2014-05-22 release

Various new terms from Phenoscape, including tooth types and ridges
2014-05-22 release image

Ontology Diff Report

  • Teeth:
    • Added multiple tooth ridge classes
    • Added synonyms for teeth (e.g. decidious / primary)
    • Added missing combos in {upper,lower}{primary,secondary}{CIPM} tooth pattern
  • Skeleton
    • NT: bony tubercle
    • Added syns for subsections of vertebral column
    • merged ‘optic foramen’ (embryonic) into optic canal
    • NT: fibula metaphysis. Fixes issue #455
  • Admin
    • split many comments into separate properties: function notes, curator notes, editor notes
    • ID typo fixed. Fixes issue #456
  • various NTs for phenotype definitions
  • Development
    • Weakened spatial disjointness constraint between Emb and Extra-Emb. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/3
    • more axioms for staging relations
  • Integration
    • NTs for epithelia and muscle of rectum analogs in inverts. Some FBbt and Wbbt classes should auto-classify here
    • made EMAPA axioms taxon-equivalent

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-05-16/uberon.owl

New Ontology

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

Report for classes

Class objects lost from source: 1

Class objects new in target: 44

New Class : bony tubercle

New Class : dorsal cloacal gland

New Class : horn of hemipenis

New Class : incisive process of premaxilla

New Class : placental caruncle

New Class : placentome of cotyledonary placenta

New Class : intertarsal sesamoid

New Class : primary premolar tooth

New Class : lower primary premolar tooth

New Class : upper primary premolar tooth

New Class : secondary premolar tooth

New Class : epithelium of terminal part of digestive tract

New Class : shoulder joint

New Class : transitional anatomical structure

New Class : entire extraembryonic component

New Class : muscle of terminal part of digestive tract

New Class : periosteum of long bone

New Class : intrahepatic branch of portal vein

New Class : rostral margin of orbit

New Class : upper premolar tooth

New Class : lower premolar tooth

New Class : mesial marginal ridge of tooth

New Class : distal marginal ridge of tooth

New Class : transverse marginal ridge of tooth

New Class : marginal ridge of tooth

New Class : oblique ridge of tooth

New Class : triangular ridge of tooth

New Class : transverse ridge of tooth

New Class : ridge of tooth

New Class : preductal region of aortic arch

New Class : postductal region of aortic arch

New Class : juxtaductal region of aortic arch

New Class : mucus body coating

New Class : mucus cocoon

New Class : metaphysis of fibula

New Class : lingual cusp of tooth

New Class : descending trunk of arch of aorta

New Class : lamina lucida

New Class : vermilion

New Class : frenulum of upper lip

New Class : frenulum of lower lip

New Class : upper vermilion

New Class : lower vermilion

New Class : frenulum of lip

Changed Class objects: 644

Changes for: levator mandibulae externus

Changes for: levator mandibulae articularis

Changes for: levator mandibulae lateralis

Changes for: levator mandibulae longus

Changes for: tonsil germinal center

Changes for: anatomical conduit space

Changes for: subarcualis rectus I

Changes for: trunk maxillary-mandibularis

Changes for: anatomical line between inner canthi

Changes for: bone of upper jaw

Changes for: dentary tooth

Changes for: cell condensation

Changes for: non-mineralized cartilage tissue

Changes for: subdivision of organism along main body axis

Changes for: thyrohyoid bone

Changes for: thyrohyoid cartilage

Changes for: tympanohyoid cartilage

Changes for: external cervical os

Changes for: intermammary line

Changes for: utriculosaccular duct

Changes for: genital swelling

Changes for: pterygoideus

Changes for: midcarpal joint

Changes for: pisiform joint

Changes for: ramus auricularis of the vagus nerve

Changes for: nasomaxillary suture

Changes for: levator quadrati

Changes for: ramus muscularis of glossopharyngeus nerve

Changes for: ramus muscularis of vagus nerve

Changes for: laryngeus ventralis

Changes for: perilymphatic channel

Changes for: umbilical smooth muscle

Changes for: gastroduodenal junction

Changes for: corpus spongiosum of penis

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

Changes for: lesser tubercle of humerus

Changes for: greater tubercle of humerus

Changes for: optic tract

  • Deleted
    • - optic tract comment editor note: relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII ‘continuous_with’
  • Added
    • + optic tract editor note relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII ‘continuous_with’

Changes for: prostatic utricle

Changes for: habenular commissure

Changes for: red nucleus

  • Deleted
    • - red nucleus comment Function notes: in animals without a significant corticospinal tract, gait is mainly controlled by the red nucleus.
  • Added
    • + red nucleus function notes in animals without a significant corticospinal tract, gait is mainly controlled by the red nucleus.

Changes for: patellofemoral joint

Changes for: nasal suture

Changes for: spheno-occipital synchondrosis

Changes for: quadrate-articular joint

Changes for: jaw joint

Changes for: mucosa-associated lymphoid tissue

Changes for: gut-associated lymphoid tissue

Changes for: sternocostal joint

Changes for: synovial joint of pectoral girdle

Changes for: synovial joint of pelvic girdle

Changes for: placenta

Changes for: tibiofibular joint

Changes for: humeroradial joint

Changes for: inferior tibiofibular joint

Changes for: humeroulnar joint

Changes for: carpometacarpal joint

Changes for: superior tibiofibular joint

Changes for: tarsometatarsal joint

Changes for: capillary

Changes for: cricothyroid joint

Changes for: laryngeal joint

Changes for: xiphisternal joint

Changes for: stifle joint

Changes for: cricoarytenoid joint

Changes for: intercarpal joint

Changes for: intermetacarpal joint

Changes for: intermetatarsal joint

Changes for: sacrococcygeal symphysis

Changes for: pubo-ischium

Changes for: retromolar triangle

Changes for: bone of jaw

  • Deleted
    • - bone of jaw comment Editor notes: Do not manually classify under here - bones are automatically classified
  • Added

Changes for: lateral olfactory tract

  • Deleted
    • - lateral olfactory tract comment Editor notes: We follow neurolex and use ‘tract’ rather than ‘stria’ as the primary label. We make this a subtype of olfactory tract. Currently this groups teleost and mammalian structures by the same name, but this may be a false grouping. For example, in zebrafish, the difference between medial and lateral depends on the region of telencephalon (dorsal or ventral). Taxon notes: In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells.[PMID:7437895]
  • Added
    • + lateral olfactory tract editor note We follow neurolex and use ‘tract’ rather than ‘stria’ as the primary label. We make this a subtype of olfactory tract. Currently this groups teleost and mammalian structures by the same name, but this may be a false grouping. For example, in zebrafish, the difference between medial and lateral depends on the region of telencephalon (dorsal or ventral). Taxon notes: In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells.[PMID:7437895]

Changes for: ora serrata of retina

Changes for: ductus reuniens

Changes for: posterior semicircular canal

Changes for: carpometacarpal joint of digit 1

Changes for: caudal-sacral region of vertebral column

Changes for: gingiva

  • Deleted
    • - gingiva comment Editor notes: FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton.
  • Added
    • + gingiva editor note FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton.

Changes for: embryonic skin basal layer

  • Deleted
    • - embryonic skin basal layer comment Editor notes: compare with ‘stratum basale of epidermis’. This class is the source for many adult structures - see WP2062. See also: ‘enveloping layer of ectoderm’
  • Added
    • + embryonic skin basal layer editor note compare with ‘stratum basale of epidermis’. This class is the source for many adult structures - see WP2062. See also: ‘enveloping layer of ectoderm’

Changes for: hyoepiglottic ligament

Changes for: prehallux skeleton

Changes for: hepatogastric ligament

Changes for: hepatoduodenal ligament

Changes for: extraembryonic cavities

Changes for: cranial ganglion

  • Deleted
    • - cranial ganglion comment Editor note: split out MA ter,. Note the MA term is part of the CNS. This needs to be checked w.r.t relationship between ganglia and the PNS, as the PNS and CNS are spatially disjoint. also meaning of MA term is not clear (appears to be union of nerve and ganglion, but MA ‘cranial nerve’ is unconnected)
  • Added
    • + cranial ganglion editor note split out MA ter,. Note the MA term is part of the CNS. This needs to be checked w.r.t relationship between ganglia and the PNS, as the PNS and CNS are spatially disjoint. also meaning of MA term is not clear (appears to be union of nerve and ganglion, but MA ‘cranial nerve’ is unconnected)

Changes for: secondary palate

  • Deleted
    • - secondary palate comment Function notes: separates respiratory and oral passages. 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 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.
    • + secondary palate function notes separates respiratory and oral passages

Changes for: geniculate ganglion

Changes for: cerebral vein

Changes for: mandible

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

Changes for: bronchoalveolar duct junction

Changes for: vestibular nuclear complex

  • Deleted
    • - vestibular nuclear complex comment Editor notes: In TA they are grouped in both the pons and medulla; WP+MA says the SVN is in the pons, and GO includes VNC development under pons development, but this is not supported by ABA. Todo - check with NIF.
  • Added
    • + vestibular nuclear complex editor note In TA they are grouped in both the pons and medulla; WP+MA says the SVN is in the pons, and GO includes VNC development under pons development, but this is not supported by ABA. Todo - check with NIF.

Changes for: preopercle vertical limb-hyomandibula joint

Changes for: fenestrated capillary

  • Deleted
    • - fenestrated capillary comment Editor notes: the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences
  • Added
    • + fenestrated capillary editor note the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences

Changes for: hyomandibula-opercle joint

Changes for: supraoccipital-parietal joint

Changes for: preopercle horizontal limb-symplectic joint

Changes for: periamygdaloid area

Changes for: bifurcation of trachea

Changes for: azygos vein

Changes for: internal thoracic vein

Changes for: esophagus muscle

Changes for: collection of basal ganglia

  • Deleted
    • - collection of basal ganglia comment Editor note: it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
  • Added
    • + collection of basal ganglia editor note it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.

Changes for: stomach non-glandular epithelium

  • Deleted
    • - stomach non-glandular epithelium comment Editor notes: OWL definition to be added later. 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

Changes for: extra-ocular muscle

Changes for: fundic gastric gland

  • Deleted
  • Added
    • + fundic gastric gland editor note Consider FMA:14923 ! Principal gland of fundus of stomach. Added part_of to mucosa to be consistent with FMA pattern (note that Kardong places this in the glandular epithelium)

Changes for: stapes cartilage element

  • Deleted
    • - stapes cartilage element comment Editor notes: TODO - check relationship to Recihert’s. 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 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.
    • + stapes cartilage element editor note TODO - check relationship to Recihert’s

Changes for: mesencephalic artery

Changes for: mucosa of dorsum of tongue

Changes for: artery

  • Deleted
    • - artery comment Editor notes: Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
  • Added
    • + artery editor note Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.

Changes for: future dermis

Changes for: optic choroid vascular plexus

Changes for: tapetum lucidum of camera-type eye

  • Deleted
    • - tapetum lucidum of camera-type eye comment Function notes: It normally functions at low light levels to provide the light-sensitive retinal cells with a second opportunity for photon-photoreceptor stimulation, thereby enhancing visual sensitivity
  • Added
    • + tapetum lucidum of camera-type eye function notes It normally functions at low light levels to provide the light-sensitive retinal cells with a second opportunity for photon-photoreceptor stimulation, thereby enhancing visual sensitivity

Changes for: distal visceral endoderm

Changes for: dermatological-muscosal system

Changes for: male prepuce epithelium

Changes for: infraspinatus tendon

Changes for: lip skeletal muscle

Changes for: intercuneiform joint

Changes for: posterior nuclear complex of thalamus

Changes for: nasion

Changes for: intergluteal cleft

Changes for: basal part of pons

Changes for: cranial placode

  • Deleted
    • - cranial placode comment Editor note: to avoid confusion, we include neurogenic placode as a subclass. Do not merge. Terminological notes: The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. Taxon notes: Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons[PMID:11523831].
  • Added
    • + cranial placode comment .
    • + cranial placode editor note to avoid confusion, we include neurogenic placode as a subclass. Do not merge. Terminological notes: The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. Taxon notes: Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons[PMID:11523831]

Changes for: upper secondary premolar tooth

Changes for: lower secondary premolar tooth

Changes for: arthropod sensillum

Changes for: post-anal tail bud

Changes for: tunica intima

  • Deleted
    • - tunica intima comment Editor note: the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
  • Added
    • + tunica intima editor note the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure

Changes for: otolith organ

  • Deleted
    • - otolith organ comment Editor notes: Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia
  • Added
    • + otolith organ editor note Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia

Changes for: epiphyseal plate

  • Deleted
    • - epiphyseal plate comment editor note: consider splitting this class into the epiphyseal plates of long bones and vertebrae
  • Added

Changes for: anterior fontanel

Changes for: skeletal system

Changes for: tongue taste bud

Changes for: metaphysis

  • Deleted
    • - metaphysis comment adjacent to or containing epiphyseal plate? Note in FMA the metaphysis is part of the diaphysis, but not in MA. In the diagram in WP, it appears to be adjacent, not part_of.
  • Added
    • + metaphysis comment adjacent to or containing epiphyseal plate? Note in FMA the metaphysis is part of the diaphysis, but not in MA.

Changes for: elbow joint

Changes for: wrist joint

Changes for: placental cotyledon

Changes for: knee joint

Changes for: temporomandibular joint

Changes for: ankle joint

Changes for: placental labyrinth villous

Changes for: hip joint

Changes for: calcaneal tendon

Changes for: glenohumeral joint

Changes for: sternoclavicular joint

Changes for: intervertebral joint

Changes for: proximal interphalangeal joint

Changes for: distal interphalangeal joint

Changes for: trachea cartilage

Changes for: cardiac mesenchyme

  • Deleted
    • - cardiac mesenchyme comment Editor note: decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
  • Added
    • + cardiac mesenchyme editor note decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts

Changes for: visceral yolk sac cavity

Changes for: radio-ulnar joint

Changes for: skin mucous gland

Changes for: upper jaw molar

Changes for: mouth floor

Changes for: left common carotid artery plus branches

Changes for: common carotid artery plus branches

  • Deleted
    • - common carotid artery plus branches comment Editor notes: we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see ‘trunk of common carotid artery’. Development notes: in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
  • Added

Changes for: right common carotid artery plus branches

Changes for: patellar ligament

Changes for: articular system

Changes for: esophageal-pneumatic duct sphincter

Changes for: bone of lower jaw

Changes for: sella turcica

  • Deleted
    • - sella turcica comment Editor notes: for consistency with FMA we have a separate class for the cavity of the sella turcica
  • Added

Changes for: segmental subdivision of nervous system

  • Deleted
    • - segmental subdivision of nervous system comment Editor note: revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
  • Added
    • + segmental subdivision of nervous system editor note revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)

Changes for: instar larval stage

Changes for: palatal muscle

Changes for: coracoid bone

  • Deleted
    • - coracoid bone comment Editor notes: check developmental relationships. Taxon notes: In Theria, coracoid bones non-existent or fused with the shoulder blades to form coracoid processes[WP]. Procoracoid+coracoid are homologuous with coracoid of teleostomi. The coracoid is a triangular shaped-bone that usually has an anteriorly directed long process that may joins its counterpart in some fish groups. It may be perforated by the coracoid foramen or it may be notched dorsally and forms the scapulo-coracoid foramen together with a similar notch of the ventral margin of the scapula[VSAO] Terminology notes: see discussion in Kardong - suggests using procoracoid (anterior coracoid) for the element in birds, reptiles, amphibians and fish, and reserving coracoid for the new synapsid/therian structure.
  • Added
    • + coracoid bone comment Terminology notes: see discussion in Kardong - suggests using procoracoid (anterior coracoid) for the element in birds, reptiles, amphibians and fish, and reserving coracoid for the new synapsid/therian structure.
    • + coracoid bone editor note check developmental relationships. Taxon notes: In Theria, coracoid bones non-existent or fused with the shoulder blades to form coracoid processes[WP]. Procoracoid+coracoid are homologuous with coracoid of teleostomi. The coracoid is a triangular shaped-bone that usually has an anteriorly directed long process that may joins its counterpart in some fish groups. It may be perforated by the coracoid foramen or it may be notched dorsally and forms the scapulo-coracoid foramen together with a similar notch of the ventral margin of the scapula[VSAO]

Changes for: pubic symphysis

Changes for: articular/anguloarticular

  • Deleted
    • - articular/anguloarticular comment Editor notes: We create different classes for articular and malleus, in contrast to VHOG. Taxon notes (from VHOG): “According to this theory [Reichert-Gaupp theory], the mammalian stapes is derived from the reptilian columella, the incus from the quadrate and the malleus from the articular […]” Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) 62:339-357. Note that TAO has a distinct class for articular - in fact we need (at least) 3 classes here - articular, anguloarticular and malleus, arranged into a single VHOG group // TODO - resolve part_of relationships
  • Added
    • + articular/anguloarticular comment TODO - resolve part_of relationships. AO Notes: TAO has a distinct class for articular - in fact we need (at least) 3 classes here - articular, anguloarticular and malleus, arranged into a single VHOG group

Changes for: subtalar joint

Changes for: metatarsophalangeal joint

Changes for: metacarpophalangeal joint

Changes for: atlanto-axial joint

Changes for: acromioclavicular joint

Changes for: conceptus

  • Deleted
    • - conceptus SubClassOf has part some extraembryonic structure
    • - conceptus comment Editor notes: EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
  • Added

Changes for: amphibian larval stage

Changes for: frontal lobe

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

Changes for: pseudodentary tooth

Changes for: Mullerian tubercle

Changes for: umbilical ring

Changes for: sacro-iliac joint

Changes for: umbilical artery

  • Deleted
    • - umbilical artery comment Editor notes: todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships
  • Added

Changes for: nematode larva

Changes for: zona limitans intrathalamica

Changes for: zone of stomach

  • Deleted
    • - zone of stomach comment Editor notes: We follow Kardong in defining stomach regions by gland, but we also include ‘body of stomach’. In future we may want to have different partitions of the stomach
  • Added
    • + zone of stomach editor note We follow Kardong in defining stomach regions by gland, but we also include ‘body of stomach’. In future we may want to have different partitions of the stomach

Changes for: femorotibial joint

Changes for: corneal blood vessel

Changes for: central sulcus

Changes for: Purkinje cell layer of cerebellar cortex

Changes for: nephron

  • Deleted
    • - nephron comment Editor note: kidney terms require review for cross-vertebrate compatibility and developmental relationships. Taxon notes: In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)[GO Kidney]
  • Added
    • + nephron editor note kidney terms require review for cross-vertebrate compatibility and developmental relationships. Taxon notes: In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)[GO Kidney]

Changes for: renal column

Changes for: intralobular bile duct

  • Deleted
    • - intralobular bile duct comment Editor notes: Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under ‘Structure of intralobular bile duct’ (i.e. the CoH is the only part of the entire IBduct)
  • Added
    • + intralobular bile duct editor note Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under ‘Structure of intralobular bile duct’ (i.e. the CoH is the only part of the entire IBduct)

Changes for: actinopterygian frontal-parietal joint

Changes for: vestibular ligament

Changes for: thyroepiglottic ligament

Changes for: cricopharyngeal ligament

Changes for: phonic lip

  • Deleted
    • - phonic lip comment Function notes: When the lips snap together during click production, vibrations in the dorsal bursae are likely produced ISBM10:0120885522. Large and cornified in sperm whales. Editor notes: requires review w.r.t location in physeter vs other odontocetes
  • Added
    • + phonic lip comment Editor notes: requires review w.r.t location in physeter vs other odontocetes
    • + phonic lip function notes When the lips snap together during click production, vibrations in the dorsal bursae are likely produced ISBM10:0120885522. Large and cornified in sperm whales

Changes for: cricotracheal ligament

Changes for: cricothyroid ligament

Changes for: cricoarytenoid ligament

Changes for: closed circulatory system

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

Changes for: maxillopalatine tooth

Changes for: anatomical line between outer canthi

Changes for: duodenal gland

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

Changes for: intestinal villus

  • Deleted
    • - intestinal villus comment Editor notes: in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all speciesi for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine. AO Notes: the BTO class refers to a generic villous
  • Added
    • + intestinal villus comment AO Notes: the BTO class refers to a generic villous
    • + intestinal villus editor note in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all speciesi for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine

Changes for: hypothalamo-hypophyseal system

Changes for: epithelium of pancreatic duct

  • Deleted
    • - epithelium of pancreatic duct comment Editor note: in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses this
  • Added

Changes for: ureterovesical junction

Changes for: ureteropelvic junction

Changes for: mesenchyme of umbilical cord

Changes for: gonadal fat pad

  • Deleted
    • - gonadal fat pad comment Editor notes: consider change relationship from part_of. AO notes: we place the amphibian structures here as their definitions state a gonadal association.
  • Added

Changes for: stato-acoustic epithelium

Changes for: antennal gland

  • Deleted
    • - antennal gland comment Editor note: consider also classifying this as a renal tubule - or separate terms for coiled/nephridial canal. Editor note: cede this term to Arthropod AO
  • Added

Changes for: vomeronasal system

  • Deleted
    • - vomeronasal system comment Editor note: check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES]
  • Added
    • + vomeronasal system editor note check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES]

Changes for: tibiotalar joint

Changes for: adenohypophyseal placode

  • Deleted
    • - adenohypophyseal placode comment Editor notes: consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm. Addtional notes: Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke’s pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke’s pouch, the anlage of the adenohypophysis. Rathke’s pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke’s pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009)
  • Added
    • + adenohypophyseal placode comment Addtional notes: Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke’s pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke’s pouch, the anlage of the adenohypophysis. Rathke’s pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke’s pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009)
    • + adenohypophyseal placode editor note consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm

Changes for: cranial sensory ganglion

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

Changes for: vestibulocochlear ganglion

  • Deleted
    • - vestibulocochlear ganglion comment Editor notes: Consider follow MA naming scheme. // The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms “cochlear nerve fiber” and “spiral ganglion cell” are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus[Wikipedia:Cochlear_nerve]
  • Added
    • + vestibulocochlear ganglion comment The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms “cochlear nerve fiber” and “spiral ganglion cell” are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus[Wikipedia:Cochlear_nerve]
    • + vestibulocochlear ganglion editor note Consider follow MA naming scheme.

Changes for: shoulder bone

Changes for: thoracic cavity nerve

  • Deleted
    • - thoracic cavity nerve comment Editor note: consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve
  • Added

Changes for: upper jaw incisor

Changes for: facial suture

Changes for: craniofacial suture

  • Deleted
    • - craniofacial suture comment Editor notes: we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA
  • Added
    • + craniofacial suture editor note we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA

Changes for: costochondral joint

Changes for: costovertebral joint

Changes for: foramen of Panizza

Changes for: accessory lacrimal gland

Changes for: tubercle of rib

Changes for: posttemporal-parietal joint

Changes for: vertebra 5-vertebra 6 joint

Changes for: vertebra 6 - vertebra 7 joint

Changes for: clavicle

Changes for: lobe of liver

  • Deleted
    • - lobe of liver comment editor note: some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts
  • Added
    • + lobe of liver editor note some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts

Changes for: corpora quadrigemina

  • Deleted
    • - corpora quadrigemina comment editor note: this section needs worked on for pan-vertebrate consistency. for now we include a mammal specific definition, even though the child terms are applicable across vertebrates
  • Added
    • + corpora quadrigemina editor note this section needs worked on for pan-vertebrate consistency. for now we include a mammal specific definition, even though the child terms are applicable across vertebrates

Changes for: lateral ethmoid-frontal joint

Changes for: prootic-pterosphenoid joint

Changes for: prootic-exoccipital joint

Changes for: basioccipital-exoccipital joint

Changes for: sternocleidomastoid

  • Deleted
    • - sternocleidomastoid comment Editor notes: TODO: sternocleidomastoid = sternomastoid + Cleidomastoideus. Origin: from manubrium sterni (sterno) and clavicle (cleido) and it’s insertion at the mastoid process of the temporal bone.
  • Added
    • + sternocleidomastoid editor note TODO: sternocleidomastoid = sternomastoid + Cleidomastoideus. Origin: from manubrium sterni (sterno) and clavicle (cleido) and it’s insertion at the mastoid process of the temporal bone.

Changes for: vertebral column

  • Deleted
    • - vertebral column comment Editor notes: Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton
  • Added
    • + vertebral column editor note Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton

Changes for: musculoskeletal system

Changes for: subfornical organ

Changes for: cardia of stomach

  • Deleted
    • - cardia of stomach comment Editor notes: We follow Kardong in defining stomach regions by glands. Boundary notes: There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that “The gastric cardia is now clearly considered to be part of the stomach”[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP].
  • Added
    • + cardia of stomach comment Boundary notes: There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that “The gastric cardia is now clearly considered to be part of the stomach”[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]
    • + cardia of stomach editor note We follow Kardong in defining stomach regions by glands.

Changes for: pylorus

  • Deleted
    • - pylorus comment Editor notes: We follow Kardong in defining stomach regions by glands
  • Added

Changes for: extraembryonic umbilical vein

Changes for: renal artery

  • Deleted
    • - renal artery comment Editor notes: renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability.
  • Added
    • + renal artery editor note renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability.

Changes for: joint of girdle

Changes for: internasal suture

Changes for: internal naris

Changes for: superior cerebellar peduncle

Changes for: area postrema

Changes for: atrioventricular valve

Changes for: tricuspid valve

Changes for: mitral valve

Changes for: respiratory system

Changes for: renal system

Changes for: circulatory system

Changes for: digestive system

Changes for: nervous system

Changes for: midgut

  • Deleted
    • - midgut comment Editor notes: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class. AO Notes: in FMA this class has no children.
  • Added
    • + midgut comment AO Notes: in FMA this class has no children.
    • + midgut editor note Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class

Changes for: hindgut

  • Deleted
    • - hindgut comment Editor notes: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - UBERONREF:0000002). We may explicitly make this a developmental class. AO Notes: in FMA this class has no children.
  • Added
    • + hindgut comment AO Notes: in FMA this class has no children.
    • + hindgut editor note Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - UBERONREF:0000002). We may explicitly make this a developmental class

Changes for: foregut

  • Deleted
    • - foregut comment Editor notes: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
  • Added
    • + foregut editor note Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure

Changes for: limb

Changes for: Malpighian tubule

Changes for: pneumatized bone

Changes for: dento-alveolar joint

Changes for: gustatory system

Changes for: flocculus

Changes for: vertebral arch joint

Changes for: ileocecal junction

Changes for: anterolateral ligament of knee

Changes for: neural spine

Changes for: water vascular system

Changes for: mesenchyme from somatopleure

  • Deleted
    • - mesenchyme from somatopleure comment Editor notes: the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
  • Added
    • + mesenchyme from somatopleure editor note the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives

Changes for: intercerebral commissure

Changes for: extraembryonic membrane mesenchyme

Changes for: coronal suture

Changes for: bregma

Changes for: deltopectoral crest

Changes for: cochlear labyrinth

  • Deleted
    • - cochlear labyrinth comment Editor notes: we follow the FMA in placing this in the membranous labyrinth. Notes: The labyrinth can be divided by layer or by region. Bony vs. membranous / Vestibular vs. cochlear
  • Added
    • + cochlear labyrinth editor note we follow the FMA in placing this in the membranous labyrinth. Notes: The labyrinth can be divided by layer or by region. Bony vs. membranous / Vestibular vs. cochlear

Changes for: frontal suture

Changes for: lambdoid suture

Changes for: sagittal suture

Changes for: preopercle-opercle joint

Changes for: os sesamoides tarsale

Changes for: extraembryonic epithelium

Changes for: supracondyle tubercle

Changes for: bicipital tuberosity

Changes for: lateral tubercle of astragalus

Changes for: ulnar tuberosity

Changes for: muscularis orbicularis

Changes for: immune system

Changes for: vertebra

  • Deleted
    • - vertebra comment Editor notes: Consider changing name to make distinction from inferred superclass ‘vertebral element’ clear // 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 comment note we follow FMA in making this an irregular bone - however vertebra have ‘epiphyses’ which are currently classified as belonging to long bones
    • + vertebra editor note Consider changing name to make distinction from inferred superclass ‘vertebral element’ clear

Changes for: integumental system

Changes for: tail

  • Deleted
    • - tail comment Editor notes: Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin
  • Added
    • + tail editor note Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin

Changes for: basal ganglion

  • Deleted
    • - basal ganglion comment Editor note: it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.
  • Added
    • + basal ganglion editor note it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done.

Changes for: hepatobiliary system

Changes for: oral epithelium

  • Deleted
    • - oral epithelium comment Editor note: consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar). Development notes: the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme [PMID:16488870]
  • Added
    • + oral epithelium editor note consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar). Development notes: the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme [PMID:16488870]

Changes for: distal sesamoid impar ligament

Changes for: pituitary stalk

Changes for: placenta junctional zone

Changes for: upper part of vagina

Changes for: placental labyrinth vasculature

Changes for: utricle duct

Changes for: saccule duct

Changes for: anterior meningeal artery

  • Deleted
    • - anterior meningeal artery comment Editor notes: this needs checking as part of a general revision of the blood vessels and their branches - unclear if the anterior meningeal artery should be treated separately from the anterior ethmoidal artery (ie as a branch) or the same thing
  • Added
    • + anterior meningeal artery editor note this needs checking as part of a general revision of the blood vessels and their branches - unclear if the anterior meningeal artery should be treated separately from the anterior ethmoidal artery (ie as a branch) or the same thing

Changes for: arthropod hepatopancreas

Changes for: pharyngeal arch mesenchymal region

  • Deleted
    • - pharyngeal arch mesenchymal region comment Editor notes: this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. [MP:0011262]
  • Added
    • + pharyngeal arch mesenchymal region editor note this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. [MP:0011262]

Changes for: mesocardium

Changes for: placenta labyrinth

Changes for: anatomical line between outer ears

Changes for: squamoparietal suture

Changes for: spiral colon

Changes for: anatomical line between pupils

Changes for: conducting system of heart

Changes for: laryngeal apparatus

Changes for: meninx

  • Deleted
    • - meninx comment Editor note: consider separate term for meninges aka collection of meninges. Note in EHDAA2 pia mater etc are part of the meninges. Also consider a new class for primary/primitive meninx. AO notes: Not consider part of the CNS/neuraxis in FMA. Taxon notes: Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx).
  • Added
    • + 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).
    • + meninx editor note consider separate term for meninges aka collection of meninges. Note in EHDAA2 pia mater etc are part of the meninges. Also consider a new class for primary/primitive meninx. AO notes: Not consider part of the CNS/neuraxis in FMA

Changes for: pia mater

  • Deleted
    • - pia mater comment Editor note: consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system
  • Added
    • + pia mater editor note consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system

Changes for: dura mater

  • Deleted
    • - dura mater comment Function notes: capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288. AO notes: in ncit this is divided into periosteal layer and meningeal layer
  • Added
    • + dura mater comment AO notes: in ncit this is divided into periosteal layer and meningeal layer
    • + dura mater function notes capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288

Changes for: mesencephalic vein

Changes for: arthropod fat body

Changes for: lesser omentum

Changes for: pharyngotympanic tube

  • Deleted
    • - pharyngotympanic tube comment Editor notes: we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship
  • Added
    • + pharyngotympanic tube editor note we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship

Changes for: extraembryonic venous system

Changes for: umbilical cord

Changes for: exocrine system

Changes for: neural crest

  • Deleted
    • - neural crest comment Editor note: consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). Taxon notes: . Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
  • Added
    • + neural crest comment Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
    • + neural crest editor note consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). Taxon notes:

Changes for: somite

  • Deleted
    • - somite comment Editor notes: currently classified as an epithelial vesicle, consistent with EHDAA2 and UBERONREF:0000002. Consider making “somitic mesoderm” a separate term and correlate with regionalization processes. Consider moving ZFA term to ‘trunk somite’ as it is part of the trunk // When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
  • Added
    • + somite comment When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
    • + somite editor note currently classified as an epithelial vesicle, consistent with EHDAA2 and UBERONREF:0000002. Consider making ‘somitic mesoderm’ a separate term and correlate with regionalization processes. Consider moving ZFA term to ‘trunk somite’ as it is part of the trunk

Changes for: interlobar duct

Changes for: striated duct of salivary gland

Changes for: extraembryonic vascular system

Changes for: hepatic portal system

Changes for: renal portal system

  • Deleted
    • - renal portal system comment Function notes: function not well understood. 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

Changes for: renal portal vein

Changes for: trunk region of vertebral column

Changes for: metacarpal/tarsal-phalangeal joint

Changes for: intraembryonic coelom

  • Deleted
    • - intraembryonic coelom comment Editor notes: consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. Todo: check ZFA, which appears to be a structure present in adults
  • Added
    • + intraembryonic coelom editor note consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. Todo: check ZFA, which appears to be a structure present in adults

Changes for: rete ovarii

Changes for: fallopian tube

Changes for: parasphenoid-pterosphenoid joint

Changes for: sphenozygomatic suture

Changes for: occipitomastoid suture

Changes for: skin mucus

Changes for: parietomastoid suture

Changes for: sphenoparietal suture

Changes for: sphenofrontal suture

Changes for: intertrochanteric crest

Changes for: premaxillary-maxillary joint

Changes for: odontogenic mesenchyme

  • Deleted
    • - odontogenic mesenchyme comment Editor notes: we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme
  • Added
    • + odontogenic mesenchyme editor note we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme

Changes for: dental epithelium

  • Deleted
    • - dental epithelium comment Editor notes: see comments for dentail organ. Development notes: In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)[PMID:10954731]. Editor notes: todo - full developmental relationships
  • Added
    • + dental epithelium comment . Editor notes: todo - full developmental relationships
    • + dental epithelium editor note see comments for dentail organ. Development notes: In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)[PMID:10954731]

Changes for: upper primary molar tooth

Changes for: frontal-pterotic joint

Changes for: opercle-interopercle joint

Changes for: crop

  • Deleted
    • - crop comment Editor notes: we follow WP and place as part of the esophagus. Taxon notes: Aves specific structure - consider adding functional grouping class. Kardong: some cetaceans have a crop-like structure
  • Added
    • + crop comment Taxon notes: Aves specific structure - consider adding functional grouping class. Kardong: some cetaceans have a crop-like structure
    • + crop editor note we follow WP and place as part of the esophagus

Changes for: ruminant stomach

Changes for: roof of mouth

  • Deleted
    • - roof of mouth comment Editor notes: check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton
  • Added
    • + roof of mouth editor note check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton

Changes for: intertarsal joint

Changes for: incus pre-cartilage condensation

  • Deleted
    • - incus pre-cartilage condensation comment Editor notes: in EHDAA2 this develops from both mandibular and maxillary mesenchyme. We have still to extend homology relationships from quadrate/incus to their ontogenic precursors (
  • Added
    • + incus pre-cartilage condensation editor note in EHDAA2 this develops from both mandibular and maxillary mesenchyme. We have still to extend homology relationships from quadrate/incus to their ontogenic precursors (

Changes for: facial bone primordium

Changes for: mural trophectoderm

Changes for: infundibular recess of 3rd ventricle

Changes for: laryngotracheal groove

Changes for: pyramid of medulla oblongata

Changes for: pleuroperitoneal canal

Changes for: polar trophectoderm

Changes for: orbitosphenoid-prootic joint

Changes for: tooth enamel organ

  • Deleted
    • - tooth enamel organ comment Editor notes: some sources treat the dental organ as epithelium - we treat it as the mereological sum of dentail epithelium plus dental papilla (consistent with treatment in many AOs), but this may be revised.Development notes: NOT develeops_from NC[UBERONREF:0000002]. Alternate definitioon: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla. Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation[WP]
  • Added
    • + tooth enamel organ editor note some sources treat the dental organ as epithelium - we treat it as the mereological sum of dentail epithelium plus dental papilla (consistent with treatment in many AOs), but this may be revised.Development notes: NOT develeops_from NC[UBERONREF:0000002]. Alternate definitioon: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla. Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation[WP]

Changes for: autopalatine-vomer joint

Changes for: dentary-anguloarticular joint

Changes for: neonate stage

Changes for: parasphenoid-basioccipital joint

Changes for: pterosphenoid-orbitosphenoid joint

Changes for: ceratohyal-dorsal hypohyal joint

Changes for: epihyal-ceratohyal joint

Changes for: dorsal hypohyal-ventral hypohyal joint

Changes for: ceratohyal-ventral hypohyal joint

Changes for: dorsal hypohyal-urohyal joint

Changes for: inter-ventral hypohyal joint

Changes for: ventral hypohyal-urohyal joint

Changes for: quadrate-hyomandibula joint

Changes for: quadrate-metapterygoid joint

Changes for: presumptive neural plate

Changes for: intervertebral disk of sixth cervical vertebra

Changes for: intervertebral disk of fifth cervical vertebra

Changes for: intervertebral disk of fourth cervical vertebra

Changes for: intervertebral disk of third cervical vertebra

Changes for: intervertebral disk of atlas

Changes for: intervertebral disk of axis

Changes for: intervertebral disk of seventh cervical vertebra

Changes for: kidney rudiment

  • Deleted
    • - kidney rudiment comment Editor notes: class added for consistency with GO - consider merging with kidney mesenchyme.
  • Added

Changes for: muscle structure

Changes for: neuropore

Changes for: anterior visceral endoderm

Changes for: chorionic plate

Changes for: spongiotrophoblast layer

Changes for: mucosa of sphenoidal sinus

Changes for: cerebellum vermis lobule I

Changes for: epibranchial 3-pharyngobranchial 3 joint

Changes for: internal male genitalia

Changes for: hairline

Changes for: anatomical conduit

Changes for: genitourinary system

Changes for: chorionic villus

Changes for: pharyngeal pouch 4

Changes for: labyrinthine layer blood vessel

Changes for: hemopoietic organ

Changes for: blood vessel smooth muscle

  • Deleted
    • - blood vessel smooth muscle comment Function notes: Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
  • Added
    • + blood vessel smooth muscle function notes Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.

Changes for: iris smooth muscle

Changes for: renal vesicle

  • Deleted
    • - renal vesicle comment Editor notes: note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107
  • Added
    • + renal vesicle editor note note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap

Changes for: autopalatine-lateral ethmoid joint

Changes for: atrioventricular canal

Changes for: sinoatrial valve

Changes for: ductus venosus

Changes for: ureteric bud tip

Changes for: communicating artery

Changes for: interpedicular line

Changes for: ectopterygoid tooth

Changes for: entopterygoid tooth

Changes for: dermis

  • Deleted
    • - dermis comment Editor notes: Consider adding a layer-of-skin grouping class for all skin layers
  • Added
    • + dermis editor note Consider adding a layer-of-skin grouping class for all skin layers

Changes for: premaxillary tooth

Changes for: embryonic structure

Changes for: mesethmoid-premaxillary joint

Changes for: mesethmoid-frontal joint

Changes for: mesethmoid-nasal joint

Changes for: mesethmoid-lateral ethmoid joint

Changes for: interchondral joint

Changes for: joint of rib

Changes for: forelimb stylopod muscle

Changes for: hindlimb zeugopod muscle

Changes for: skin muscle

  • Deleted
    • - skin muscle comment Editor notes: review as part of general integumentary system review - part of skin, or more generally, integumental system
  • Added
    • + skin muscle editor note review as part of general integumentary system review - part of skin, or more generally, integumental system

Changes for: mesethmoid-vomer joint

Changes for: trabecular network of bone

Changes for: temporal part of head

Changes for: amniotic ectoderm

  • Deleted
    • - amniotic ectoderm SubClassOf extraembryonic tissue
    • - amniotic ectoderm comment Editor note: we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk—the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion.
  • Added
    • + amniotic ectoderm editor note we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk—the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion.

Changes for: placenta metrial gland

Changes for: rostral migratory stream

Changes for: amniotic mesoderm

  • Deleted
    • - amniotic mesoderm SubClassOf extraembryonic tissue
    • - amniotic mesoderm comment Editor note: we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk—the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion.
  • Added
    • + amniotic mesoderm editor note we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk—the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion.

Changes for: tooth of upper jaw

Changes for: chorionic mesenchyme

Changes for: mesoderm of yolk sac

Changes for: trophectoderm

  • Deleted
    • - trophectoderm comment Editor notes: distinction between trophectoderm and trophoblast unclear/inconsistent in many sources. AO notes: BTO has this has part of the trophoblast
  • Added

Changes for: vault of skull

  • Deleted
    • - vault of skull comment Editor notes: We follow http://www.ncbi.nlm.nih.gov/pubmed/11523816 (Morriss-Kay) in definingenumerating the components of the skull vault. Note that there is a conflict with Kardong; e.g. in fig 7.10, Kardong places the squamosal in the temporal series. We cannot place the vault as entirely part of the dermatocranium as it has a small splanchnocranium contribution and a sclerotomal contribution. Terminology notes. we include calvarium as a synonym, but Gray’s Anatomy’s list includes the Ethmoid and Sphenoid bone in the Calvaria. Some books (and HPO) state that calvaria consists of just the frontal bone, parietal bone, temporal bone, and occipital bone. Note vault may not be precisely equivalent to calvaria
  • Added
    • + vault of skull comment Terminology notes. we include calvarium as a synonym, but Gray’s Anatomy’s list includes the Ethmoid and Sphenoid bone in the Calvaria. Some books (and HPO) state that calvaria consists of just the frontal bone, parietal bone, temporal bone, and occipital bone. Note vault may not be precisely equivalent to calvaria
    • + vault of skull editor note We follow http://www.ncbi.nlm.nih.gov/pubmed/11523816 (Morriss-Kay) in definingenumerating the components of the skull vault. Note that there is a conflict with Kardong; e.g. in fig 7.10, Kardong places the squamosal in the temporal series. We cannot place the vault as entirely part of the dermatocranium as it has a small splanchnocranium contribution and a sclerotomal contribution

Changes for: metatarsophalangeal joint of pedal digit 5

Changes for: Reichert’s membrane

Changes for: extraembryonic ectoderm

  • Deleted
    • - extraembryonic ectoderm comment Editor note: we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk—the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion.
  • Added
    • + extraembryonic ectoderm editor note we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk—the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion.

Changes for: stylohyoid ligament

Changes for: interphalangeal joint of manus

Changes for: interphalangeal joint of pes

Changes for: interphalangeal joint of pedal digit 3

Changes for: interphalangeal joint of pedal digit 2

Changes for: interphalangeal joint of pedal digit 1

Changes for: interphalangeal joint of manual digit 1

Changes for: interphalangeal joint of manual digit 2

Changes for: interphalangeal joint of pedal digit 4

Changes for: interphalangeal joint of pedal digit 5

Changes for: interphalangeal joint of manual digit 4

Changes for: interphalangeal joint of manual digit 3

Changes for: life cycle stage

  • Deleted
    • - life cycle stage comment Editor notes: we map the ZFS unknown stage here as it is logically equivalent to saying some life cycle stage
  • Added

Changes for: interphalangeal joint of manual digit 5

Changes for: metacarpophalangeal joint of manual digit 1

Changes for: blastula stage

Changes for: metacarpophalangeal joint of manual digit 2

Changes for: metacarpophalangeal joint of manual digit 5

Changes for: metacarpophalangeal joint of manual digit 4

Changes for: metacarpophalangeal joint of manual digit 3

Changes for: metatarsophalangeal joint of pedal digit 3

Changes for: metatarsophalangeal joint of pedal digit 4

Changes for: metatarsophalangeal joint of pedal digit 2

Changes for: metatarsophalangeal joint of pedal digit 1

Changes for: dorsal anterior lateral line ganglion

Changes for: tract of brain

  • Deleted
    • - tract of brain comment Editor notes: the NIFSTD class ‘nerve tract’ is classified under ‘regional part of brain’, so it may seem like it belongs here, but actually includes spinal cord tracts
  • Added
    • + tract of brain editor note the NIFSTD class ‘nerve tract’ is classified under ‘regional part of brain’, so it may seem like it belongs here, but actually includes spinal cord tracts

Changes for: anal canal

  • Deleted
    • - anal canal comment Editor notes: requires alignment with EHDAA2 and complete developmental relationships
  • Added

Changes for: mouth

Changes for: intestine

  • Deleted
    • - intestine comment Editor notes: This class is probably too inclusive. Taxon notes: [in zebrafish] No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
  • Added
    • + intestine comment No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
    • + intestine editor note This class is probably too inclusive. Taxon notes: [in zebrafish]

Changes for: haemolymphatic fluid

Changes for: parietal endoderm

Changes for: meninx of midbrain

Changes for: meninx of telencephalon

Changes for: meninx of hindbrain

Changes for: meninx of diencephalon

Changes for: metapodial pad

Changes for: skeletal ligament

Changes for: smooth muscle of eye

Changes for: periosteum of epiphysis

Changes for: epithelium of rectum

Changes for: mesenchyme of yolk sac

Changes for: ligamentum arteriosum

Changes for: future meninx

  • Deleted
    • - future meninx comment Editor notes: decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx
  • Added
    • + future meninx editor note decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx

Changes for: metacarpus region

  • Deleted
    • - metacarpus region comment Editor notes: Note that along with FMA we treat this as a limb segment rather than a purely skeletal element. AO notes: Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
  • Added
    • + metacarpus region comment AO notes: Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
    • + metacarpus region editor note Note that along with FMA we treat this as a limb segment rather than a purely skeletal element

Changes for: cavity lining

  • Deleted
    • - cavity lining comment Editor notes: consider merging with serous membrane. AO notes: in MA this groups pericardium, pleura and periotoneal cavity lining
  • Added

Changes for: entire sense organ system

Changes for: ligament

Changes for: atlanto-occipital joint

Changes for: anatomical projection

  • Deleted
    • - anatomical projection comment Editor notes: should be declared sijoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)
  • Added
    • + anatomical projection editor note should be declared sijoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)

Changes for: anterior commissure anterior part

Changes for: pontine tegmentum

Changes for: regenerating anatomical structure

Changes for: subdivision of vertebral column

Changes for: caudal region of vertebral column

Changes for: sacral region of vertebral column

Changes for: lumbar region of vertebral column

Changes for: thoracic region of vertebral column

Changes for: cervical region of vertebral column

Changes for: process of vertebra

Changes for: posterior part of anterior commissure

Changes for: midbrain-hindbrain boundary

Changes for: heart primordium

Changes for: anterior neural tube

Changes for: dorsal fin

Changes for: dermatocranium

  • Deleted
    • - dermatocranium comment Editor notes: wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
  • Added
    • + dermatocranium editor note wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007

Changes for: suspensorium

  • Deleted
    • - suspensorium comment Editor notes: requires review, possible split; TAO/ZFA structure is splanchoncranium (but includes some dermal bones as parts). Note AAO also includes ‘palatoquadrate and suspensorium’ as a class
  • Added
    • + suspensorium editor note requires review, possible split; TAO/ZFA structure is splanchoncranium (but includes some dermal bones as parts). Note AAO also includes ‘palatoquadrate and suspensorium’ as a class

Changes for: keratin-based acellular structure

  • Deleted
    • - keratin-based acellular structure comment Editor note: should all structures composed primarily of keratin be classified here? At what stage of cornification are keratin-filled cells no longer considered cells
  • Added

Changes for: mammalian cervical vertebra 3

Changes for: equine glandular stomach

  • Deleted
    • - equine glandular stomach comment Editor notes: We have a distinct class for ‘glandular region of stomach’. We may want to merge into this class, even though this is not considered a distinct stomach.
  • Added
    • + equine glandular stomach editor note We have a distinct class for ‘glandular region of stomach’. We may want to merge into this class, even though this is not considered a distinct stomach.

Changes for: prepupa

Changes for: fascia

Changes for: arthropod hypopharynx

Changes for: arthropod tibia

  • Deleted
    • - arthropod tibia comment Editor notes: this term should be ceded to the arthropod anatomy ontology. Homology notes: homology of leg segments between groups are difficult to prove and are the source of much argument. Some authors posit up to eleven segments per leg for the most recent common ancestor of extant arthropods [1], but modern arthropods have eight or fewer. It has been argued [2][3] that the ancestral leg need not have been so complex, and that other events, such as the successive loss of function of a Hox-gene could result in parallel gains of leg segments.
  • Added
    • + arthropod tibia comment that the ancestral leg need not have been so complex, and that other events, such as the successive loss of function of a Hox-gene could result in parallel gains of leg segments.
    • + arthropod tibia editor note this term should be ceded to the arthropod anatomy ontology. Homology notes: homology of leg segments between groups are difficult to prove and are the source of much argument. Some authors posit up to eleven segments per leg for the most recent common ancestor of extant arthropods [1], but modern arthropods have eight or fewer. It has been argued [2][3]

Changes for: arthropod sternum

Changes for: gastro-splenic ligament

Changes for: tendon

Changes for: choledocho-duodenal junction

Changes for: camera-type eye

Changes for: forelimb bone

Changes for: extraembryonic endoderm

Changes for: upper lobe of lung

  • Deleted
    • - upper lobe of lung comment Editor notes: the logical definition must have a clause stating position relative to a lower lobe, otherwise a single lobed side (such as the left lobe in the mouse) trivially classifies as an upper lobe
  • Added
    • + upper lobe of lung editor note the logical definition must have a clause stating position relative to a lower lobe, otherwise a single lobed side (such as the left lobe in the mouse) trivially classifies as an upper lobe

Changes for: lower lobe of lung

Changes for: external ectoderm

  • Deleted
    • - external ectoderm comment Editor note: merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube). Development notes: (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
  • Added
    • + external ectoderm comment Development notes: (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
    • + external ectoderm editor note merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)

Changes for: metanephros

Changes for: perichordal bone

  • Deleted
    • - perichordal bone comment Editor notes: We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under ‘replacement bone’, for consistency with ZFA
  • Added
    • + perichordal bone editor note We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under ‘replacement bone’, for consistency with ZFA

Changes for: tricuspid valve cusp

Changes for: insect labrum

Changes for: head mesenchyme from mesoderm

Changes for: mandibular prominence

Changes for: stomach glandular epithelium

  • Deleted
    • - stomach glandular epithelium comment Editor notes: we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has ‘epithelium of gastric gland’, which is part of the gastric gland. Consider also: stomach glandular region as a part-of parent
  • Added
    • + stomach glandular epithelium editor note we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has ‘epithelium of gastric gland’, which is part of the gastric gland. Consider also: stomach glandular region as a part-of parent

Changes for: cuneate fasciculus of spinal cord

  • Deleted
    • - cuneate fasciculus of spinal cord comment editor note: check ontology structure, isa parentage to fasciculus of spinal cord should be inferred. TODO - change definition to be the whole of the CF in the SC
  • Added

Changes for: cranial appendage

  • Deleted
    • - cranial appendage comment Editor notes: revisit after CARO2 appendage issue is sorted. Note that antennae are appendages that protrude from the head
  • Added
    • + cranial appendage editor note revisit after CARO2 appendage issue is sorted. Note that antennae are appendages that protrude from the head

Changes for: spinal cord segment

  • Deleted
    • - spinal cord segment comment Editor notes: This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term
  • Added
    • + spinal cord segment editor note This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term

Changes for: cervical vertebra 1 anterior tubercle

Changes for: anterior tubercle of transverse process of cervical vertebra

Changes for: posterior tubercle of transverse process of cervical vertebra

Changes for: oropharyngeal papilla

Changes for: integumentary papilla

Changes for: cochlear ganglion

  • Deleted
    • - cochlear ganglion comment Editor notes: in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems
  • Added
    • + cochlear ganglion editor note in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems

Changes for: lens nucleus

Changes for: epiglottis

  • Deleted
    • - epiglottis comment Editor note: refine definition to better distinguish cartilage from the whole structure
  • Added

Changes for: renal medulla

Changes for: ulnar sesamoid bone

Changes for: myelin

Changes for: limbic system

Changes for: urorectal septum

Changes for: optic canal

Changes for: visual cortex

Changes for: integumentary skeleton

Changes for: extraembryonic mesoderm

Changes for: olfactory system

Changes for: paired limb/fin field

  • Deleted
    • - paired limb/fin field comment Editor notes: we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
  • Added
    • + paired limb/fin field editor note we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.

Changes for: median fin

Changes for: connecting stalk vasculature

Changes for: major vestibular gland

Changes for: regular connective tissue

  • Deleted
    • - regular connective tissue comment Editor notes: the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
  • Added
    • + regular connective tissue editor note the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).

Changes for: simple cuboidal epithelium

Changes for: organism subdivision

  • Deleted
    • - organism subdivision comment Editor note: Reflects CARO2. todo - check the inclusion of FMA ‘cardinal body part here’, and check child terms for consistency
  • Added
    • + organism subdivision editor note Reflects CARO2. todo - check the inclusion of FMA ‘cardinal body part here’, and check child terms for consistency

Changes for: extraembryonic structure

Changes for: tissue

  • Deleted
    • - tissue comment Editor note: changed label and definition to reflect CARO2
  • Added

Changes for: extraembryonic membrane

Changes for: connecting stalk mesoderm

Changes for: forelimb zeugopod skeleton

Changes for: carina of trachea

Changes for: frenulum of tongue

Changes for: posterior fontanelle

Changes for: supraglenoid tubercle

Changes for: ceratobranchial 5 tooth

Changes for: shell

  • Deleted
    • - shell comment Editor notes: may be obsoleted after integumental system overhaul
  • Added

Changes for: mandibular symphysis

Changes for: appendix testis

  • Deleted
    • - appendix testis comment Editor notes: the label hydatid of morgagni is ambiguous w.r.t male vs female. The ncita structure ‘hydatic of morgani[sic]’ is male and thus belongs here. See also ‘vesicular appendage of epoophoron’
  • Added
    • + appendix testis comment ‘ is male and thus belongs here. See also ‘vesicular appendage of epoophoron’
    • + appendix testis editor note the label hydatid of morgagni is ambiguous w.r.t male vs female. The ncita structure ‘hydatic of morgani[sic]

Changes for: interphalangeal joint

Changes for: trigeminal neural crest

Changes for: thymus primordium

  • Deleted
    • - thymus primordium comment Editor notes: we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn’t reflected in EHDAA2. Development notes: Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. Taxon notes: variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals[ISBN-10:0781714125]
  • Added
    • + thymus primordium editor note we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn’t reflected in EHDAA2. Development notes: Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. Taxon notes: variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals[ISBN-10:0781714125]

Changes for: pedal digit metatarsal cartilage element

  • Deleted
    • - pedal digit metatarsal cartilage element comment Editor note: EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton
  • Added
    • + pedal digit metatarsal cartilage element editor note EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton

Changes for: venous dural sinus

Changes for: valve of inferior vena cava

Changes for: urinary system structure

  • Deleted
    • - urinary system structure comment editor note: note that we do not explicitly exclude entities such as WBbt:0005777 (excretory duct) here, but they will be automatically classified under this class after reasoning
  • Added
    • + urinary system structure editor note note that we do not explicitly exclude entities such as WBbt:0005777 (excretory duct) here, but they will be automatically classified under this class after reasoning

Changes for: gastrointestinal system

Changes for: frontonasal suture

Changes for: dorsal telencephalic commissure

Changes for: nasal cavity epithelium

  • Deleted
    • - nasal cavity epithelium comment Editor note: this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism
  • Added
    • + nasal cavity epithelium editor note this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism

Changes for: terminal part of digestive tract

Changes for: adrenal/interrenal gland

Changes for: interrenal gland

  • Deleted
    • - interrenal gland comment Editor notes: check isa - not a true gland? There are two types of interrenal cells identified (1) The noradrenaline type, which contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane. (2) The adrenaline type, in which the vesicles are smaller and contain homogenous electron-lucent granules that are separated from the vesicular membrane by a visible – halo http://dev.biologists.org/content/130/10/2107.full
  • Added
    • + interrenal gland editor note check isa - not a true gland? There are two types of interrenal cells identified (1) The noradrenaline type, which contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane. (2) The adrenaline type, in which the vesicles are smaller and contain homogenous electron-lucent granules that are separated from the vesicular membrane by a visible – halo http://dev.biologists.org/content/130/10/2107.full

Changes for: cerebellar commissure

Changes for: root of cranial nerve

Changes for: arthropod oviduct

  • Deleted
    • - arthropod oviduct comment Editor notes: this term should be ceded to the arthropod anatomy ontology. Note that this is not even analagous to the class ‘oviduct’ in uberon (as the oviduct is the entire tube, from gonad to outside)
  • Added
    • + arthropod oviduct editor note this term should be ceded to the arthropod anatomy ontology. Note that this is not even analagous to the class ‘oviduct’ in uberon (as the oviduct is the entire tube, from gonad to outside)

Changes for: inter-basipterygium joint

Changes for: inter-premaxillary joint

Changes for: hyomandibular-otic region joint

Changes for: orbitosphenoid-lateral ethmoid joint

Changes for: autopalatine-maxillary joint

Changes for: vertebra 4-vertebra 5 joint

Changes for: hyomandibula-metapterygoid joint

Changes for: chorion-containing eggshell

Changes for: plantaris

  • Deleted
    • - plantaris comment Editor notes: todo - coordinate with phenoscape-ext on representation of amphibian plantaris longus and profundus
  • Added
    • + plantaris editor note todo - coordinate with phenoscape-ext on representation of amphibian plantaris longus and profundus

Changes for: manual digit mesenchyme

  • Deleted
    • - manual digit mesenchyme comment Editor notes: In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation
  • Added
    • + manual digit mesenchyme editor note In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation

Changes for: acetabular labrum

  • Deleted
    • - acetabular labrum comment Function notes: Its function is to deepen the acetabulum, making it more difficult for the head of the femur to slip out of place (sublux). Structure notes: some sources treat this as fibrocartilage
  • Added

Changes for: pectoral complex muscle

Changes for: calcaneofibular ligament

Changes for: medial ligament of ankle joint

Changes for: talofibular ligament

Changes for: extraembryonic tissue

Changes for: talocalcaneonavicular joint

Changes for: calcaneocuboid joint