gas gland

New Class : calcified structure of brain

New Class : choroid plexus corpora arenacea

New Class : pineal corpora arenacea

New Class : xenarthrale

Changed Class objects: 933

Changes for: rostral linear nucleus

  • Deleted
    • - rostral linear nucleus comment Editorial note: Brain Info does not list the linear nuclei as part of the ventral tegmental area but as a co-area of the midbrain tegmentum. Am assuming the rostral linear nucleus of the raphe is synonymous, but needs further review. (NIF)
  • Added
    • + rostral linear nucleus editor note Brain Info does not list the linear nuclei as part of the ventral tegmental area but as a co-area of the midbrain tegmentum. Am assuming the rostral linear nucleus of the raphe is synonymous, but needs further review. (NIF)

Changes for: base of crypt of lieberkuhn

  • Deleted
    • - base of crypt of lieberkuhn comment 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. [ISBN:9780521617147]

Changes for: dartos muscle of scrotum

  • Deleted
    • - dartos muscle of scrotum comment AO 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]
  • Added
    • + 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 }

Changes for: branch of ilio-marsupialis muscle

Changes for: fetal tooth

Changes for: flexural organ

  • Deleted
    • - flexural organ comment Taxon notes: may be an ontogenetical remnant of the infundibular organ in cephalochordates. Editor notes: we cannot classify as a secretory circumventricular organ, as this leads to unsatisfiability
  • Added

Changes for: limb gland

Changes for: platypus calcaneus spur

  • Deleted
    • - platypus calcaneus spur comment Taxon notes: The female platypus, in common with echidnas, has rudimentary spur buds which do not develop (dropping off before the end of their first year) and lack functional crural glands. Not to be confused with ‘calcaneal spur’, a small osteophyte (bone spur) located on the calcaneus (heel bone)
  • Added
    • + platypus calcaneus spur taxon notes The female platypus, in common with echidnas, has rudimentary spur buds which do not develop (dropping off before the end of their first year) and lack functional crural glands. Not to be confused with ‘calcaneal spur’, a small osteophyte (bone spur) located on the calcaneus (heel bone)

Changes for: hyomandibular cartilage

  • Deleted
    • - hyomandibular cartilage comment Taxon notes: The stapes is homologous to the hyomandibula. In this ontology, we use the class ‘hyomandibular cartilage’ generally to include the future stapes, the future hyomandibular bone of teleosts and the unossified cartilage in sharks.
  • Added
    • + hyomandibular cartilage taxon notes The stapes is homologous to the hyomandibula. In this ontology, we use the class ‘hyomandibular cartilage’ generally to include the future stapes, the future hyomandibular bone of teleosts and the unossified cartilage in sharks.

Changes for: stylohyoid bone

  • Deleted
    • - stylohyoid bone comment 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[MURDOCH]

Changes for: epipleural series

Changes for: surangular bone

  • Deleted
    • - surangular bone comment Taxon notes: “Nevertheless, it is not completely clear that this[osteichthyans] surangular is homologous with the surangular in tetrapods”[paleos] In some lepospondyls, and in frogs and salamanders, the surangular is absent. However, it becomes increasingly significant in the anthracosaur lineage. In turtles, it is one of the two principle bones of the lower jaw. In lepidosaurs, it is less important because of the development of a separate coronoid bone. In advanced lizards and pythonomorphs, it may fuse with the articular and perhaps other bones and loses its separate identity. In syanapsids, a secondary jaw joint develops between the surangular and the squamosal, which becomes the unique mammalian jaw articulation. However, the surangular fuses with the dentary and becomes the unitary mammalian “mandible” without a separate identity
  • Added
    • + surangular bone comment In some lepospondyls, and in frogs and salamanders, the surangular is absent. However, it becomes increasingly significant in the anthracosaur lineage. In turtles, it is one of the two principle bones of the lower jaw. In lepidosaurs, it is less important because of the development of a separate coronoid bone. In advanced lizards and pythonomorphs, it may fuse with the articular and perhaps other bones and loses its separate identity. In syanapsids, a secondary jaw joint develops between the surangular and the squamosal, which becomes the unique mammalian jaw articulation. However, the surangular fuses with the dentary and becomes the unitary mammalian “mandible” without a separate identity
    • + surangular bone taxon notes Nevertheless, it is not completely clear that this[osteichthyans] surangular is homologous with the surangular in tetrapods[paleos]

Changes for: oviduct artery

Changes for: depressor mandibulae muscle

  • Deleted
    • - depressor mandibulae muscle comment 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
    • + 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]

Changes for: puboischiofemoralis externus muscle

Changes for: puboischiofemoralis internus muscle

Changes for: dorsal head of rib

  • Deleted
    • - dorsal head of rib comment Taxon notes: Ribs of primitive tetrapods are bicipital (having two heads)[Kardong]. Terminology notes: sometimes called the tuberculum, but not to be confused with the tubercle, which is between body and neck
  • Added

Changes for: ventral head of rib

Changes for: pineal gland stalk

Changes for: motor nucleus of vagal nerve

  • Deleted
    • - motor nucleus of vagal nerve comment Usage notes: in ZFA this is the superclass of dorsolateral and medial (which have not been generalized above ZFA). In this ontology it is a broad grouping class covering these zebrafish structures as well as the generalized dorsal motor nucleus
  • Added
    • + motor nucleus of vagal nerve curator notes in ZFA this is the superclass of dorsolateral and medial (which have not been generalized above ZFA). In this ontology it is a broad grouping class covering these zebrafish structures as well as the generalized dorsal motor nucleus

Changes for: spinal cord dorsal commissural nucleus

Changes for: secondary remex feather

Changes for: dermal condensation of feather follicle

  • Deleted
    • - dermal condensation of feather follicle comment Taxon notes: The development of placodes where dermal condensations occur, an evolutionary novelty, required changes in gene expression and timing. However, such changes are known to be an important mechanism in the origin of morphological innovations in many other organisms (True and Carroll 2002, Prum 2005)
  • Added
    • + dermal condensation of feather follicle taxon notes The development of placodes where dermal condensations occur, an evolutionary novelty, required changes in gene expression and timing. However, such changes are known to be an important mechanism in the origin of morphological innovations in many other organisms (True and Carroll 2002, Prum 2005)

Changes for: areolar gland

Changes for: acinus of lactiferous gland

Changes for: vertebra cartilage element

Changes for: endocardium of auricle

Changes for: omosternum

Changes for: epicoracoid

Changes for: vasculature of respiratory integument

Changes for: obsolete external carotid

Changes for: obsolete internal carotid

Changes for: obsolete carotid

Changes for: prepollical protuberances

Changes for: tibial protuberances

Changes for: medial forebrain bundle

Changes for: mammary gland

Changes for: colostrum

Changes for: lobule of lactiferous gland

Changes for: obsolete nuptial pads

Changes for: milk

Changes for: epithelium of crypt of lieberkuhn

Changes for: ulnar protuberances

Changes for: thalamic reticular nucleus

Changes for: metacarpal fold

Changes for: ulnar fold

Changes for: metatarsal fold

Changes for: tarsal fringe

Changes for: lateral geniculate body

Changes for: jaw depressor muscle

  • Deleted
    • - jaw depressor muscle comment 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.’[doi:10.1006/bijl.2000.0436]

Changes for: semen

  • Deleted
    • - semen comment 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 a taxonomically generic way (see comments for UBERON:0006530).

Changes for: quadrate-articular joint

  • Deleted
    • - quadrate-articular joint comment Usage 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
    • + 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]

Changes for: gut-associated lymphoid tissue

Changes for: periarterial lymphatic sheath

Changes for: elastic cartilage tissue

Changes for: sternocostal joint

Changes for: synovial joint of pectoral girdle

Changes for: papillary layer of dermis

Changes for: placenta

  • Deleted
    • - placenta comment Taxon notes: Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother’s uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 “Vertebrates, Kardong”]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: http://dx.doi.org/10.1002/jmor.11011 // Marsupials possess only a rudimentary placenta, with reduced nutrient and oxygen exchanging capabilities.
  • Added
    • + placenta comment Marsupials possess only a rudimentary placenta, with reduced nutrient and oxygen exchanging capabilities.
    • + placenta taxon notes Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother’s uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: http://dx.doi.org/10.1002/jmor.11011

Changes for: crypt of Lieberkuhn

  • Deleted
    • - crypt of Lieberkuhn comment 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[ISBN:9780521617147]

Changes for: blood vessel

  • Deleted
    • - blood vessel comment note that FMA:63183 Blood vessel is categorized as ‘general anatomical term’. Suggestion to map to region of vascular tree from Terry H at JAX. Taxon notes: annelids have blood vessels, but this class is not applicable to annelids.
  • Added

Changes for: finger fringes

Changes for: obsolete lower eyelid texture

Changes for: mental gland

Changes for: epithelium of lens

  • Deleted
    • - epithelium of lens comment Usage notes: this class is the superclass of the anterior epithelium and equatorial epithlium, although the term ‘lens epithelium’ may refer specifically to the former
  • Added
    • + epithelium of lens curator notes this class is the superclass of the anterior epithelium and equatorial epithlium, although the term ‘lens epithelium’ may refer specifically to the former

Changes for: capsule of lens

  • Deleted
    • - capsule of lens homology notes (…) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (…) A watery aqueous humor fills the spaces in the eye in front of the lens (…) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000550 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 }
  • Added
    • + capsule of lens homology notes (…) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (…) A watery aqueous humor fills the spaces in the eye in front of the lens (…) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000550 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 }

Changes for: pedal acropodium region

Changes for: acropodium region

Changes for: manual acropodium region

Changes for: transverse cervical artery

Changes for: diencephalon

Changes for: midbrain

  • Deleted
    • - midbrain comment Editors note: developmental relationships need revised. AO notes: part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships
  • Added

Changes for: ethmoid region

  • Deleted
    • - ethmoid region comment Usage notes: currently this is not restricted to skeletal elements, unlike UBERONREF:0000007
  • Added

Changes for: dorsal plus ventral thalamus

Changes for: hypothalamus

Changes for: olfactory tubercle

Changes for: levator claviculae muscle

  • Deleted
    • - levator claviculae muscle comment 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.[WP]

Changes for: amygdala

  • Deleted
    • - amygdala comment AO notes: MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype
  • Added

Changes for: cortex

Changes for: rostral organ

Changes for: semicircular canal

  • Deleted
    • - semicircular canal comment Note that MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal
  • Added
    • + semicircular canal external ontology notes MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal { external ontology=MA }

Changes for: cochlea

  • Deleted
    • - cochlea comment AO notes: sources vary in connection to bony labyrinth. Taxon notes: The association with ‘lagena’ in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: “In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)”
  • Added
    • + cochlea external ontology notes sources vary in connection to bony labyrinth { external ontology=XAO }
    • + cochlea taxon notes The association with ‘lagena’ in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: ‘In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)’

Changes for: carpometacarpal joint of digit 1

  • Deleted
    • - carpometacarpal joint of digit 1 comment 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[WP]

Changes for: femoral pore

  • Deleted
    • - femoral pore comment Taxon notes: Femoral pores are present in all genera in the families Cordylidae, Crotaphytidae, Hoplocercidae, Iguanidae, Phrynosomatidae, and Xantusiidae.[1] 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[WP]

Changes for: sebaceous gland

  • Deleted
    • - sebaceous gland comment Usage notes: sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called ‘modified’ sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass.
  • Added
    • + sebaceous gland SubClassOf part of some pilosebaceous unit
    • + sebaceous gland curator notes sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called ‘modified’ sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass.

Changes for: photoreceptor layer of retina

  • Deleted
    • - photoreceptor layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001165 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + photoreceptor layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001165 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: outer nuclear layer of retina

  • Deleted
    • - outer nuclear layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001170 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + outer nuclear layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001170 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: optic disc

  • Deleted
    • - optic disc homology notes (…) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000551 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 }
  • Added
    • + optic disc homology notes (…) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000551 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 }

Changes for: cranial nerve

  • Deleted
    • - cranial nerve comment Editors note: classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Note EMAPA subdivides nerve into CNS nerve and PNS nerve, with all cranial nerves classified as CNS nerves.
  • Added
    • + cranial nerve editor note classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Note EMAPA subdivides nerve into CNS nerve and PNS nerve, with all cranial nerves classified as CNS nerves.

Changes for: layer of retina

  • Deleted
    • - layer of retina comment Note that MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
  • Added
    • + layer of retina external ontology notes MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers { external ontology=MA }

Changes for: pigmented layer of retina

  • Deleted
    • - pigmented layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000536 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + pigmented layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000536 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: tunicate tunic

  • Deleted
    • - tunicate tunic comment Taxon notes: In some species tunicin occurs in small amounts. Some species calcium salts are deposited as spicules. In ascidians, the tunic is supplied with blood vessels.
  • Added
    • + tunicate tunic taxon notes In some species tunicin occurs in small amounts. Some species calcium salts are deposited as spicules. In ascidians, the tunic is supplied with blood vessels.

Changes for: tunicate postabdomen

Changes for: aqueous humor of eyeball

  • Deleted
    • - aqueous humor of eyeball comment Note that FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
    • - aqueous humor of eyeball homology notes (…) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (…) A watery aqueous humor fills the spaces in the eye in front of the lens (…) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000548 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 }
  • Added
    • + aqueous humor of eyeball external ontology notes FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. { external ontology=FMA }
    • + aqueous humor of eyeball homology notes (…) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (…) A watery aqueous humor fills the spaces in the eye in front of the lens (…) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000548 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 }

Changes for: vitreous humor

Changes for: inner plexiform layer of retina

  • Deleted
    • - inner plexiform layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001168 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + inner plexiform layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001168 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: ganglionic layer of retina

  • Deleted
    • - ganglionic layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001166 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + ganglionic layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001166 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: nerve fiber layer of retina

  • Deleted
    • - nerve fiber layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001169 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + nerve fiber layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001169 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: outer plexiform layer of retina

  • Deleted
    • - outer plexiform layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001171 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + outer plexiform layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001171 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: inner nuclear layer of retina

  • Deleted
    • - inner nuclear layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001167 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + inner nuclear layer of retina homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001167 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: short microvillus layer

Changes for: striated border microvillus layer

Changes for: brush border layer

Changes for: layer of microvilli

Changes for: urodeum

  • Deleted
    • - urodeum comment Taxon notes: This is where the urates collect. In the hen the oviduct opens into this compartment.[http://caiquesite.com/glossary.htm]
  • Added
    • + urodeum taxon notes This is where the urates collect. In the hen the oviduct opens into this compartment.[http://caiquesite.com/glossary.htm]

Changes for: zonal element

Changes for: muscular artery

Changes for: head external integument structure

Changes for: body external integument structure

Changes for: limb external integument structure

Changes for: tail external integument structure

Changes for: lateral pretrosal artery

Changes for: mandibular artery

Changes for: external integument structure

Changes for: podotheca

Changes for: Ruffini nerve ending

Changes for: proctodeum portion of cloaca

  • Deleted
    • - proctodeum portion of cloaca comment Taxon notes: For most birds this is where the phallus is located, but male parrots do not have a phallus. The Bursa of Fabricus is located here.[http://caiquesite.com/glossary.htm]
  • Added
    • + proctodeum portion of cloaca taxon notes For most birds this is where the phallus is located, but male parrots do not have a phallus. The Bursa of Fabricius is located here.[http://caiquesite.com/glossary.htm]

Changes for: pterygomandibular raphe

Changes for: palatine raphe

Changes for: enamel

  • Deleted
    • - enamel comment AO notes: part_of tooth enamel organ in MA. Editor notes: current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)
  • Added

Changes for: periodontium

Changes for: pharyngeal raphe

Changes for: Reissner’s fiber

  • Deleted
    • - Reissner’s fiber comment Taxon notes: Reissner’s fiber is present in the central canal of species in all chordate subphyla[Olsson R. (1993) Reissner’s fiber mechanisms: some common denominators. In The Subcommissural Organ: An Ependymal Brain Gland ]
  • Added
    • + Reissner’s fiber taxon notes Reissner’s fiber is present in the central canal of species in all chordate subphyla[Olsson R. (1993) Reissner’s fiber mechanisms: some common denominators. In The Subcommissural Organ: An Ependymal Brain Gland ]

Changes for: epiglottic cartilage

Changes for: sclera

  • Deleted
    • - sclera comment 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] 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
  • Added
    • + 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]

Changes for: corneal epithelium

Changes for: male external urethral sphincter

Changes for: nasal concha

  • Deleted
    • - nasal concha comment Note that FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here // Turbinals are only ossified in birds and derived synapsids.
  • Added

Changes for: frontal sinus

  • Deleted
    • - frontal sinus comment 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[MURDOCh]

Changes for: iris

  • Deleted
    • - iris comment Taxon notes: The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development - dx.doi.org/10.1006/dbio.1998.9019
  • Added
    • + iris taxon notes The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development - dx.doi.org/10.1006/dbio.1998.9019

Changes for: anterior chamber of eyeball

Changes for: prepuce

  • Deleted
    • - prepuce comment Usage notes: this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue
  • Added
    • + prepuce curator notes this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue

Changes for: mesencephalic nucleus of trigeminal nerve

  • Deleted
    • - mesencephalic nucleus of trigeminal nerve comment Development notes: develops from NC in some species[UBERONREF:0000002] Not of NC origin[doi:10.1002/dvdy.1197]. AO notes: part of midbrain tegmentum in NIF and MA. the neurons of the mesencephalic trigeminal nucleus are the only centrally located primary sensory neurons in amniotes; all others are extramedullary[PMID:11747082]
  • Added
    • + mesencephalic nucleus of trigeminal nerve development notes develops from NC in some species[UBERONREF:0000002] Not of NC origin[doi:10.1002/dvdy.1197]. AO notes: part of midbrain tegmentum in NIF and MA. the neurons of the mesencephalic trigeminal nucleus are the only centrally located primary sensory neurons in amniotes; all others are extramedullary[PMID:11747082]

Changes for: lower jaw region

Changes for: secondary palate

  • Deleted
    • - secondary palate comment Taxon notes: present in mammals and some reptiles. A similar structure is found in crocodilians, but, in most other tetrapods, the oral and nasal cavities are not truly separate. The secondary palate is formed by bilateral medial extensions of maxillary processes. The extensions (palatine processes) meet at the midline, merging dorsally with nasal septum and rostrally with primary palate. The secondary palate (hard palate) separates nasal and oral cavities. Caudal extension of the secondary palate into the pharynx, forms a soft palate which divides the rostral pharynx into dorsal (nasopharynx) and ventral (oropharynx) chamber.
  • Added
    • + secondary palate taxon notes present in mammals and some reptiles. A similar structure is found in crocodilians, but, in most other tetrapods, the oral and nasal cavities are not truly separate. The secondary palate is formed by bilateral medial extensions of maxillary processes. The extensions (palatine processes) meet at the midline, merging dorsally with nasal septum and rostrally with primary palate. The secondary palate (hard palate) separates nasal and oral cavities. Caudal extension of the secondary palate into the pharynx, forms a soft palate which divides the rostral pharynx into dorsal (nasopharynx) and ventral (oropharynx) chamber.

Changes for: upper jaw region

Changes for: neurocranium

  • Deleted
    • - neurocranium comment Development notes: The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. Composition notes: It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton[WP] AO notes: It seems MA uses ‘neurocranium’ as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, …
  • Added
    • + neurocranium comment AO notes: It seems MA uses ‘neurocranium’ as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, …
    • + 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]

Changes for: cavity of pharynx

  • Deleted
    • - cavity of pharynx comment Taxon notes: See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship. Development notes: TOODO check
  • Added

Changes for: larynx

  • Deleted
    • - larynx homology notes (In anura) a dorsal pair of arytenoid cartilages (…), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (…). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (…) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (…) and a cartilage in the epiglottis.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001279 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 }
  • Added
    • + larynx homology notes (In anura) a dorsal pair of arytenoid cartilages (…), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (…). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (…) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (…) and a cartilage in the epiglottis.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001279 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 }

Changes for: laryngeal cartilage

  • Deleted
    • - laryngeal cartilage homology notes (In anura) a dorsal pair of arytenoid cartilages (…), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (…). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (…) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (…) and a cartilage in the epiglottis.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001550 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 }
  • Added
    • + laryngeal cartilage homology notes (In anura) a dorsal pair of arytenoid cartilages (…), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (…). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (…) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (…) and a cartilage in the epiglottis.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001550 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 }

Changes for: taste bud

  • Deleted
    • - taste bud comment Development notes: arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN10:1607950324 (todo - request cell terms from CL) Taste buds form in greatest concentration on the dorsal surface of the tongue
  • Added
    • + taste bud development notes arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN10:1607950324 (todo - request cell terms from CL) Taste buds form in greatest concentration on the dorsal surface of the tongue

Changes for: maxillary vein

  • Deleted
    • - maxillary vein comment Taxon notes: in horses, a branch of the external jugular gives off the occipital and caudal auricular vein
  • Added

Changes for: ethmoid bone

  • Deleted
    • - ethmoid bone comment AO notes: Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA. Taxon notes: todo - homology e.g. mesethmoid of teleost
  • Added
    • + ethmoid bone external ontology notes Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA { external ontology=MA }
    • + ethmoid bone taxon notes todo - homology e.g. mesethmoid of teleost

Changes for: occipital bone

  • Deleted
    • - occipital bone comment 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 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]

Changes for: nasal bone

  • Deleted
    • - nasal bone comment Taxon notes: In primitive bony fish and tetrapods, the nasal bones are the most anterior of a set of four paired bones forming the roof of the skull, being followed in sequence by the frontals, the parietals, and the postparietals. Their form in living species is highly variable, depending on the shape of the head, but they generally form the roof of the snout or beak, running from the nostrils to a position short of the orbits. In most animals, they are generally therefore proportionally larger than in humans or great apes, because of the shortened faces of the latter. Turtles, unusually, lack nasal bones, with the prefrontal bones of the orbit reaching all the way to the nostrils (ISBN 0-03-910284-X)
  • Added
    • + nasal bone taxon notes In primitive bony fish and tetrapods, the nasal bones are the most anterior of a set of four paired bones forming the roof of the skull, being followed in sequence by the frontals, the parietals, and the postparietals. Their form in living species is highly variable, depending on the shape of the head, but they generally form the roof of the snout or beak, running from the nostrils to a position short of the orbits. In most animals, they are generally therefore proportionally larger than in humans or great apes, because of the shortened faces of the latter. Turtles, unusually, lack nasal bones, with the prefrontal bones of the orbit reaching all the way to the nostrils (ISBN 0-03-910284-X)

Changes for: jugal bone

Changes for: mandible

  • Deleted
    • - mandible comment AO notes: Note in ZFA ‘mandible’ is a syn for the ventral mandibular arch, which is a portion of the 1st pharyngeal arch; however the term ‘mandibular symphysis’ refers to the dentary
  • Added
    • + mandible external ontology notes Note in ZFA ‘mandible’ is a syn for the ventral mandibular arch, which is a portion of the 1st pharyngeal arch; however the term ‘mandibular symphysis’ refers to the dentary { external ontology=ZFA }

Changes for: hyoid bone

  • Deleted
    • - hyoid bone comment 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.[WP]

Changes for: orbital region

Changes for: squamous part of temporal bone

  • Deleted
    • - squamous part of temporal bone comment Taxon notes: The squamosal bone, which is homologous with the squama, and forms the side of the cranium in many bony fish and tetrapods. Primitively, it is a flattened plate-like bone, but in many animals it is narrower in form, for example, where it forms the boundary between the two temporal fenestrae of diapsid reptiles. Editor notes: consider separate class for squamosal OR making squamosal the primary label
  • Added
    • + squamous part of temporal bone editor note consider separate class for squamosal OR making squamosal the primary label
    • + squamous part of temporal bone taxon notes The squamosal bone, which is homologous with the squama, and forms the side of the cranium in many bony fish and tetrapods. Primitively, it is a flattened plate-like bone, but in many animals it is narrower in form, for example, where it forms the boundary between the two temporal fenestrae of diapsid reptiles

Changes for: obsolete branchial arch skeleton

Changes for: supraoptic crest

Changes for: epithelium of gonad

  • Deleted
    • - epithelium of gonad comment Note that after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
  • Added
    • + epithelium of gonad editor note after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts

Changes for: epithelium of female gonad

  • Deleted
    • - epithelium of female gonad comment Note that after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
  • Added
    • + epithelium of female gonad editor note after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts

Changes for: parieto-occipital sulcus

Changes for: epithelium of male gonad

  • Deleted
    • - epithelium of male gonad comment Note that after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
  • Added
    • + epithelium of male gonad editor note after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts

Changes for: cranial division of the internal carotid artery

Changes for: caudal division of the internal carotid artery

Changes for: future internal carotid artery

Changes for: septal nuclear complex

Changes for: digestive tract

  • Deleted
    • - digestive tract comment Terminology notes: we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the ‘alimentary canal’, consider adding an extra class for this. AO notes: FMA also has a term ‘gastrointestinal tract’, but this includes the liver.
  • Added
    • + digestive tract comment AO notes: FMA also has a term ‘gastrointestinal tract’, but this includes the liver.
    • + digestive tract terminology notes we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the ‘alimentary canal’, consider adding an extra class for this

Changes for: skin of hip

Changes for: vein of hindlimb zeugopod

  • Deleted
    • - vein of hindlimb zeugopod comment Terminology notes: The term “sural veins” is not sufficient to appropriately designate the complex venous system of the calf. This should be designated as soleal veins (venae solealis), the veins of the soleus muscle and gastrocnemius veins (venae gastrocnemii)[http://www.veinsurg.com/fr/biblio/echodoppler/echodoppler_11.php]
  • Added
    • + vein of hindlimb zeugopod terminology notes The term ‘sural veins’ is not sufficient to appropriately designate the complex venous system of the calf. This should be designated as soleal veins (venae solealis), the veins of the soleus muscle and gastrocnemius veins (venae gastrocnemii)[http://www.veinsurg.com/fr/biblio/echodoppler/echodoppler_11.php]

Changes for: parapineal organ

  • Deleted
    • - parapineal organ comment Taxon notes: In lampreys and apparently in some fossil fish, the parapineal body and the pineal body (epiphysis) are a bilateral pair of structures rather than being located in series, one in front of the other. A pair of visual structures may have been the ancestral condition of this pineal complex (Weichert, 1970, p.622). The parapineal organs of lampreys, tadpoles, and lizards possess cells similar to rods and cones. Frogs possess a brow spot or frontal organ where ancestral pineal eye might have been (Weichert, 1970, p.622)
  • Added
    • + parapineal organ taxon notes In lampreys and apparently in some fossil fish, the parapineal body and the pineal body (epiphysis) are a bilateral pair of structures rather than being located in series, one in front of the other. A pair of visual structures may have been the ancestral condition of this pineal complex (Weichert, 1970, p.622). The parapineal organs of lampreys, tadpoles, and lizards possess cells similar to rods and cones. Frogs possess a brow spot or frontal organ where ancestral pineal eye might have been (Weichert, 1970, p.622)

Changes for: genioglossus muscle

  • Deleted
    • - genioglossus muscle comment taxon notes: Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians. [AAO:0010660]
  • Added

Changes for: olfactory nerve

Changes for: os basale

Changes for: extrinsic auricular muscle

Changes for: left subclavian artery

Changes for: palmar/plantar sweat gland

Changes for: lateral structure

Changes for: urethra muscle

Changes for: hindlimb zeugopod

  • Deleted
    • - hindlimb zeugopod comment note that FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion // Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
  • Added

Changes for: mouth mucosa

  • Deleted
    • - mouth mucosa comment Usage notes: this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
  • Added
    • + mouth mucosa curator notes this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)

Changes for: ventral part of pharyngeal pouch 2

Changes for: dorsal part of pharyngeal pouch 3

  • Deleted
    • - dorsal part of pharyngeal pouch 3 comment Development notes: Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III)[MP]
  • Added

Changes for: ventral part of pharyngeal pouch 1

Changes for: dorsal part of pharyngeal pouch 2

  • Deleted
    • - dorsal part of pharyngeal pouch 2 comment 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[MP]

Changes for: dorsal part of pharyngeal pouch 1

Changes for: ventral part of pharyngeal pouch 3

Changes for: skeleton of digitopodium

Changes for: skeleton of manual digitopodium

Changes for: basal nucleus of telencephalon

Changes for: skeleton of pedal digitopodium

Changes for: spiracle

  • Deleted
    • - spiracle comment 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]. In elasmobranchs (sharks and rays), a spiracle is found behind each eye, and is often used to pump water through the gills while the animal is at rest (Fouts, 2003). A spiracle is also found in primitive bony fishes as the chirrups. TODO - check GO:0035277-spiracle morphogenesis, open tracheal system - taxon constraint in GO
  • Added

Changes for: spiral valve of conus arteriosus

Changes for: spiral valve of cystic duct

Changes for: muscle of iris

  • Deleted
  • Added
    • + muscle of iris comment 331
    • + muscle of iris taxon notes The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]

Changes for: stomach non-glandular epithelium

  • Deleted
    • - stomach non-glandular epithelium comment Taxon notes: this region may develop from the base of the esophagus (some herbivores) - in rodents, loss of the gastric glands in the mucosa leavea a nonglandular epithelial stomach in which smooth muscle contractions knead and mix digesta. This can be keratinized.
  • Added
    • + stomach non-glandular epithelium taxon notes this region may develop from the base of the esophagus (some herbivores) - in rodents, loss of the gastric glands in the mucosa leavea a nonglandular epithelial stomach in which smooth muscle contractions knead and mix digesta. This can be keratinized.

Changes for: sphincter pupillae

Changes for: median ovary

  • Deleted
    • - median ovary comment [In other animals]](Taxon notes: 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
    • + 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])

Changes for: extra-ocular muscle

  • Deleted
    • - extra-ocular muscle comment AO notes: BTO and MA consider this part of the eye; we follow them here (inferred from skeletal muscle). Not clear if omission from FMA is deliberate. Editor notes: todo - resolve discrepancies in which muscles are considered extra-ocular. Taxon notes: Mammals have 7 extra-ocular muscles, but humans lack the M. retractor bulbi. Note in ZFA this is the set of muscles.
  • Added
    • + extra-ocular muscle external ontology notes BTO and MA consider this part of the eye; we follow them here (inferred from skeletal muscle). Not clear if omission from FMA is deliberate. Editor notes: todo - resolve discrepancies in which muscles are considered extra-ocular { external ontology=BTO }
    • + extra-ocular muscle taxon notes Mammals have 7 extra-ocular muscles, but humans lack the M. retractor bulbi. Note in ZFA this is the set of muscles.

Changes for: maxillary artery

  • Deleted
    • - maxillary artery comment Development notes: …1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries [http://download.videohelp.com/vitualis/med/Vascular_Devt.html]
  • Added
    • + maxillary artery development notes …1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries [http://download.videohelp.com/vitualis/med/Vascular_Devt.html]

Changes for: anterior part of tongue

Changes for: ophthalmic artery

Changes for: lacrimal artery

Changes for: posterior communicating artery

Changes for: stapes cartilage element

  • Deleted
    • - stapes cartilage element comment Taxon notes: The stapes is homologous to the hyomandibula. In this ontology, we use the class ‘hyomandibular cartilage’ generally to include the future stapes, the future hyomandibular bone of teleosts and the unossified cartilage in sharks.
  • Added
    • + stapes cartilage element taxon notes The stapes is homologous to the hyomandibula. In this ontology, we use the class ‘hyomandibular cartilage’ generally to include the future stapes, the future hyomandibular bone of teleosts and the unossified cartilage in sharks.

Changes for: mucosa of dorsum of tongue

Changes for: trigeminal nerve

  • Deleted
    • - trigeminal nerve comment 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[ISBN10:0471888893]

Changes for: abducens nerve

  • Deleted
    • - abducens nerve comment 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[WP]

Changes for: intermediate layer of tympanic membrane

Changes for: chromaffin system

  • Deleted
    • - chromaffin system comment Taxon notes: in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies
  • Added

Changes for: cuboidal epithelium

Changes for: hypoglossal nerve

  • Deleted
    • - hypoglossal nerve comment AO notes: we use a broad definition of cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves
  • Added

Changes for: collateral sulcus

Changes for: orbital cavity

Changes for: splanchnic layer of lateral plate mesoderm

Changes for: visceral endoderm

Changes for: somatopleure

  • Deleted
    • - somatopleure comment AO notes: sources differ as to whether this is part-of or develops-from the LPM. Development notes: Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
  • Added
    • + somatopleure development notes Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
    • + somatopleure external ontology notes sources differ as to whether this is part-of or develops-from the LPM

Changes for: suspensory ligament of breast

Changes for: chordamesoderm

  • Deleted
    • - chordamesoderm comment note that WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
  • Added

Changes for: hilum

Changes for: accessory XI nerve cranial component

  • Deleted
    • - accessory XI nerve cranial component comment Editors/usage notes: 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] Thus in contemporary discussions of the accessory nerve, the common practice is to dismiss the cranial part altogether, referring to the accessory nerve specifically as the spinal accessory nerve.
  • Added
    • + accessory XI nerve cranial component comment Thus in contemporary discussions of the accessory nerve, the common practice is to dismiss the cranial part altogether, referring to the accessory nerve specifically as the spinal accessory nerve.
    • + 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]

Changes for: ingested food

Changes for: dental comb

  • Deleted
    • - dental comb comment Taxon notes: The toothcomb occurs in lemuriform primates (which includes lemurs and lorisoids), treeshrews, colugos, hyraxes, and some African antelopes. The structures evolved independently in different types of mammals through convergent evolution and vary both in dental composition and structure. In most mammals the comb is formed by a group of teeth with fine spaces between them. The toothcombs in most mammals include incisors only, while in lemuriform primates they include incisors and canine teeth that tilt forward at the front of the lower jaw, followed by a canine-shaped first premolar. The toothcombs of colugos and hyraxes take a different form with the individual incisors being serrated, providing multiple tines per tooth
  • Added
    • + dental comb taxon notes The toothcomb occurs in lemuriform primates (which includes lemurs and lorisoids), treeshrews, colugos, hyraxes, and some African antelopes. The structures evolved independently in different types of mammals through convergent evolution and vary both in dental composition and structure. In most mammals the comb is formed by a group of teeth with fine spaces between them. The toothcombs in most mammals include incisors only, while in lemuriform primates they include incisors and canine teeth that tilt forward at the front of the lower jaw, followed by a canine-shaped first premolar. The toothcombs of colugos and hyraxes take a different form with the individual incisors being serrated, providing multiple tines per tooth

Changes for: lumen of pharyngotympanic tube

Changes for: pedal digitopodium region

Changes for: manual digitopodium region

Changes for: digitopodium region

  • Deleted
    • - digitopodium region comment Terminology notes: some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod
  • Added

Changes for: centrale

  • Deleted
    • - centrale comment Usage notes: This term corresponds both to the navicular bone in the pes and the similar central carpals in the manus. AO notes: the FMA term is under ‘general anatomical term’.
  • Added

Changes for: intercuneiform joint

  • Deleted
    • - intercuneiform joint comment 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[WP]

Changes for: medullary reticular formation

Changes for: scale

  • Deleted
    • - scale comment Usage notes: currently defined in a very inclusive fashion - may be obsoleted and replaced by more specific classes in future versions. The TAO, VSAO amd ZFA classes by this name are classified as ‘dermal scales’. Can also be classified by composition - e.g. pangolin keratin scales.
  • Added
    • + scale curator notes currently defined in a very inclusive fashion - may be obsoleted and replaced by more specific classes in future versions. The TAO, VSAO amd ZFA classes by this name are classified as ‘dermal scales’. Can also be classified by composition - e.g. pangolin keratin scales.

Changes for: digit

  • Deleted
    • - digit comment Usage notes: this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term ‘digit’ has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion
  • Added
    • + digit curator notes this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term ‘digit’ has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion

Changes for: post-anal tail bud

  • Deleted
  • Added

Changes for: endochondral bone

Changes for: corpus luteum

  • Deleted
    • - corpus luteum comment 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[PMID:20959416]

Changes for: trabecula carnea

Changes for: navicular bone of pes

  • Deleted
    • - navicular bone of pes comment 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]. TODO - add correct VSAO xref (currently broken)
  • Added
    • + navicular bone of pes comment . TODO - add correct VSAO xref (currently broken)
    • + 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]

Changes for: face

  • Deleted
    • - face comment 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)[vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf]

Changes for: distal carpal bone 3

  • Deleted
    • - distal carpal bone 3 comment 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[WP]

Changes for: distal carpal bone 2

  • Deleted
    • - distal carpal bone 2 comment 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)[AAO]

Changes for: skeletal system

  • Deleted
    • - skeletal system comment Note that GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
  • Added
    • + skeletal system external ontology notes GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates { external ontology=GO }

Changes for: distal carpal bone 4

  • Deleted
    • - distal carpal bone 4 comment 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[AAO]

Changes for: distal carpal bone 1

  • Deleted
    • - distal carpal bone 1 comment 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[WP]

Changes for: pectoral girdle region

  • Deleted
    • - pectoral girdle region comment Note that this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
  • Added
    • + pectoral girdle region comment Usage Notes: this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).

Changes for: lunate

  • Deleted
    • - lunate comment 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: wrist joint

Changes for: vasa vasorum

Changes for: muscle of pelvic girdle

Changes for: Pacinian corpuscle

Changes for: distal carpal bone

  • Deleted
    • - distal carpal bone comment Taxon notes: Primitively, each of the distal bones appears to have articulated with a single metacarpal[WP]
  • Added

Changes for: articular capsule

Changes for: skin of shoulder

Changes for: ankle joint

Changes for: Meckel’s diverticulum

Changes for: calcaneal tendon

Changes for: glenohumeral joint

  • Deleted
    • - glenohumeral joint comment AO notes: in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle. Editor notes: note that in this ontology ‘glenoid fossa’ is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship
  • Added

Changes for: infraspinatus muscle

  • Deleted
    • - infraspinatus muscle comment 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.[WP]

Changes for: shoulder

  • Deleted
    • - shoulder comment AO notes: In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone
    • - shoulder homology notes (…) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a ‘coracoid’.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000342 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332 }
  • Added

Changes for: intervertebral joint

  • Deleted
    • - intervertebral joint comment AO notes: FMA has ‘intervertebral joint’ as a GAT, and has two distinct classes ‘intervertebral symphysis’ and ‘intervertebral syndesmosis’, but note that the latter do not connect the centra
  • Added

Changes for: urethral crest

  • Deleted
    • - urethral crest comment AO notes: in the FMA this is part of the prostatic urethra - but this leads to inconsistencies as ‘urethral crest’ in sex-neutral, with male and female subtypes
  • Added

Changes for: left common cardinal vein

Changes for: hemisphere of embryo

  • Deleted
    • - hemisphere of embryo comment Usage notes: Like many of the early_development classes in this ontology, this class requires review for its applicability across vertebrates. See the tracker item for further discussion.
  • Added
    • + hemisphere of embryo curator notes Like many of the early_development classes in this ontology, this class requires review for its applicability across vertebrates. See the tracker item for further discussion.

Changes for: trachea cartilage

Changes for: paraganglion

Changes for: limb mesenchyme

Changes for: flexor digitorum profundus

Changes for: extensor carpi ulnaris muscle

  • Deleted
    • - extensor carpi ulnaris muscle comment Taxon notes: Amphibians - def: “Muscle of the forearm: It shares a common origin with two other muscles of the forearm. It arises from the lateral epicondyle of the humerus by two tendons: the first one is in common with the m. extensor digitorum communis longus, and the second one is broad and in common with the m. epicondylocubitalis. It is pinnately attached to the dorsal surface of the distal carpal 5-4-3.” [AAO:0010281]. Note that we make the insertion relationship a GCI until digit numbering issues are resolved
  • Added

Changes for: skin mucous gland

Changes for: forelimb muscle

Changes for: prostate gland secretion

  • Deleted
    • - prostate gland secretion comment Taxon notes: Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline.
  • Added

Changes for: flexor carpi radialis muscle

  • Deleted
    • - flexor carpi radialis muscle comment AO notes - we group the AAO class here, despite the different insertion site - requires vetting “Muscle which originates on the inner border of the humerus and inserts on the carpus.” [AAO:0010733]
  • Added

Changes for: flexor carpi ulnaris muscle

  • Deleted
    • - flexor carpi ulnaris muscle comment AO notes: AAO has a class with the same name, the exact insertion point is unclear; consider grouping “Muscle which originates from the medial condyle of the humerus and inserts on the carpus.” [AAO:0010734]
  • Added

Changes for: tail muscle

Changes for: left common carotid artery plus branches

Changes for: right subclavian artery

Changes for: internal carotid artery

Changes for: subclavian artery

Changes for: common carotid artery plus branches

Changes for: cuspid

Changes for: right common carotid artery plus branches

Changes for: arch of aorta

Changes for: intermaxillary process

  • Deleted
    • - intermaxillary process comment Editors note: requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip
  • Added

Changes for: eyelid tarsus

  • Deleted
    • - eyelid tarsus comment 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). [PMID:16496288]

Changes for: descending aorta

Changes for: abdominal aorta

  • Deleted
    • - abdominal aorta comment Editors note: Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
  • Added
    • + abdominal aorta editor note Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates

Changes for: scapulocoracoid

  • Deleted
    • - scapulocoracoid comment AO notes: ZFA defines as precursor to scapula and coracoid. Cartilage in TAO. Editor notes: todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present
  • Added

Changes for: rectal salt gland

Changes for: cartilaginous neurocranium

  • Deleted
    • - cartilaginous neurocranium comment note that in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
  • Added
    • + cartilaginous neurocranium external ontology notes in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) { external ontology=FMA }

Changes for: cranial bone

Changes for: vomerine tooth

Changes for: auditory system

Changes for: palatal muscle

Changes for: masticatory muscle

  • Deleted
    • - masticatory muscle comment Usage 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
    • + 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]

Changes for: dentary

  • Deleted
    • - dentary comment Taxon notes: In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.
  • Added
    • + dentary taxon notes In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.

Changes for: cleithrum

  • Deleted
    • - cleithrum comment 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.[VSAO]

Changes for: epidural space

  • Deleted
    • - epidural space comment AO notes: in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail
  • Added

Changes for: amphibian larval stage

Changes for: digestive syncytial vacuole

  • Deleted
    • - digestive syncytial vacuole comment 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[WP]

Changes for: ectocervix

Changes for: nuptial pad

Changes for: bone fossa

  • Deleted
    • - bone fossa comment AO notes: General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named ‘fossa’ are cavities in FMA, hence placement here
  • Added

Changes for: dorsal motor nucleus of vagus nerve

Changes for: olfactory cortex

  • Deleted
    • - olfactory cortex homology notes (In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000325 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008) }
  • Added
    • + olfactory cortex homology notes (In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000325 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008) }

Changes for: hippocampal sulcus

Changes for: muscle of leg

Changes for: optic artery

Changes for: dorsal longitudinal vein

Changes for: central artery

Changes for: venom gland duct

Changes for: cerebrospinal fluid

  • Deleted
    • - cerebrospinal fluid comment AO notes: the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
  • Added
    • + cerebrospinal fluid external ontology notes the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. { external ontology=FMA }

Changes for: efferent lamellar arteriole

Changes for: efferent filamental artery

Changes for: afferent lamellar arteriole

Changes for: concurrent branch afferent branchial artery

Changes for: recurrent branch afferent branchial artery

Changes for: external acoustic meatus

  • Deleted
    • - external acoustic meatus comment AO notes: subdivision of head in FMA. Editor note: consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct. Development notes: tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469]
  • Added
    • + external acoustic meatus external ontology notes subdivision of head in FMA. Editor note: consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct. Development notes: tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469] { external ontology=FMA }

Changes for: afferent filamental artery

Changes for: lesser sac

  • Deleted
    • - lesser sac comment AO notes: classified as a cavity in EHDAA2, so this truly corresponds to FMA ‘Cavity of lesser sac’ - we hedge for now; todo - treat same as greater sac
  • Added

Changes for: epididymis

  • Deleted
    • - epididymis comment Taxon notes: A similar, but probably non-homologous, structure is found in cartilaginous fishes[WP]. Kardong has epididymis in elasmobranch.Structures notes: Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
  • Added
    • + epididymis comment . Kardong has epididymis in elasmobranch.Structures notes: Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
    • + epididymis taxon notes A similar, but probably non-homologous, structure is found in cartilaginous fishes[WP]

Changes for: membranous urethra of male or female

Changes for: levator ani muscle

Changes for: sciatic nerve

  • Deleted
    • - sciatic nerve comment Taxon notes: mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/
  • Added
    • + sciatic nerve taxon notes mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/

Changes for: longissimus thoracis muscle

Changes for: tarsal skeleton

  • Deleted
    • - tarsal skeleton comment 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]. AO notes: we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
  • Added
    • + tarsal skeleton comment . AO notes: we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
    • + 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]

Changes for: nephrogenic zone

  • Deleted
    • - nephrogenic zone comment Taxon notes: see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish.
  • Added

Changes for: centrale endochondral element

Changes for: ischial spine

Changes for: secondary heart field

  • Deleted
    • - secondary heart field comment 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 [PMID:17276708]

Changes for: medullary ray

  • Deleted
    • - medullary ray comment Termonology notes: Their name is potentially misleading – the “medullary” refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla. AO notes: FMA says parenchyma, MP says cortex
  • Added
    • + medullary ray comment Terminology notes: Their name is potentially misleading – the “medullary” refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla. AO notes: FMA says parenchyma, MP says cortex

Changes for: carpal skeleton

  • Deleted
    • - carpal skeleton comment [Evolutionary variations]](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]. 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 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])

Changes for: dermal annular fold

Changes for: tectospinal tract

Changes for: upper lip protuberances

Changes for: mammary gland connective tissue

Changes for: molecular layer of cerebellar cortex

Changes for: upper eyelid protuberances

Changes for: ventral nuclear group

  • Deleted
    • - ventral nuclear group comment AO notes: consider splitting nucleus from nuclear group (FMA has ‘nucleus of subthalamus’) - but note this is also treated as a nucleus (singular) in FMA. ZFA:0005576 represents an individual nucleus within the group
  • Added

Changes for: interdental plate

  • Deleted
    • - interdental plate comment 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[WP]

Changes for: endometrium

  • Deleted
    • - endometrium comment Taxon notes: Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead. AO notes: in FMA this is subdivided into basal and outer. In MA there is a single child term, endometrium epithelium
  • Added
    • + endometrium external ontology notes in FMA this is subdivided into basal and outer. In MA there is a single child term, endometrium epithelium { external ontology=FMA }
    • + endometrium taxon notes Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead

Changes for: inner medulla of kidney

Changes for: monkey lips dorsal bursa complex

Changes for: loop of Henle

  • Deleted
    • - loop of Henle comment Note that the definitions of some kidney parts refer to Henle’s loop, even in species where this may not be present. Requires review.
  • Added
    • + loop of Henle comment Taxon Notes: the definitions of some kidney parts refer to Henle’s loop, even in species where this may not be present. Requires review.

Changes for: hepatic sinusoid

  • Deleted
    • - hepatic sinusoid homology notes (…) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (…) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000708 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) }
  • Added
    • + hepatic sinusoid homology notes (…) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (…) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000708 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) }

Changes for: pubis

Changes for: ischium

Changes for: ilium

  • Deleted
    • - ilium comment Note that this is_a hip bone in MA. Taxon notes: All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium[WP]
  • Added

Changes for: innominate bone

  • Deleted
    • - innominate bone comment AO 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] Editor notes: currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage
  • Added
    • + innominate bone comment Editor notes: currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage
    • + 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 }

Changes for: pelvic girdle region

  • Deleted
    • - pelvic girdle region comment Note that this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list
  • Added
    • + pelvic girdle region comment Usage Notes: this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list

Changes for: wall of intestine

  • Deleted
    • - wall of intestine comment Editors note: we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different
  • Added
    • + wall of intestine editor note we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different

Changes for: pancreas

  • Deleted
    • - pancreas comment 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]. The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract (Figures 16 and 17 ). The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
    • - pancreas definition An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans[PMID]. { database cross reference=http://en.wikipedia.org/wiki/Pancreas , database cross reference=http://www.ncbi.nlm.nih.gov/pubmed/16417468 , database cross reference=GO:0031016 }
  • Added
    • + pancreas definition An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. { database cross reference=GO:0031016 }
    • + pancreas function notes The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans { source=http://www.ncbi.nlm.nih.gov/pubmed/16417468 }
    • + 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]
    • + pancreas taxon notes The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm

Changes for: phonic lip

  • Deleted
    • - phonic lip comment Editor notes: requires review w.r.t location in physeter vs other odontocetes
  • Added

Changes for: urothelium of ureter

  • Deleted
    • - urothelium of ureter comment AO notes: MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium
  • Added

Changes for: trigone of urinary bladder

  • Deleted
    • - trigone of urinary bladder comment 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[WP]

Changes for: anus

  • Deleted
    • - anus comment Taxon notes: In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish’s throat. – http://www.earthlife.net/fish/digestion.html
  • Added
    • + anus taxon notes In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish’s throat. – http://www.earthlife.net/fish/digestion.html

Changes for: adrenal cortex

  • Deleted
    • - adrenal cortex comment Taxon notes: Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO
  • Added
    • + adrenal cortex taxon notes Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO

Changes for: nephron tubule

  • Deleted
    • - nephron tubule comment note that in ISBN10:0073040584 “Vertebrates, Kardong”, the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA
  • Added

Changes for: collecting duct of renal tubule

  • Deleted
    • - collecting duct of renal tubule comment note that in ISBN10:0073040584 “Vertebrates, Kardong”, the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron
  • Added
    • + collecting duct of renal tubule external ontology notes in ISBN10:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron { external ontology=FMA }

Changes for: Peyer’s patch

  • Deleted
    • - Peyer’s patch comment AO notes: FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc] - Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs. Taxon notes: Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer’s patches (Zapata and Solas).
  • Added
    • + 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).
    • + Peyer’s patch external ontology notes FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc] { external ontology=FMA }

Changes for: pancreatic tributary of splenic vein

Changes for: intestinal villus

Changes for: renal lobe

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

Changes for: remnant of lumen of Rathke’s pouch

Changes for: hypothalamo-hypophyseal system

  • Deleted
    • - hypothalamo-hypophyseal system comment 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 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]

Changes for: principal gastric gland

Changes for: gonadal fat pad

Changes for: coxal gland

  • Deleted
    • - coxal gland comment Taxon notes: They are found in all arachnids (with the exception of some Acari), and in other chelicerates, such as horseshoe crabs. Homology: The coxal gland is thought to be homologous with the antennal gland of crustaceans. Editor note: cede this term to Arthropod AO
  • Added
    • + coxal gland editor note cede this term to Arthropod AO
    • + coxal gland taxon notes They are found in all arachnids (with the exception of some Acari), and in other chelicerates, such as horseshoe crabs. Homology: The coxal gland is thought to be homologous with the antennal gland of crustaceans

Changes for: crustacean maxillary gland

  • Deleted
    • - crustacean maxillary gland comment Taxon notes: consider generalizing to include millipedes, centipedes. Function: Two different excretory organs are found among crustaceans: the antennal gland and the maxillary gland. Both have the same basic structure: an end sac and a convoluted duct that may expand into a bladder before opening to the outside. In most adult crustaceans only one or the other gland functions. The functional gland may change during the life cycle. Terminology note: http://crustacea.nhm.org/glossary/define.html?termID=327 suggests green gland as the generic term and antennal as the decapoda term. Editor note: cede this term to Arthropod AO
  • Added
    • + crustacean maxillary gland editor note cede this term to Arthropod AO
    • + crustacean maxillary gland taxon notes consider generalizing to include millipedes, centipedes. Function: Two different excretory organs are found among crustaceans: the antennal gland and the maxillary gland. Both have the same basic structure: an end sac and a convoluted duct that may expand into a bladder before opening to the outside. In most adult crustaceans only one or the other gland functions. The functional gland may change during the life cycle. Terminology note: http://crustacea.nhm.org/glossary/define.html?termID=327 suggests green gland as the generic term and antennal as the decapoda term

Changes for: supraorbital artery

Changes for: antennal gland

Changes for: terminal branch of ophthalmic artery

Changes for: palate bone

  • Deleted
  • Added
    • + palate bone comment Usage notes: this is distinct (but not disjoint) from palatine bone

Changes for: tibiotalar joint

Changes for: right common cardinal vein

Changes for: vestibulocochlear ganglion

  • Deleted
    • - vestibulocochlear ganglion homology notes (During the development of the inner ear in a vertebrate embryo) As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000696 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:21452441 Park BY, Saint-Jeannet JP, Induction and Segregation of the Vertebrate Cranial Placodes. Developmental Biology (2010) }
  • Added
    • + vestibulocochlear ganglion homology notes (During the development of the inner ear in a vertebrate embryo) As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000696 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:21452441 Park BY, Saint-Jeannet JP, Induction and Segregation of the Vertebrate Cranial Placodes. Developmental Biology (2010) }

Changes for: tail vein

Changes for: abdominal mammary gland

  • Deleted
    • - abdominal mammary gland comment Taxon notes: Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml
  • Added
    • + abdominal mammary gland taxon notes Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml

Changes for: facial bone

Changes for: hindlimb bone

Changes for: shoulder bone

Changes for: thoracic cavity artery

Changes for: ankle nerve

Changes for: small intestine Peyer’s patch

Changes for: large intestine Peyer’s patch

Changes for: bony plate series

Changes for: lateral line scale series

Changes for: hemal spine series

Changes for: hyponychium

Changes for: stria vascularis of cochlear duct

Changes for: midbrain cerebral aqueduct

Changes for: third ventricle

Changes for: metanephros induced blastemal cells

Changes for: costochondral joint

  • Deleted
    • - costochondral joint comment Taxon notes: In humans, Joints between costal cartilages of ribs 6-9 are plane synovial joints. Articulation between costal cartilage of rib 9 and rib 10 is fibrous
  • Added
    • + costochondral joint taxon notes In humans, Joints between costal cartilages of ribs 6-9 are plane synovial joints. Articulation between costal cartilage of rib 9 and rib 10 is fibrous

Changes for: costovertebral joint

Changes for: sternohyoid muscle

Changes for: clavicle

  • Deleted
    • - clavicle comment 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 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]

Changes for: cutaneous vein

Changes for: premaxilla

  • Deleted
    • - premaxilla comment Editors note: requires checking embryonic vs adult; isa fetal organ part in FMA; adult bone of upper jaw in AAO and ZFA; split. Note that we have loops if we add develops_from UBERON:0005620 { source=EHDAA2 }
    • - premaxilla homology notes (…) in all higher vertebrates a premaxilla is present (…) (reference 1); Although the presence of a tooth-bearing outer buccal arcade (premaxilla, maxilla, dentary) is cited as a common character of Osteichthyes, dipnoans lack all three bones (…) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000426 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1017/S0022215100025585 O’Malley JF, Evolution of the nasal cavities and sinuses in relation to function. The Journal of Laryngology and Otology (1924), ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.105 }
  • Added
    • + premaxilla editor note requires checking embryonic vs adult; isa fetal organ part in FMA; adult bone of upper jaw in AAO and ZFA; split. Note that we have loops if we add develops_from UBERON:0005620 primary palate
    • + premaxilla homology notes (…) in all higher vertebrates a premaxilla is present (…) (reference 1); Although the presence of a tooth-bearing outer buccal arcade (premaxilla, maxilla, dentary) is cited as a common character of Osteichthyes, dipnoans lack all three bones (…) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000426 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1017/S0022215100025585 O’Malley JF, Evolution of the nasal cavities and sinuses in relation to function. The Journal of Laryngology and Otology (1924), ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.105 }

Changes for: chondrocranium

  • Deleted
    • - chondrocranium comment Editor/AO notes: we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls ‘chondrocranium’ must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal). Taxon notes: covers the brain dorsally in chondrichthyans
  • Added
    • + chondrocranium editor note we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls ‘chondrocranium’ must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
    • + chondrocranium taxon notes covers the brain dorsally in chondrichthyans

Changes for: nucleus pulposus

Changes for: spinal cord

  • Deleted
    • - spinal cord homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000601 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 }
  • Added
    • + spinal cord homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000601 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 }

Changes for: nuchal plate series

Changes for: caudate lobe of liver

Changes for: vomeronasal organ

  • Deleted
    • - vomeronasal organ comment Taxon notes: Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.)
    • - vomeronasal organ homology notes (…) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (…) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (…) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (…) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (…) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000665 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669 (ref.1), http://www.ncbi.nlm.nih.gov/pubmed/9866877 Doving KB, Trotier D, Review: Structure and function of the vomeronasal organ. The Journal of Experimental Biology (1998) (ref.2), DOI:10.1046/j.1469-7580.2001.19810077.x Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001) (ref.3) , DOI:10.1002/ar.22415 Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K, Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) (2012) (ref.4) }
  • Added
    • + vomeronasal organ homology notes (…) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (…) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (…) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (…) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (…) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000665 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669 (ref.1), http://www.ncbi.nlm.nih.gov/pubmed/9866877 Doving KB, Trotier D, Review: Structure and function of the vomeronasal organ. The Journal of Experimental Biology (1998) (ref.2), DOI:10.1046/j.1469-7580.2001.19810077.x Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001) (ref.3) , DOI:10.1002/ar.22415 Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K, Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) (2012) (ref.4) }
    • + vomeronasal organ taxon notes Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.)

Changes for: olfactory tract

  • Deleted
    • - olfactory tract comment AO notes: sources differ as to whether this is part of the bulb (BTO), or cortex (MA). We represent this as the connection between the two, and is thus entirely part of neither, yet overlaps both. Note that the NIF class has been retired
  • Added
    • + olfactory tract external ontology notes sources differ as to whether this is part of the bulb (BTO), or cortex (MA). We represent this as the connection between the two, and is thus entirely part of neither, yet overlaps both. Note that the NIF class has been retired { external ontology=BTO }

Changes for: lentiform nucleus

Changes for: parathyroid gland

  • Deleted
    • - parathyroid gland comment 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 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]

Changes for: smooth muscle tissue

  • Deleted
    • - smooth muscle tissue comment terminological note: GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
    • - smooth muscle tissue homology notes (…) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (…) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an ‘acoel-like’ smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001246 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) }
  • Added
    • + smooth muscle tissue homology notes (…) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (…) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an ‘acoel-like’ smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001246 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) }
    • + smooth muscle tissue terminology notes GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.

Changes for: dorsum

  • Deleted
    • - dorsum comment Taxon notes: In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
  • Added
    • + dorsum taxon notes In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body

Changes for: main olfactory organ

  • Deleted
    • - main olfactory organ comment note - fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
  • Added
    • + main olfactory organ external ontology notes fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint

Changes for: renal vein

Changes for: ascending colon

Changes for: caecum

  • Deleted
    • - caecum comment 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] Kardong: in some herbivorous lizards, a cecum is present between small and large intestines
  • Added
    • + caecum comment Kardong: in some herbivorous lizards, a cecum is present between small and large intestines
    • + 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]

Changes for: tympanic ring

  • Deleted
    • - tympanic ring comment AO notes: in FMA, the tympanic ring is an anatomical line. Howevever http://www.ncbi.nlm.nih.gov/pubmed/11237469 states: “the tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane”. Taxon notes: check amphibians - in AAO “Funnel-like ring structure located lateral to the ventral ramus of the squamosal, beneath the skin; it provides support to the tympanic membrane”. Gene notes: Gsc and Prx1 are essential for tympanic ring development
  • Added
    • + tympanic ring comment Gene notes: Gsc and Prx1 are essential for tympanic ring development
    • + tympanic ring editor note check amphibians
    • + tympanic ring external ontology notes in AAO ‘Funnel-like ring structure located lateral to the ventral ramus of the squamosal, beneath the skin; it provides support to the tympanic membrane’. { external ontology=AAO }
    • + tympanic ring external ontology notes in FMA, the tympanic ring is an anatomical line. Howevever http://www.ncbi.nlm.nih.gov/pubmed/11237469 states: ‘the tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane’. { external ontology=FMA }

Changes for: symphysis

Changes for: body of stomach

  • Deleted
    • - body of stomach comment Note that we include this as zone of stomach even though it is not distinguished by gland type
  • Added

Changes for: nerve root

  • Deleted
    • - nerve root comment Note that this ontology enforces strict part-disjointness between the CNS and PNS which poses challenges for modeling roots of nerves in a way that is consistent with other ontologies. Sometimes the root may be modeled as being entirely part of the brain or spinal cord, in other cases, part of the (peripheral) nerve. We make nerve root continuous_with nerve to avoid inconsistencies. FMA has segment of nerve with subtypes: segment of sympathetic trunk, nerve root, nerve rootlet, nerve root proper
  • Added
    • + nerve root external ontology notes this ontology enforces strict part-disjointness between the CNS and PNS which poses challenges for modeling roots of nerves in a way that is consistent with other ontologies. Sometimes the root may be modeled as being entirely part of the brain or spinal cord, in other cases, part of the (peripheral) nerve. We make nerve root continuous_with nerve to avoid inconsistencies. FMA has segment of nerve with subtypes: segment of sympathetic trunk, nerve root, nerve rootlet, nerve root proper { external ontology=FMA }

Changes for: synchondrosis

Changes for: interparietal bone

  • Deleted
    • - interparietal bone comment Taxon notes: rarely present in humans[PMID:3654370]. Editor notes: consider splitting classes for inter-parietal and post-parietal. postparietals paired in reptiles, fused in mammals.
  • Added

Changes for: endolymphatic sac

Changes for: costal arch

  • Deleted
    • - costal arch comment AO notes: we treat margin and arch in FMA as equivalent here, as a temporary measure. This may be split in future. We follow MA in making this a part of the rib.
  • Added

Changes for: meningeal dura mater

  • Deleted
    • - meningeal dura mater comment Editors note: not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area
  • Added
    • + meningeal dura mater editor note not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area

Changes for: layer of dura mater

  • Deleted
    • - layer of dura mater comment Editors note: not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area
  • Added
    • + layer of dura mater editor note not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area

Changes for: superior recess of lesser sac

Changes for: hepatic artery

Changes for: head electric organ

Changes for: electroreceptor organ

Changes for: brille

  • Deleted
    • - brille comment Taxon notes: In snakes, there is no eyelid and the brille is clear and cannot be distinguished except when the animal is becoming ready for ecdysis. At that time, it becomes cloudy and is visible as a cover over the eye. When the snake moults, the brille is also shed as part of its skin. The Brilles protect their eyes from dust and dirt and gives them a “glassy-eyed” blank appearance Snakes, flap-footed lizards, night lizards, and some skinks have brilles. All geckos except those in the subfamily Eublepharinae (eyelid geckos) possess brilles. Fish also have transparent eyelids called adipose eyelids. // there are transitional stages between total lid loss and full brille formation (Bellairs & Boyd, 1947).
  • Added
    • + brille comment there are transitional stages between total lid loss and full brille formation (Bellairs & Boyd, 1947).
    • + brille taxon notes In snakes, there is no eyelid and the brille is clear and cannot be distinguished except when the animal is becoming ready for ecdysis. At that time, it becomes cloudy and is visible as a cover over the eye. When the snake moults, the brille is also shed as part of its skin. The Brilles protect their eyes from dust and dirt and gives them a ‘glassy-eyed’ blank appearance Snakes, flap-footed lizards, night lizards, and some skinks have brilles. All geckos except those in the subfamily Eublepharinae (eyelid geckos) possess brilles. Fish also have transparent eyelids called adipose eyelids.

Changes for: strand of duvet hair

Changes for: clasper

  • Deleted
    • - clasper comment Taxon notes: the term is also used for insect claspers, but we reserve it for the elasmobranchii structure
  • Added
    • + clasper taxon notes the term is also used for insect claspers, but we reserve it for the elasmobranchii structure

Changes for: joint articular surface

Changes for: pseudostratified columnar epithelium

Changes for: branchiostegal ray series

Changes for: epibranchial series

Changes for: limb epidermis

Changes for: respiratory bronchiole

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

Changes for: oropharyngeal choana

Changes for: superior cerebellar peduncle

Changes for: atrioventricular valve

Changes for: tricuspid valve

Changes for: mitral valve

Changes for: skin epidermis

Changes for: habenulo-interpeduncular tract

Changes for: digestive system

  • Deleted
    • - digestive system comment note that many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
  • Added
    • + digestive system external ontology notes many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class { external ontology=MA }

Changes for: parabigeminal nucleus

Changes for: peripeduncular nucleus

  • Deleted
    • - peripeduncular nucleus comment Note that FMA and NIF support this being part of midbrain tegmentum; MA places this in the thalamus and ABA supports thalamus. todo - check. for now we take a conservative position and assert overlaps for both rather than part of
  • Added

Changes for: adipose tissue

  • Deleted
    • - adipose tissue comment Note in FMA this is dense irregular connective tissue. Taxon notes: n humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
  • Added
    • + adipose tissue comment Taxon notes: n humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
    • + adipose tissue external ontology notes in FMA this is dense irregular connective tissue { external ontology=FMA }

Changes for: musculature

  • Deleted
    • - musculature comment AO notes: In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (not MA:musculature). AAO is generally confused here.
  • Added
    • + musculature external ontology notes In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (not MA:musculature). AAO is generally confused here. { external ontology=FMA }

Changes for: central nervous system

  • Deleted
    • - central nervous system homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000293 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud’homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) }
  • Added
    • + central nervous system homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000293 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud’homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) }

Changes for: left ovary

  • Deleted
    • - left ovary comment [In other animals]](Taxon notes: In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo[Wikipedia:Ovary#In_other_animals])
  • Added
    • + 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])

Changes for: chordate pharynx

Changes for: esophagus

  • Deleted
    • - esophagus comment AO notes: esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
  • Added
    • + esophagus external ontology notes esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) { external ontology=MA }

Changes for: nail plate

Changes for: tarsometatarsus

Changes for: muscle of pectoral girdle

Changes for: midgut

Changes for: hindgut

Changes for: neural tube

  • Deleted
    • - neural tube homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000307 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }
  • Added
    • + neural tube homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000307 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }

Changes for: yolk sac

  • Deleted
    • - yolk sac comment Taxon notes: In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN10:0073040584 “Vertebrates, Kardong”]
  • Added
    • + yolk sac taxon notes In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN10:0073040584 (Vertebrates, Kardong)]

Changes for: spleen

  • Deleted
    • - spleen comment Taxon notes: Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) [PMID:20959416]
  • Added
    • + spleen taxon notes Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) [PMID:20959416]

Changes for: liver

  • Deleted
    • - liver comment AO notes: Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it’s only a subset of cells that have clear immune function. Taxon notes: WP: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.[7] An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. // The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
  • Added
    • + liver comment The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
    • + liver external ontology notes Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it’s only a subset of cells that have clear immune function. Taxon notes: WP: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.[7] An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. { external ontology=ZFA }

Changes for: pair of nares

Changes for: hindlimb

  • Deleted
    • - hindlimb comment AO notes: note that this corresponds to FMA:’free lower limb’ (a limb segment), NOT ‘lower limb’. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton
  • Added
    • + hindlimb external ontology notes note that this corresponds to FMA:’free lower limb’ (a limb segment), NOT ‘lower limb’. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton { external ontology=FMA }

Changes for: forelimb

  • Deleted
    • - forelimb comment AO notes: note that this corresponds to FMA:’free upper limb’ (a limb segment), NOT FMA:’upper limb’. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Usage notes: Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm
  • Added
    • + forelimb curator notes Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm
    • + forelimb external ontology notes note that this corresponds to FMA:’free upper limb’ (a limb segment), NOT FMA:’upper limb’. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb { external ontology=FMA }

Changes for: mushroom body

  • Deleted
    • - mushroom body comment Taxon notes: Also in annelids. “Comparison to the verte- brate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times” [PMID:20813265]
  • Added
    • + mushroom body taxon notes Also in annelids. ‘Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times’ [PMID:20813265]

Changes for: rectum

  • Deleted
    • - rectum comment Taxon notes: In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish’s throat. – http://www.earthlife.net/fish/digestion.html
  • Added
    • + rectum taxon notes In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish’s throat. – http://www.earthlife.net/fish/digestion.html

Changes for: sensory system

  • Deleted
    • - sensory system comment note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
  • Added

Changes for: calcareous tooth

  • Deleted
    • - calcareous tooth comment Editors note: we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeous tooth. Note that sea cucumbers develop calcareous tooth-like structures
  • Added
    • + calcareous tooth editor note we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeous tooth. Note that sea cucumbers develop calcareous tooth-like structures

Changes for: vertebral bone 2

Changes for: flocculus

  • Deleted
    • - flocculus comment AO Notes: flocculus is an exact label for two distinct classes in NIF. Function notes: At its base, the flocculus receives input from the middle ears vestibular system and regulates balance. Many floccular projections descend to the spinal cord and connect to the motor nuclei involved in control of eye movement.[WP]. Taxon notes: enlarged in pterosaurs[PMID:14586467]
  • Added
    • + flocculus external ontology notes flocculus is an exact label for two distinct classes in NIF. Function notes: At its base, the flocculus receives input from the middle ears vestibular system and regulates balance. Many floccular projections descend to the spinal cord and connect to the motor nuclei involved in control of eye movement.[WP]. Taxon notes: enlarged in pterosaurs[PMID:14586467] { external ontology=NIF }

Changes for: ventral pancreatic duct

  • Deleted
    • - ventral pancreatic duct comment Development notes: Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.[WP]
  • Added
    • + ventral pancreatic duct development notes Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.[WP]

Changes for: external carotid artery

Changes for: bony vertebral centrum

Changes for: pennate muscle

Changes for: intersomitic vessel

Changes for: filoplume feather

Changes for: cerebral cortex marginal layer

Changes for: periodontal ligament

  • Deleted
    • - periodontal ligament comment AO notes: FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA
  • Added

Changes for: spine appendage

Changes for: braincase and auditory apparatus

Changes for: superior tarsal muscle

  • Deleted
    • - superior tarsal muscle comment Editors note: declaring this to be both smooth muscle and part of the LPS leads to a disjointness violation (smooth muscle and striated muscle)
  • Added
    • + superior tarsal muscle editor note declaring this to be both smooth muscle and part of the LPS leads to a disjointness violation (smooth muscle and striated muscle)

Changes for: ventricular system choroidal fissure

  • Deleted
    • - ventricular system choroidal fissure comment Usage notes: not to be confused with optic fissure. the choroidal fissure is a subarachnoid space (via subarachnoid fissure in FMA). AO notes: Most ontologies appear to have switched to using less confusing primary terms for optic and choroidal fissues. Still need to check FMA - two possible terms? CARO notes: is this a groove or a space or a line? Structure notes: relate to lateral ventricle?
  • Added

Changes for: adenohypophysis

  • Deleted
    • - adenohypophysis comment Taxon notes: “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”[NBK53175]. In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke’s pouch in zebrafish[ZFA].
  • Added
    • + adenohypophysis comment .
    • + adenohypophysis taxon notes In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke’s pouch in zebrafish[ZFA]
    • + adenohypophysis taxon notes 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[NBK53175].

Changes for: integument

  • Deleted
    • - integument comment Usage notes: in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term ‘integument’ used in invertebrates; consider ‘integumental system’. Note that the VSAO class appears to include adnexa by its definition.
  • Added
    • + integument curator notes in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term ‘integument’ used in invertebrates; consider ‘integumental system’. Note that the VSAO class appears to include adnexa by its definition.

Changes for: bone marrow cavity

Changes for: ossification center

Changes for: arch of centrum of vertebra

Changes for: body marking

Changes for: epithelial scleral papilla layer

  • Deleted
    • - epithelial scleral papilla layer comment Development notes: The scleral ossicles are of dermal (neural crest) origin, develop intramembranously within the scleral mesenchyme, and are induced to form by overlying (transient) epithelial scleral papillae (Nelson, 1942; Murray, 1943; Fyfe and Hall, 1981, 1983; Hall, 1981, 2005; Pinto and Hall, 1991). Taxon notes: Scleral papillae (which induce scleral ossicles in birds) have not been reported in teleosts, but evidence for their presence may not have been sought
  • Added
    • + epithelial scleral papilla layer comment Taxon notes: Scleral papillae (which induce scleral ossicles in birds) have not been reported in teleosts, but evidence for their presence may not have been sought
    • + epithelial scleral papilla layer development notes The scleral ossicles are of dermal (neural crest) origin, develop intramembranously within the scleral mesenchyme, and are induced to form by overlying (transient) epithelial scleral papillae (Nelson, 1942; Murray, 1943; Fyfe and Hall, 1981, 1983; Hall, 1981, 2005; Pinto and Hall, 1991)

Changes for: simian shelf

Changes for: palpebral bone

  • Deleted
    • - palpebral bone comment Taxon notes: The most extreme development of the palpebral is found in the armored dino- saur Euoplocephalus tutus, where the bone forms a quarter-sphere and adducts to completely occlude the or- bit (Coombs, 1972; Vickaryous and Russell, 2003). Notwithstanding the superficially similar position, palpe- brals and tarsal plates differ both anatomically and developmentally and are not considered homologous (Gauthier et al., 1988). Editor notes http://www.ncbi.nlm.nih.gov/pubmed/16496288 says ‘invests’ the eyelid, is this consistent across taxa?
  • Added
    • + palpebral bone comment Editor notes http://www.ncbi.nlm.nih.gov/pubmed/16496288 says ‘invests’ the eyelid, is this consistent across taxa?
    • + palpebral bone taxon notes The most extreme development of the palpebral is found in the armored dino- saur Euoplocephalus tutus, where the bone forms a quarter-sphere and adducts to completely occlude the or- bit (Coombs, 1972; Vickaryous and Russell, 2003). Notwithstanding the superficially similar position, palpe- brals and tarsal plates differ both anatomically and developmentally and are not considered homologous (Gauthier et al., 1988)

Changes for: amnioserosa

  • Deleted
    • - amnioserosa comment Editor’s notes: May be obsoleted once added to insect ontology. Coordinate with cell type in CL
  • Added

Changes for: non-keratinized stratified squamous epithelium

Changes for: os opticus

  • Deleted
    • - os opticus comment Taxon notes: At present, it has been documented in 219 species from 35 families, including perching birds, woodpeckers, hummingbirds, toucans, kingfishers, and falcons (Tiemeier, 1950). Morphologically, this element varies in shape from a complete encircling element in some woodpeckers (e.g., Melanerpes eryth- rocephalus) to an abbreviated arc in Gallus
  • Added
    • + os opticus taxon notes At present, it has been documented in 219 species from 35 families, including perching birds, woodpeckers, hummingbirds, toucans, kingfishers, and falcons (Tiemeier, 1950). Morphologically, this element varies in shape from a complete encircling element in some woodpeckers (e.g., Melanerpes eryth- rocephalus) to an abbreviated arc in Gallus

Changes for: sagittal keel

  • Deleted
    • - sagittal keel taxon notes Sagittal keels occur in Homo erectus and occasionally Homo heidelbergensis, where they probably served as an armour against shock to the roof of the skull, and as the attachment point for the temporalis muscles. Most Homo sapiens lost them likely as part of the general trend toward thinning of the cranial bones during the Pleistocene, to make room for larger brains. However there is a very small portion of modern humans who have this, but its function and etiology are unknown. Patrick Stewart of Star Trek and the martial artist Shi Yan Ming present good examples of modern humans with this feature. { source=http://en.wikipedia.org/wiki/Occipital_bun , taxon=Homo erectus }
  • Added
    • + sagittal keel taxon notes Sagittal keels occur in Homo erectus and occasionally Homo heidelbergensis, where they probably served as an armour against shock to the roof of the skull, and as the attachment point for the temporalis muscles. Most Homo sapiens lost them likely as part of the general trend toward thinning of the cranial bones during the Pleistocene, to make room for larger brains. However there is a very small portion of modern humans who have this, but its function and etiology are unknown. Patrick Stewart of Star Trek and the martial artist Shi Yan Ming present good examples of modern humans with this feature. { source=http://en.wikipedia.org/wiki/Occipital_bun , taxon=Homo erectus }

Changes for: hindlimb interepipodial space

Changes for: blowhole

  • Deleted
    • - blowhole comment Taxon notes: Baleen whales have two blowholes positioned in a V-shape while toothed whales have only one blowhole. The blowhole of a sperm whale, a toothed whale, is located left of centre in the frontal area of the snout, and is actually its left nostril, while the right nostril lacks an opening to the surface despite the fact that its nasal passage is otherwise well developed.
  • Added
    • + blowhole taxon notes Baleen whales have two blowholes positioned in a V-shape while toothed whales have only one blowhole. The blowhole of a sperm whale, a toothed whale, is located left of centre in the frontal area of the snout, and is actually its left nostril, while the right nostril lacks an opening to the surface despite the fact that its nasal passage is otherwise well developed.

Changes for: cranial skeletal system

  • Deleted
    • - cranial skeletal system comment Note that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called ‘skull’ belongs here, as it includes the whole splanchnocranium. Editor notes: we use ‘cranial skeletal system’, so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
  • Added
    • + cranial skeletal system comment Usage notes: that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called ‘skull’ belongs here, as it includes the whole splanchnocranium. Editor notes: we use ‘cranial skeletal system’, so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)

Changes for: nictitating membrane lamina

  • Deleted
    • - nictitating membrane lamina comment Taxon notes: these laminae may consist of purely hyaline cartilage (cats and horses) or may be heavily invested with elastic fibers (dogs, pigs, and cows; Schlegel et al., 2001)
  • Added
    • + nictitating membrane lamina taxon notes these laminae may consist of purely hyaline cartilage (cats and horses) or may be heavily invested with elastic fibers (dogs, pigs, and cows; Schlegel et al., 2001)

Changes for: pedal toe disc

Changes for: manual toe disc

Changes for: vestibulo-cochlear VIII ganglion complex

Changes for: barbed keratin-coated spine

  • Deleted
    • - barbed keratin-coated spine comment Taxon notes: Porcupines’ quills, or spines, take on various forms, depending on the species, but all are modified hairs coated with thick plates of keratin, and they are embedded in the skin musculature. Old World porcupines (Hystricidae) have quills embedded in clusters, whereas in New World porcupines (Erethizontidae), single quills are interspersed with bristles, underfur and hair.
  • Added
    • + barbed keratin-coated spine taxon notes Porcupines’ quills, or spines, take on various forms, depending on the species, but all are modified hairs coated with thick plates of keratin, and they are embedded in the skin musculature. Old World porcupines (Hystricidae) have quills embedded in clusters, whereas in New World porcupines (Erethizontidae), single quills are interspersed with bristles, underfur and hair.

Changes for: epidermal ridge of digit

Changes for: vertebra

  • Deleted
    • - vertebra comment note we follow FMA in making this an irregular bone - however vertebra have ‘epiphyses’ which are currently classified as belonging to long bones
  • Added
    • + vertebra editor note we follow FMA in making this an irregular bone - however vertebra have ‘epiphyses’ which are currently classified as belonging to long bones

Changes for: integumental system

  • Deleted
    • - integumental system homology notes (…) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000403 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) }
  • Added
    • + integumental system homology notes (…) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000403 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) }

Changes for: hippocampal formation

  • Deleted
    • - hippocampal formation comment Usage notes: The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum[NIF]. BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says “hippocampus” it means “hippocampal formation”. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
  • Added
    • + hippocampal formation comment . BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says “hippocampus” it means “hippocampal formation”. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
    • + hippocampal formation curator notes The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum[NIF]

Changes for: limb bone

  • Deleted
    • - limb bone comment AO notes: NCITA includes clavicle. MA:’limb bone’ is actually a bone of limb or girdle // Note that the formal definition is very inclusive, and includes sesamoids
  • Added

Changes for: striatum

  • Deleted
    • - striatum comment [History. Check caudoputamen](AO notes: FMA divides ‘striatum of neuraxis’ into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see http://en.wikipedia.org/wiki/Striatum#History. Check caudoputamen)
  • Added
    • + striatum external ontology notes [History. Check caudoputamen](FMA divides ‘striatum of neuraxis’ into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see http://en.wikipedia.org/wiki/Striatum#History. Check caudoputamen) { external ontology=FMA }

Changes for: ventral tegmental nucleus

  • Deleted
    • - ventral tegmental nucleus comment AO notes: ventral and anterior tegmental nucleus are synonyms in FMA, but we split these into seperate classes. This is consistent with MA, ABA and neuronames, which treat these as distinct (NN suggest the anterior is a rodent specific structure). Location notes: this is part of pons and brainstem in MA, but this leads to an inconsistency with ABA. We err on the side of safety, and exclude the relationship to the pons here.
  • Added
    • + ventral tegmental nucleus comment Location notes: this is part of pons and brainstem in MA, but this leads to an inconsistency with ABA. We err on the side of safety, and exclude the relationship to the pons here.
    • + ventral tegmental nucleus external ontology notes ventral and anterior tegmental nucleus are synonyms in FMA, but we split these into seperate classes. This is consistent with MA, ABA and neuronames, which treat these as distinct (NN suggest the anterior is a rodent specific structure) { external ontology=FMA }

Changes for: myenteric nerve plexus

Changes for: cerebral hemisphere white matter

Changes for: lens fiber

  • Deleted
    • - lens fiber homology notes (…) the line, or Y, or star sutures common to mammalian lenses, including those of primates. In the case of line or Y sutures, the overlapping of lens fibers in each successive shell is coincident and results in the formation of four or six three-dimensional suture planes that extend from the lens nucleus to the periphery.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000444 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1167/iovs.03-0466 Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004) }
  • Added
    • + lens fiber homology notes (…) the line, or Y, or star sutures common to mammalian lenses, including those of primates. In the case of line or Y sutures, the overlapping of lens fibers in each successive shell is coincident and results in the formation of four or six three-dimensional suture planes that extend from the lens nucleus to the periphery.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000444 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1167/iovs.03-0466 Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004) }

Changes for: lenticular fasciculus

Changes for: erector spinae muscle group

Changes for: scleral ossicle

  • Deleted
    • - scleral ossicle comment Taxon notes: The distribution of scleral ossicles and scleral cartilage among verte- brate taxa is not the same. Some taxa (e.g., birds) have both elements; some only have one element (e.g., crocodiles only have a scleral cartilage); while others (e.g., snakes) have neither element (Walls, 1942) number of ossicles making up the sclerotic ring as well as the shape of both the individual plates and the sclerotic ring is variable among tetrapod taxa…. It is therefore extremely likely that scleral skeletal elements (ossicles and cartilage) of all rep- tiles (including birds) are homologous (but cannot be assumed for reptiles and teleosts). Function notes: The function of these elements is to support the eye from within the sclera; scleral ossicles play an additional important role during accommodation in terrestrial vertebrates (Lemmrich, 1931; Walls, 1942; King and McLelland, 1984).
  • Added
    • + scleral ossicle function notes The function of these elements is to support the eye from within the sclera; scleral ossicles play an additional important role during accommodation in terrestrial vertebrates (Lemmrich, 1931; Walls, 1942; King and McLelland, 1984).
    • + scleral ossicle taxon notes The distribution of scleral ossicles and scleral cartilage among verte- brate taxa is not the same. Some taxa (e.g., birds) have both elements; some only have one element (e.g., crocodiles only have a scleral cartilage); while others (e.g., snakes) have neither element (Walls, 1942) number of ossicles making up the sclerotic ring as well as the shape of both the individual plates and the sclerotic ring is variable among tetrapod taxa…. It is therefore extremely likely that scleral skeletal elements (ossicles and cartilage) of all rep- tiles (including birds) are homologous (but cannot be assumed for reptiles and teleosts)

Changes for: endochondral scleral ossicle

  • Deleted
    • - endochondral scleral ossicle comment Taxon notes: The scleral ossicles [of teleosts] are reported to form indirectly by endochondral (Hall and Miyake, 1992) or by perichondral ossification (Patterson, 1977) from a cartilage element that is also present in the sclera. This is unlike the scleral ossicles of reptiles, which develop directly from ectomesenchyme (i.e., intramembranous ossification) and independently from the scleral cartilage[PMID:17051547]
  • Added
    • + endochondral scleral ossicle taxon notes The scleral ossicles [of teleosts] are reported to form indirectly by endochondral (Hall and Miyake, 1992) or by perichondral ossification (Patterson, 1977) from a cartilage element that is also present in the sclera. This is unlike the scleral ossicles of reptiles, which develop directly from ectomesenchyme (i.e., intramembranous ossification) and independently from the scleral cartilage[PMID:17051547]

Changes for: intramembranous scleral ossicle

  • Deleted
    • - intramembranous scleral ossicle comment Development notes: The scleral ossicles [in reptiles] are of dermal (neural crest) origin, develop intramembranously within the scleral mesenchyme, and are induced to form by overlying (transient) epithelial scleral papillae (Nelson, 1942; Murray, 1943; Fyfe and Hall, 1981, 1983; Hall, 1981, 2005; Pinto and Hall, 1991)
  • Added

Changes for: scleral mesenchyme

  • Deleted
    • - scleral mesenchyme comment Development notes: The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
  • Added
    • + scleral mesenchyme development notes The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288

Changes for: nasal concha of ethmoid bone

Changes for: associated mesenchyme of midgut

Changes for: gonial bone

Changes for: interventricular foramen of CNS

Changes for: hyoid apparatus

  • Deleted
    • - hyoid apparatus comment Taxon notes: In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process).
  • Added
    • + hyoid apparatus taxon notes In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process).

Changes for: musculus retractor bulbi

Changes for: vertebral column opening

Changes for: conus arteriosus

  • Deleted
    • - conus arteriosus comment Terminology notes: we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally[Kardong] Taxon notes: Kardong says absent in adult tetrapods, check AAO
  • Added

Changes for: scleral cartilage

  • Deleted
    • - scleral cartilage comment Taxon notes: May be calcified in chondrichthyans. Tetrapods without this element (e.g., snakes and mammals) have a collagenous sclera. May not be homologous - see http://www.ncbi.nlm.nih.gov/pubmed/17051547. cup-shaped in birds. Present in monotremes. Editor notes: consider distinguishing cup from predecessor of ossicle. Hall: The scleral cartilaginous cup is a distinctly sepa- rate element composed of hyaline cartilage. Editors notes: relationship to sclera - overlaps?
  • Added
    • + scleral cartilage editor note relationship to sclera - overlaps?
    • + scleral cartilage taxon notes May be calcified in chondrichthyans. Tetrapods without this element (e.g., snakes and mammals) have a collagenous sclera. May not be homologous - see http://www.ncbi.nlm.nih.gov/pubmed/17051547. cup-shaped in birds. Present in monotremes. Editor notes: consider distinguishing cup from predecessor of ossicle. Hall: The scleral cartilaginous cup is a distinctly sepa- rate element composed of hyaline cartilage

Changes for: choroid tapetum lucidum

Changes for: retinal tapetum lucidum

Changes for: placenta labyrinth

  • Deleted
    • - placenta labyrinth comment Taxon notes: Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively … The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[doi: 10.1073/pnas.96.14.8138 ]. See also: http://placentation.ucsd.edu/placenta.html
  • Added
    • + placenta labyrinth comment . See also: http://placentation.ucsd.edu/placenta.html
    • + placenta labyrinth taxon notes Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively … The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[doi: 10.1073/pnas.96.14.8138 ]

Changes for: tonsil

  • Deleted
    • - tonsil comment Usage notes: the term ‘tonsil’ can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region
  • Added
    • + tonsil curator notes the term ‘tonsil’ can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region

Changes for: palatine tonsil

  • Deleted
    • - palatine tonsil comment Development notes: tonsillar fossa develops from dorsal portion of pouch 2. Note that pharyngeal and lingual tonsils do not develop from pharyngeal pouches[ISBN10:1607950324]
  • Added
    • + palatine tonsil development notes tonsillar fossa develops from dorsal portion of pouch 2. Note that pharyngeal and lingual tonsils do not develop from pharyngeal pouches[ISBN10:1607950324]

Changes for: cricoid cartilage

  • Deleted
    • - cricoid cartilage homology notes (In anura) a dorsal pair of arytenoid cartilages (…), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (…). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (…) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (…) and a cartilage in the epiglottis.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001308 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 }
  • Added
    • + cricoid cartilage homology notes (In anura) a dorsal pair of arytenoid cartilages (…), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (…). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (…) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (…) and a cartilage in the epiglottis.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001308 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 }

Changes for: choroidal guanine tapetum

Changes for: choroidal tapetum fibrosum

Changes for: rete testis

  • Deleted
    • - rete testis comment Editors note: add more specific classification e.g. anastomosing network - consider FMA:3726
  • Added

Changes for: caudal principal ray set

Changes for: pes

  • Deleted
    • - pes comment Editors note: consider renaming using less human-centric terminology
  • Added
    • + pes editor note consider renaming using less human-centric terminology

Changes for: connective tissue

Changes for: pancreas primordium

  • Deleted
    • - pancreas primordium comment AO notes: in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds. Terminology notes: revisit after standardizing terms ‘primordium’, ‘anlagen’, ‘bud’
  • Added

Changes for: ventral pancreatic bud

  • Deleted
    • - ventral pancreatic bud comment Development notes: the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship. // The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]
  • Added

Changes for: photoreceptor inner segment layer

  • Deleted
    • - photoreceptor inner segment layer homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001172 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + photoreceptor inner segment layer homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001172 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: photoreceptor outer segment layer

  • Deleted
    • - photoreceptor outer segment layer homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001173 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + photoreceptor outer segment layer homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001173 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: conducting system of heart

Changes for: pelvis

  • Deleted
    • - pelvis comment Note that MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
  • Added

Changes for: perineum

Changes for: meninx

  • Deleted
    • - meninx comment Taxon notes: Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx).
  • Added
    • + meninx taxon notes Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx).

Changes for: adrenal gland

  • Deleted
    • - adrenal gland comment Taxon notes: The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole. Function notes: suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
  • Added
    • + adrenal gland function notes suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
    • + adrenal gland taxon notes The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole

Changes for: arytenoid swellings

Changes for: exocrine gland

  • Deleted
    • - exocrine gland comment Editor’s note: Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
  • Added
    • + exocrine gland editor note Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses

Changes for: dura mater

Changes for: right atrioventricular canal

Changes for: left atrioventricular canal

Changes for: sinusoid

  • Deleted
    • - sinusoid comment AO notes - some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined).
  • Added

Changes for: retinal neural layer

  • Deleted
    • - retinal neural layer homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000535 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + retinal neural layer homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000535 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: nictitating membrane

  • Deleted
    • - nictitating membrane comment Taxon notes: Some reptiles, birds, and sharks have full nictitating membranes; in many mammals, a small, vestigial portion of the membrane remains in the corner of the eye. Some mammals, such as camels, polar bears, seals, and aardvarks, have full nictitating membranes[WP]. Editor notes: We exclude the shark structure for this via a taxon constraint.
  • Added
    • + nictitating membrane comment . Editor notes: We exclude the shark structure for this via a taxon constraint.
    • + nictitating membrane taxon notes Some reptiles, birds, and sharks have full nictitating membranes; in many mammals, a small, vestigial portion of the membrane remains in the corner of the eye. Some mammals, such as camels, polar bears, seals, and aardvarks, have full nictitating membranes[WP]

Changes for: tail vasculature

Changes for: fat pad

  • Deleted
    • - fat pad comment AO notes: FMA says isa fascia organ. Note that XAO and AAO have structures called fat pad/body, but these are gonad-associated, so we place them with the gonad-specific subclass
  • Added

Changes for: splenic sinusoid

  • Deleted
    • - splenic sinusoid comment Taxon notes: Whereas man and the rat are in the “sinusal” group, the mouse belongs in the “nonsinusal” group. The red pulp of spleens of rat, dog, man, and many other mammals contains an elaborate plexus of sinuses; that of mouse, cat, pig and others has no true sinuses and relatively few veins leading from the meshes into collecting veins - http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml
  • Added

Changes for: talus

  • Deleted
    • - talus comment Taxon notes: The talus is apparently derived from the fusion of three separate bones in the feet of primitive amphibians; the tibiale, articulating with tibia, the intermedium, between the bases of the tibia and fibula, and the fourth centrale, lying in the mid-part of the tarsus. These bones are still partially separate in modern amphibians, which therefore do not have a true talus. The talus forms a considerably more flexible joint in mammals than it does in reptiles. This reaches its greatest extent in artiodactyls, where the distal surface of the bone has a smooth keel to allow greater freedom of movement of the foot, and thus increase running speed[WP]
  • Added
    • + talus taxon notes The talus is apparently derived from the fusion of three separate bones in the feet of primitive amphibians; the tibiale, articulating with tibia, the intermedium, between the bases of the tibia and fibula, and the fourth centrale, lying in the mid-part of the tarsus. These bones are still partially separate in modern amphibians, which therefore do not have a true talus. The talus forms a considerably more flexible joint in mammals than it does in reptiles. This reaches its greatest extent in artiodactyls, where the distal surface of the bone has a smooth keel to allow greater freedom of movement of the foot, and thus increase running speed[WP]

Changes for: manus

  • Deleted
    • - manus comment Usage notes: like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton
  • Added
    • + manus curator notes like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton

Changes for: bile duct

  • Deleted
    • - bile duct homology notes (…) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (…) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000212 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) }
  • Added
    • + bile duct homology notes (…) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (…) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000212 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) }

Changes for: anterior choroidal artery

Changes for: astragalus-calcaneum unit

Changes for: submandibular duct

Changes for: neural crest

  • Deleted
    • - neural crest editor note consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). Taxon notes:
  • Added
    • + neural crest editor note consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).

Changes for: neurectoderm

  • Deleted
    • - neurectoderm comment Terminology notes: we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
  • Added

Changes for: white matter of cerebellum

  • Deleted
    • - white matter of cerebellum comment note that in NIF this is a composite structure; in MA and FMA it is explicitly part of cerebellum. This leads to consistency problems with strict parcellation schemes like ABA, see cerebellar peduncles. In NIF this is a composite structure, this is followed partially here in weakening the relationship to overlaps
  • Added
    • + white matter of cerebellum external ontology notes in NIF this is a composite structure; in MA and FMA it is explicitly part of cerebellum. This leads to consistency problems with strict parcellation schemes like ABA, see cerebellar peduncles. In NIF this is a composite structure, this is followed partially here in weakening the relationship to overlaps { external ontology=NIF }

Changes for: coelemic cavity lumen

Changes for: notochord

  • Deleted
    • - notochord comment Development notes: In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. // The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
    • - notochord homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000199 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }
  • Added
    • + notochord comment The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
    • + notochord development notes In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
    • + notochord homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000199 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }

Changes for: somite

  • Deleted
    • - somite homology notes (…) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (…) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000191 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) }
  • Added
    • + somite homology notes (…) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (…) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000191 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) }

Changes for: interlobar duct

Changes for: renal portal system

  • Deleted
    • - renal portal system comment Taxon notes: present in all classes of vertebrates except mammals; the mammalian kidney has a low pressure vascular network that may be its counterpart [ISBN10:0073040584]
  • Added
    • + renal portal system taxon notes present in all classes of vertebrates except mammals; the mammalian kidney has a low pressure vascular network that may be its counterpart [ISBN10:0073040584]

Changes for: Mullerian duct

  • Deleted
    • - Mullerian duct comment Development notes: Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct
  • Added

Changes for: liver primordium

  • Deleted
    • - liver primordium comment Editor’s note: consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it’s not clear how they differ
  • Added
    • + liver primordium editor note consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it’s not clear how they differ

Changes for: intraembryonic coelom

  • Deleted
    • - intraembryonic coelom homology notes (…) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (…) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000316 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 }
  • Added
    • + intraembryonic coelom homology notes (…) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (…) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000316 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 }

Changes for: right atrium venous valve

Changes for: neural arch

  • Deleted
    • - neural arch comment Taxon notes: tiny neural arches present in Hagfish (which lack a true vertebraal column).
    • - neural arch homology notes (…) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001670 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270 }
  • Added
    • + neural arch homology notes (…) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001670 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270 }
    • + neural arch taxon notes tiny neural arches present in Hagfish (which lack a true vertebraal column).

Changes for: eyebrow

Changes for: spinal cord neural plate

  • Deleted
    • - spinal cord neural plate homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…)[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000439 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }
  • Added
    • + spinal cord neural plate homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (4) a single, tubular nerve cord that is located dorsal to the notochord (…)[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000439 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }

Changes for: upper jaw cingulum

Changes for: lower jaw cingulum

Changes for: paraurethral duct

Changes for: paraurethral gland

  • Deleted
    • - paraurethral gland comment AO notes: in MP female urethral gland, Skene gland and paraurethral gland are exact syns. Note that NCITA seems to use the term in a more generic way, as a parent for skene gland, cowper gland (which may be the same as the male bulbo-urethral gland)
  • Added
    • + paraurethral gland external ontology notes in MP female urethral gland, Skene gland and paraurethral gland are exact syns. Note that NCITA seems to use the term in a more generic way, as a parent for skene gland, cowper gland (which may be the same as the male bulbo-urethral gland) { external ontology=MP }

Changes for: seminal vesicle fluid

Changes for: primitive sex cord of indifferent gonad

Changes for: pancreatic duct

  • Deleted
    • - pancreatic duct comment note that this class groups together accessory (dorsal) and main (ventral) pancreatic ducts. AO notes: in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms
  • Added
    • + pancreatic duct comment Usage notes: this class groups together accessory (dorsal) and main (ventral) pancreatic ducts. AO notes: in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms

Changes for: rhamphotheca

Changes for: infraorbital series

Changes for: ruminant forestomach

  • Deleted
    • - ruminant forestomach comment Development/homology notes: You will still see the statement in some texts that the parts of the forestomach are derived from the embryonic esophagus, and that’s the reason why (like the esophagus) they’re lined with stratified squamous epithelium. This is open to doubt. While there is no doubt that the rumen, reticulum, and omasum are all derived from the embryonic foregut, there is evidence to indicate that all three come from that an area of the foregut homologous to the part that develops into the single stomach of non-ruminants. If this is so, then the forestomach can be considered diverticula (or derivatives) of the stomach proper, not the esophagus, despite the nature of the lining – http://www.vetmed.vt.edu/education/curriculum/vm8054/labs/lab21/Examples/exrumen.htm
  • Added
    • + ruminant forestomach development notes You will still see the statement in some texts that the parts of the forestomach are derived from the embryonic esophagus, and that’s the reason why (like the esophagus) they’re lined with stratified squamous epithelium. This is open to doubt. While there is no doubt that the rumen, reticulum, and omasum are all derived from the embryonic foregut, there is evidence to indicate that all three come from that an area of the foregut homologous to the part that develops into the single stomach of non-ruminants. If this is so, then the forestomach can be considered diverticula (or derivatives) of the stomach proper, not the esophagus, despite the nature of the lining – http://www.vetmed.vt.edu/education/curriculum/vm8054/labs/lab21/Examples/exrumen.htm

Changes for: crop

  • Deleted
    • - crop comment Taxon notes: Aves specific structure - consider adding functional grouping class. Kardong: some cetaceans have a crop-like structure
  • Added
    • + crop taxon notes Aves specific structure - consider adding functional grouping class. Kardong: some cetaceans have a crop-like structure

Changes for: proventriculus

Changes for: cremaster muscle

  • Deleted
    • - cremaster muscle comment Usage notes: in females it is represented by only a few muscle loops that envelop the round ligament of the uterus. This class represents the male structure
  • Added
    • + cremaster muscle curator notes in females it is represented by only a few muscle loops that envelop the round ligament of the uterus. This class represents the male structure

Changes for: outer epithelium

Changes for: dermal scale

Changes for: enveloping layer of ectoderm

  • Deleted
    • - enveloping layer of ectoderm comment Taxon notes: Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
  • Added
    • + enveloping layer of ectoderm taxon notes Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.

Changes for: epidermal scale

Changes for: flexor pollicis longus muscle

  • Deleted
    • - flexor pollicis longus muscle comment Taxon notes: Modern humans are unique among hominids in having a flexor pollicis longus (FPL) muscle belly that is separate from that of the flexor digitorum profundus (FDP). While the FPL is not a separate muscle belly in extant great apes, a distinct tendon from the FDP belly might be present. In some individuals this tendon tend to act more like a ligament which restricts extension of the interphalangeal joint of the thumb. In orangutans there is a tendon similar in insertion and function to the FPL in humans, but which has an intrinsic origin on the oblique head of the adductor pollicis[WP]
  • Added
    • + flexor pollicis longus muscle taxon notes Modern humans are unique among hominids in having a flexor pollicis longus (FPL) muscle belly that is separate from that of the flexor digitorum profundus (FDP). While the FPL is not a separate muscle belly in extant great apes, a distinct tendon from the FDP belly might be present. In some individuals this tendon tend to act more like a ligament which restricts extension of the interphalangeal joint of the thumb. In orangutans there is a tendon similar in insertion and function to the FPL in humans, but which has an intrinsic origin on the oblique head of the adductor pollicis[WP]

Changes for: efferent portion of pharyngeal arch artery

Changes for: future central tendon

  • Deleted
    • - future central tendon comment Development notes: The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm.
  • Added
    • + future central tendon development notes The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm.

Changes for: mural trophectoderm

  • Deleted
    • - mural trophectoderm homology notes (…) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of ‘lower’ vertebrates.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000597 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0721676685 Romer AS, Parsons T, Vertebrate body (1977) p.105-106 }
  • Added
    • + mural trophectoderm homology notes (…) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of ‘lower’ vertebrates.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000597 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0721676685 Romer AS, Parsons T, Vertebrate body (1977) p.105-106 }

Changes for: Meckel’s cartilage pre-cartilage condensation

Changes for: embryonic intraretinal space

  • Deleted
    • - embryonic intraretinal space homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000534 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + embryonic intraretinal space homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (…) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000534 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: radius-ulna pre-cartilage condensation

Changes for: scapula pre-cartilage condensation

  • Deleted
    • - scapula pre-cartilage condensation comment Development notes: the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005).[PMID:21455939]
  • Added
    • + scapula pre-cartilage condensation development notes the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005).[PMID:21455939]

Changes for: pleuropericardial folds

  • Deleted
    • - pleuropericardial folds comment Development notes: As the folds grow towards the midline, carrying the phrenic nerve, the root of the folds migrate ventrally[http://www.indiana.edu/~anat550/cvanim/pericard/pericard.html]
  • Added
    • + pleuropericardial folds development notes As the folds grow towards the midline, carrying the phrenic nerve, the root of the folds migrate ventrally[http://www.indiana.edu/~anat550/cvanim/pericard/pericard.html]

Changes for: optic pit

  • Deleted
    • - optic pit homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles (reference 1); The first morphological sign of eye development in vertebrates is the bilateral evagination of diencephalon in the early neurula. In mammals, this is marked by the appearance of the optic pit, whereas in fish and amphibians a bulging of the optic primordia is observed. Continued evagination of the optic primordia leads to the formation of the optic vesicles (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001162 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, DOI:10.1146/annurev.cellbio.17.1.255 Chow RL and Lang RA, Early eye development in vertebrates. Annual Review of Cell and Developmental Biology (2001) }
  • Added
    • + optic pit homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles (reference 1); The first morphological sign of eye development in vertebrates is the bilateral evagination of diencephalon in the early neurula. In mammals, this is marked by the appearance of the optic pit, whereas in fish and amphibians a bulging of the optic primordia is observed. Continued evagination of the optic primordia leads to the formation of the optic vesicles (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001162 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, DOI:10.1146/annurev.cellbio.17.1.255 Chow RL and Lang RA, Early eye development in vertebrates. Annual Review of Cell and Developmental Biology (2001) }

Changes for: polar trophectoderm

  • Deleted
    • - polar trophectoderm homology notes (…) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of ‘lower’ vertebrates.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000980 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106 }
  • Added
    • + polar trophectoderm homology notes (…) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of ‘lower’ vertebrates.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000980 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106 }

Changes for: interstitial tissue

Changes for: spleen primordium

Changes for: shoulder joint primordium

Changes for: multi cell component structure

Changes for: 1st arch mandibular component

Changes for: 1st arch maxillary component

Changes for: muscle structure

  • Deleted
    • - muscle structure comment Usage notes: in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
  • Added
    • + muscle structure curator notes in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila

Changes for: nipple sheath

Changes for: gizzard

  • Deleted
    • - gizzard comment Taxon notes: currently restricted to Aves, but may be found outside - e.g. Pangolins. AO notes: BTO also includes: A thickened part of the alimentary canal in some animals (as an insect or an earthworm) that is similar in function to the crop of a bird. However, we are refering to the Aves structure here.
  • Added
    • + gizzard external ontology notes BTO also includes: A thickened part of the alimentary canal in some animals (as an insect or an earthworm) that is similar in function to the crop of a bird. However, we are refering to the Aves structure here. { external ontology=BTO }
    • + gizzard taxon notes currently restricted to Aves, but may be found outside - e.g. Pangolins

Changes for: spleen primary B follicle

Changes for: mesonephric distal tubule

Changes for: mesonephric proximal tubule

Changes for: inner epithelial layer of tympanic membrane

Changes for: spongiotrophoblast layer

  • Deleted
    • - spongiotrophoblast layer comment Taxon notes: restriction to Rodentia may be too strong - we apply it for now as we are inheriting the MP definition. Development notes: In the absence of direct lineage analysis, it has been assumed, from his- tological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone[PMID:19829370]
  • Added
    • + spongiotrophoblast layer taxon notes restriction to Rodentia may be too strong - we apply it for now as we are inheriting the MP definition. Development notes: In the absence of direct lineage analysis, it has been assumed, from his- tological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone[PMID:19829370]

Changes for: periocular mesenchyme

  • Deleted
    • - periocular mesenchyme comment AO notes: Check XAO once it has a definition. Taxon notes: Periocular mesenchyme (PM) is a mesencephalic neural crest derived cell population which as a result of an interaction with the retinal pigment epithelium forms the scleral cartilage of the avian eye[PMID:3709965]
  • Added
    • + periocular mesenchyme external ontology notes Check XAO once it has a definition. Taxon notes: Periocular mesenchyme (PM) is a mesencephalic neural crest derived cell population which as a result of an interaction with the retinal pigment epithelium forms the scleral cartilage of the avian eye[PMID:3709965] { external ontology=XAO }

Changes for: brain ventricle

  • Deleted
    • - brain ventricle comment Note that FMA draws the distinction between e.g. ‘fourth ventricle’ and ‘cavity of fourth ventricle’. The latter is a cavity, and part of the former, which is a region. The superclass of ‘fourth ventricle’ is_a ‘region of ventricular system of the brain’. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies.
  • Added
    • + brain ventricle external ontology notes FMA draws the distinction between e.g. ‘fourth ventricle’ and ‘cavity of fourth ventricle’. The latter is a cavity, and part of the former, which is a region. The superclass of ‘fourth ventricle’ is_a ‘region of ventricular system of the brain’. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. { external ontology=FMA }

Changes for: midface

  • Deleted
    • - midface comment editors note: this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface.
  • Added
    • + midface editor note this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface.

Changes for: periorbital region

Changes for: subarachnoid cistern

Changes for: posterior auricular vein

Changes for: auricular vein

  • Deleted
    • - auricular vein comment Taxon notes: In humans this refers to either the anterior or posterior auricular vein, passing in front of or behind the ear. This class also groups other auricular veins, including the greater, ventral, central auricular nerves. These may exhibit different branching structures. In the pig, the external jugular branches to the maxillary to the caudal auricular to the middle auricular, then onto various unique patterns
  • Added
    • + auricular vein taxon notes In humans this refers to either the anterior or posterior auricular vein, passing in front of or behind the ear. This class also groups other auricular veins, including the greater, ventral, central auricular nerves. These may exhibit different branching structures. In the pig, the external jugular branches to the maxillary to the caudal auricular to the middle auricular, then onto various unique patterns

Changes for: alveolar ridge

Changes for: anatomical conduit

Changes for: optic vesicle

  • Deleted
    • - optic vesicle homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000165 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }
  • Added
    • + optic vesicle homology notes (…) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000165 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 }

Changes for: chorionic villus

  • Deleted
    • - chorionic villus comment Taxon notes: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively. Histology notes: The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present.
  • Added
    • + chorionic villus comment Histology notes: The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present.
    • + chorionic villus taxon notes The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively

Changes for: primary circulatory organ

  • Deleted
    • - primary circulatory organ comment Taxon notes: note we reserve the subclass ‘heart’ from the vertebrate multi-chambered heart. “The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian”. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis. Gene notes: Bmp, Nkx, Gata
  • Added
    • + primary circulatory organ comment Gene notes: Bmp, Nkx, Gata
    • + primary circulatory organ taxon notes note we reserve the subclass ‘heart’ from the vertebrate multi-chambered heart. ‘The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian’. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis

Changes for: pharyngeal pouch 3

  • Deleted
    • - pharyngeal pouch 3 comment Development notes: The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve[WP]
  • Added
    • + pharyngeal pouch 3 development notes The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve[WP]

Changes for: pharyngeal pouch 2

  • Deleted
    • - pharyngeal pouch 2 comment Development notes: Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve[WP] 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.
  • Added
    • + pharyngeal pouch 2 comment 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.
    • + pharyngeal pouch 2 development notes Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve[WP]

Changes for: pharyngeal pouch 1

  • Deleted
    • - pharyngeal pouch 1 comment AO notes: we use adjacency relations rather than part_of, as in EHDAA2. Development notes: The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery[WP]
  • Added
    • + pharyngeal pouch 1 external ontology notes we use adjacency relations rather than part_of, as in EHDAA2. Development notes: The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery[WP] { external ontology=EHDAA2 }

Changes for: pharyngeal pouch 4

  • Deleted
    • - pharyngeal pouch 4 comment Development notes: Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands.[MP]
  • Added
    • + pharyngeal pouch 4 development notes Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands.[MP]

Changes for: os penis

  • Deleted
    • - os penis comment Taxon notes: found in most mammals, with the exception of humans
  • Added

Changes for: olfactory bulb mitral cell layer

Changes for: hemopoietic organ

Changes for: primary heart field

  • Deleted
    • - primary heart field comment note that this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
  • Added

Changes for: cardiogenic plate

  • Deleted
    • - cardiogenic plate homology notes (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000975 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) }
  • Added
    • + cardiogenic plate homology notes (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000975 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) }

Changes for: septum transversum

  • Deleted
    • - septum transversum comment Note that in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum. Development notes: The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
  • Added
    • + septum transversum development notes The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
    • + septum transversum external ontology notes in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum { external ontology=EHDAA2 }

Changes for: orbitofrontal cortex

Changes for: atrial septum primum

Changes for: mammary gland smooth muscle

Changes for: apex of heart

Changes for: appendicular skeleton

  • Deleted
    • - appendicular skeleton comment Note that ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of ‘subdivision of appendicular skeleton’). We have separate classes such as ‘skeleton of limb’, and ‘skeleton of hindlimb’ for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
  • Added
    • + appendicular skeleton external ontology notes ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of ‘subdivision of appendicular skeleton’). We have separate classes such as ‘skeleton of limb’, and ‘skeleton of hindlimb’ for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. { external ontology=FMA }

Changes for: mesentery

  • Deleted
    • - mesentery comment Note that in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: “In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.”. TODO - check. Consider FMA:259286 - Region of mesentery.
  • Added
    • + mesentery external ontology notes in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: ‘In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.’. TODO - check. Consider FMA:259286 - Region of mesentery. { external ontology=FMA }

Changes for: interventricular septum

  • Deleted
    • - interventricular septum comment Development notes: involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)[17064678]
  • Added

Changes for: skin of body

  • Deleted
    • - skin of body comment Usage notes: consider ‘integumentary system’ for invertebrates. AO notes: Note that FMA uses ‘skin’ for the entire organ. XAO seems consistent. MA seems to use it analagously to zone of skin
  • Added

Changes for: kidney pyramid

Changes for: hypodermis

  • Deleted
    • - hypodermis comment AO Notes: BTO has ‘subcutis’, as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
  • Added

Changes for: atrioventricular canal

Changes for: sinoatrial valve

  • Deleted
    • - sinoatrial valve comment Usage notes: in humans and mouse this is the opening from SV into right atrium. This class represents the valve connecting the SV to any atrium and is applicable to animals with a single atrium
  • Added
    • + sinoatrial valve curator notes in humans and mouse this is the opening from SV into right atrium. This class represents the valve connecting the SV to any atrium and is applicable to animals with a single atrium

Changes for: nasal capsule

  • Deleted
    • - nasal capsule comment Taxon notes: In most mammals, the nasal capsule remains unossified, except in mammals where the ethmoid portion ossifies to form the turbinates[Kardong]. In avians, the mesethmoid supports upper beak formation, whereas the ectethmoid comprises elements of the olfactory system, including the lamina cribosa, the crista galli apophysis and the conchae. Editor’s note - consider splitting this class. Developing cartilage in mammals? Connective tissue sheath in TAO. Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium[AAO]. Cartilaginous envelope containing the nasal organ[FishBase] Multi-tissue structure composed of connective tissue that surrounds, the internal portions of the olfactory epithelium[ZFA]. Avian def: The nasal capsule is dorsoventrally divided into two parts: the upper part, the ectethmoid, serves olfaction and is composed of the lamina cribosa, the crista galli apophysis and the conchae. The lower part, the mesethmoid, is a thick cartilage bar extending from the corpus sphenoidalis to the rostral extremity of the nose (Fig. 1A-B). In the avian embryo, the mesethmoid constitutes the cartilage primordium of the upper beak
  • Added
    • + nasal capsule comment . Avian def: The nasal capsule is dorsoventrally divided into two parts: the upper part, the ectethmoid, serves olfaction and is composed of the lamina cribosa, the crista galli apophysis and the conchae. The lower part, the mesethmoid, is a thick cartilage bar extending from the corpus sphenoidalis to the rostral extremity of the nose (Fig. 1A-B). In the avian embryo, the mesethmoid constitutes the cartilage primordium of the upper beak
    • + nasal capsule taxon notes In most mammals, the nasal capsule remains unossified, except in mammals where the ethmoid portion ossifies to form the turbinates[Kardong]. In avians, the mesethmoid supports upper beak formation, whereas the ectethmoid comprises elements of the olfactory system, including the lamina cribosa, the crista galli apophysis and the conchae. Editor’s note - consider splitting this class. Developing cartilage in mammals? Connective tissue sheath in TAO. Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium[AAO]. Cartilaginous envelope containing the nasal organ[FishBase] Multi-tissue structure composed of connective tissue that surrounds, the internal portions of the olfactory epithelium[ZFA]

Changes for: lateral ventricle choroid plexus stroma

Changes for: incisor dental pulp

Changes for: molar dental pulp

Changes for: truncus arteriosus

Changes for: endocardial cushion

  • Deleted
    • - endocardial cushion homology notes (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000932 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3 }
  • Added
    • + endocardial cushion homology notes (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000932 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3 }

Changes for: common cardinal vein

  • Deleted
    • - common cardinal vein comment Taxon notes: Paired in gnathostomes; with only a vestige of the right duct in the adult hagfish (21) and the left duct atrophying at metamorphosis in the lamprey (22)[PMID:20959416, S1]
  • Added
    • + common cardinal vein taxon notes Paired in gnathostomes; with only a vestige of the right duct in the adult hagfish (21) and the left duct atrophying at metamorphosis in the lamprey (22)[PMID:20959416, S1]

Changes for: epithelium of bronchiole

Changes for: upper pharyngeal 5 tooth

Changes for: upper pharyngeal tooth

Changes for: pharyngobranchial 3 tooth

Changes for: upper pharyngeal 4 tooth

Changes for: pharyngobranchial 2 tooth

Changes for: thyroid gland

  • Deleted
    • - thyroid gland homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000418 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }
  • Added
    • + thyroid gland homology notes (…) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (…) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (…).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000418 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 }

Changes for: nipple

Changes for: areola

Changes for: substantia nigra

Changes for: cerebellum

  • Deleted
    • - cerebellum comment note that almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem
  • Added
    • + cerebellum external ontology notes almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem { external ontology=ABA }

Changes for: insula

Changes for: basibranchial 2 tooth

Changes for: accessory XI nerve

  • Deleted
    • - accessory XI nerve comment Taxon notes: In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve[GO]
  • Added
    • + accessory XI nerve taxon notes In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve[GO]

Changes for: basibranchial 4 tooth

Changes for: basibranchial tooth

Changes for: gluteal muscle

  • Deleted
    • - gluteal muscle comment AO notes: FMA includes tensor fasciae latae and other buttock muscles. BTO def: Any one of three large skeletal muscles that form the buttock and move the thigh.
  • Added

Changes for: interchondral joint

Changes for: outflow tract myocardium

  • Deleted
    • - outflow tract myocardium homology notes (…) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (…) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000603 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997) }
  • Added
    • + outflow tract myocardium homology notes (…) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (…) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000603 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997) }

Changes for: bony shelf above orbit

Changes for: pyloric gastric gland

Changes for: epithelium of mammary gland

Changes for: osteoid

  • Deleted
    • - osteoid comment AO notes: Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class ‘bone condensation’. is_a intercellular matrix in FMA.
  • Added
    • + osteoid external ontology notes Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class ‘bone condensation’. is_a intercellular matrix in FMA. { external ontology=VSAO }

Changes for: rostral migratory stream

  • Deleted
    • - rostral migratory stream comment Taxon notes: In rodents, the anterior region of the SVZ produces neuroblasts that migrate in chain toward the olfactory bulb along the so-called rostral migratory stream (RMS)[BTO]
  • Added
    • + rostral migratory stream taxon notes In rodents, the anterior region of the SVZ produces neuroblasts that migrate in chain toward the olfactory bulb along the so-called rostral migratory stream (RMS)[BTO]

Changes for: mammary gland alveolus

Changes for: splanchnocranium

  • Deleted
    • - splanchnocranium comment AO notes: VSAO labels this term ‘pharyngeal arch’ (2012-06-01) - however, it clearly means pharyngeal arch skeleton. Editor/AO notes: many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
  • Added
    • + splanchnocranium external ontology notes VSAO labels this term ‘pharyngeal arch’ (2012-06-01) - however, it clearly means pharyngeal arch skeleton. Editor/AO notes: many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both { external ontology=VSAO }

Changes for: phalanx

  • Deleted
    • - phalanx comment Taxon notes: In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three[WP]
  • Added
    • + phalanx taxon notes In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three[WP]

Changes for: distal phalanx

  • Deleted
    • - distal phalanx comment Taxon notes: In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans.
  • Added
    • + distal phalanx taxon notes In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans.

Changes for: middle phalanx

  • Deleted
    • - middle phalanx comment Taxon notes: in some groups such as whales, there are multiple intermediate phalanges. Editors note: consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed ‘intermediate phalanx’, leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit
  • Added
    • + middle phalanx editor note consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed ‘intermediate phalanx’, leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit
    • + middle phalanx taxon notes in some groups such as whales, there are multiple intermediate phalanges

Changes for: trophectoderm

Changes for: cardinal vein

Changes for: primitive streak

  • Deleted
    • - primitive streak comment AO notes: VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826
    • - primitive streak homology notes (…) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (…) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001202 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 }
  • Added
    • + primitive streak external ontology notes VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 { external ontology=VHOG }
    • + primitive streak homology notes (…) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (…) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001202 , ontology=VHOG , source=http://bgee.unil.ch/ , source=PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 }

Changes for: allantois

  • Deleted
    • - allantois comment a diverticulum of the hindgut endoderm [ISBN10:0073040584 “Vertebrates, Kardong”]. AO notes: part_of embryo in EHDAA2 - note differences in humans
  • Added
    • + allantois comment a diverticulum of the hindgut endoderm [ISBN10:0073040584 (Vertebrates, Kardong)]. AO notes: part_of embryo in EHDAA2 - note differences in humans

Changes for: distal phalanx of manual digit 1

  • Deleted
    • - distal phalanx of manual digit 1 comment Taxon notes: The human pollical distal phalanx (PDP) has a pronounced insertion for the flexor pollicis longus (asymmetric towards the radial side), an ungual fossa, and a pair of dissymmetric ungual spines (the ulnar being more prominent). This asymmetry is necessary to ensure that the thumb pulp is always facing the pulps of the other digits, an osteological configuration which provides the maximum contact surface with held objects.[WP]
  • Added
    • + distal phalanx of manual digit 1 taxon notes The human pollical distal phalanx (PDP) has a pronounced insertion for the flexor pollicis longus (asymmetric towards the radial side), an ungual fossa, and a pair of dissymmetric ungual spines (the ulnar being more prominent). This asymmetry is necessary to ensure that the thumb pulp is always facing the pulps of the other digits, an osteological configuration which provides the maximum contact surface with held objects.[WP]

Changes for: Reichert’s cartilage

  • Deleted
    • - Reichert’s cartilage comment AO notes: in EHDAA2 this also develops from 3rd arch Mes from NC. Development notes: Classically defined as: a structure… develop the stapes, the styloid processes, the stylohyoid ligaments, and the lesser cornua of the hyoid bone; its proximal end gives rise to the stylohyoid ligament. Relationship to stapes disputed.
  • Added

Changes for: ectoplacental cone

  • Deleted
    • - ectoplacental cone comment Development notes: derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast.[PMID:19829370]
  • Added

Changes for: pallium

  • Deleted
    • - pallium comment Taxon notes: In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus[WP]
  • Added
    • + pallium taxon notes In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus[WP]

Changes for: ventral part of telencephalon

Changes for: pharyngeal arch artery

  • Deleted
    • - pharyngeal arch artery comment Usage notes: Do not confuse with arch of aorta. Editor notes: add specific artery derivatives. Development notes: The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches. Taxon notes: Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
  • Added
    • + pharyngeal arch artery curator notes Do not confuse with arch of aorta. Editor notes: add specific artery derivatives. Development notes: The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
    • + pharyngeal arch artery taxon notes Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods

Changes for: tetrapod frontal bone

  • Deleted
    • - tetrapod frontal bone comment Taxon notes: fused in humans, paired in other animals Development notes: In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993).
  • Added
    • + tetrapod frontal bone taxon notes fused in humans, paired in other animals Development notes: In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993).

Changes for: apical ectodermal ridge

  • Deleted
    • - apical ectodermal ridge comment Usage notes: note that media, dorsal fins etc have AERs. Taxon/development notes: The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold[PMID:20574421]. Function notes: maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
  • Added
    • + apical ectodermal ridge comment . Function notes: maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
    • + apical ectodermal ridge curator notes note that media, dorsal fins etc have AERs. Taxon/development notes: The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold[PMID:20574421]

Changes for: male inguinal canal

Changes for: female inguinal canal