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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Replace ZFA-sourced defs with TAO generalized def if available #64

Closed cmungall closed 12 years ago

cmungall commented 12 years ago

Uberon has 128 text defs that are taken directly from ZFA or in which the ZFA text was used. For 7 of these, there was a TAO-sourced definition that should be used in its place (or generalized further).


[Term]
id: UBERON:0004747
name: supraoccipital bone
alt_id: UBERON:0005237
def: "In humans: a bone on the dorsal side of the great foramen of the skull, usually forming a part of the occipital in the adult, but distinct in the young[DF]. In teleosts: Large shield-shaped unpaired median cartilage bone that contact the parietal anteriorly, and the exocciptial and epiotic laterally. Forms the posterodorsal most point of the cranium. The supraoccipital usually bears a crest that extends posterodorsally." [ZFA:0000595]
comment: Taxon notes (via VHOG): See Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution, Fourth Edition (2006) McGraw-Hill, p.237 Table 7.1; we follow 
subset: vertebrate_core
synonym: "supraoccipital" EXACT [VHOG:0001150]
xref: ZFA:0000595 ! supraoccipital
xref: VHOG:0001150 ! supraoccipital bone
xref: MA:0001474 ! supraoccipital bone
is_a: UBERON:0002513 ! endochondral bone
relationship: part_of UBERON:0002241 ! chondrocranium
relationship: part_of UBERON:0001703 ! neurocranium
relationship: part_of UBERON:0005902 {source="TAO"} ! occipital region
relationship: part_of UBERON:0001676 {source="Kardong", gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! occipital bone
xref: SCTID:95947006 ! Entire supraoccipital bone
xref: TAO:0000595 ! supraoccipital
relationship: develops_from UBERON:0011162 ! supraoccipital bone cartilaginous condensation
property_value: external_definition "Endochondral bone that is located at the dorsal part of the occipital region of the cranium or the dorso-posterior part of the skull. It forms the dorsal margin of the foramen magnum. Commonly the supraoccipital articulates with the parietals anteriorly, the epiotics laterally, and the exoccipitals posteroventrally. The supraoccipital is an unpaired median bone.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000595", date_retrieved="2012-08-14", source="TAO:GA_TG"}
property_value: axiom_lost_from_external_ontology "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000595", date_retrieved="2012-08-14"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps supraoccipital-parietal joint (TAO:0005264)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000595", date_retrieved="2012-08-14"}
synonym: "acrinial@fr" RELATED [TAO:0000595]
synonym: "acrinioste@fr" RELATED [TAO:0000595]
synonym: "supraoccipital@fr" RELATED [TAO:0000595]

[Term]
id: UBERON:0001692
name: basioccipital bone
def: "Large median unpaired cartilage bone that contacts the exocciptal, epiotic and pterotic dorsally, and the parasphenoid anteriorly. Forms the posteroventral hind margin of the cranium, articulates with the centrum of the first vertebra. Bears a posteroventral pharyngeal process that is flattened ventrally and opposes the pharyngeal teeth of the fifth pair of ceratobranchials[ZFA]." [Wikipedia:Basilar_part_of_occipital_bone, ZFIN:curator]
comment: TODO - check FMA
subset: uberon_slim
subset: vertebrate_core
synonym: "basioccipital bone" EXACT []
synonym: "basioccipital" EXACT []
synonym: "basi-occipital" EXACT []
synonym: "basilar part of occipital bone" EXACT []
xref: AAO:0000039 ! basioccipital
xref: FMA:52858 ! Basilar part of occipital bone
xref: VHOG:0001152 ! basioccipital bone
xref: MA:0001462 ! basioccipital bone
xref: TAO:0000472 ! basioccipital
xref: ZFA:0000472 ! basioccipital
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c4/Parsbasilaris%28young%29.PNG/200px-Parsbasilaris%28young%29.PNG
xref: EMAPA:18705 ! basioccipital bone
is_a: UBERON:0002513 ! endochondral bone
relationship: part_of UBERON:0005902 {source="TAO"} ! occipital region
relationship: part_of UBERON:0001676 {source="Kardong", gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! occipital bone
relationship: part_of UBERON:0002517 {source="FMA"} ! basicranium
relationship: part_of UBERON:0002241 ! chondrocranium
relationship: develops_from UBERON:0006209 ! basioccipital cartilage condensation
xref: SCTID:138976007 ! Entire basilar part of occipital bone
synonym: "pars basilaris ossis occipitalis" RELATED LATIN [Wikipedia:Basilar_part_of_occipital_bone]
xref: http://upload.wikimedia.org/wikipedia/commons/c/c4/Parsbasilaris%28young%29.PNG
property_value: external_definition "An unpaired medial bone contributing to the ventral margin of the foramen magnum that extends into the floor of the brain cavity. It can contribute to the centromedial portion of the occipital condyle.[AAO]" xsd:string {ontology="AAO", external_class="AAO:0000039", date_retrieved="2012-06-20", source="AAO:EJS"}
property_value: external_definition "Chondral bone that articulates with the exoccipitals dorsally, the prootics anteriorly, the parasphenoid ventrally, and the first free vertebra posteriorly. The basioccipital forms the floor of the foramen magnum. The basioccipital is an unpaired medial bone.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000472", date_retrieved="2012-08-14", source="TAO:GA_TG"}
property_value: axiom_lost_from_external_ontology "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000472", date_retrieved="2012-08-14"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps parasphenoid-basioccipital joint (TAO:0001832)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000472", date_retrieved="2012-08-14"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps basioccipital-exoccipital joint (TAO:0002038)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000472", date_retrieved="2012-08-14"}
synonym: "basinial@fr" RELATED [TAO:0000472]
synonym: "basinioste@fr" RELATED [TAO:0000472]
synonym: "basioccipital@fr" RELATED [TAO:0000472]

[Term]
id: UBERON:0001703
name: neurocranium
def: "Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof." [Wikipedia:Neuroranium, ZFA:0001580, PMID:11523816]
comment: Development notes: The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. Composition notes: It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton[WP] AO notes: It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
subset: uberon_slim
subset: vertebrate_core
synonym: "brain box" EXACT []
synonym: "brain case" RELATED [ZFA:0001580]
synonym: "braincase" RELATED [ZFA:0001580]
synonym: "brain pan" RELATED [http://www.thefreedictionary.com/braincase]
xref: MA:0000317 ! chondrocranium
xref: FMA:53672 ! Neurocranium
xref: TAO:0001580 ! neurocranium
xref: ZFA:0001580 ! neurocranium
xref: XAO:0003170 ! neurocranium
xref: EHDAA2:0000243 ! chondrocranium
xref: AAO:0010153 ! neurocranium
is_a: UBERON:0011158 {source="FMA"} ! subdivision of skull
relationship: part_of UBERON:0003128 ! cranium
relationship: develops_from UBERON:0004761 ! cartilaginous neurocranium
relationship: encloses UBERON:0000955 ! brain
xref: SCTID:361731002 ! Entire neurocranium
property_value: external_definition "Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001580", date_retrieved="2012-08-14", source="TAO:MAH"}

[Term]
id: UBERON:0006606
name: mandibular symphysis
def: "A cartilaginous joint that connects left and right mandibles/dentary bones" [ZFA:0005488, Wikipedia:Symphysis_menti]
comment: Taxon notes: in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible[Kardong] Editor notes: this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints
subset: vertebrate_core
synonym: "mental symphysis" RELATED [Wikipedia:Symphysis_menti]
synonym: "symphysis menti" EXACT [MA:0001490]
xref: AAO:0000277 ! mandibular symphysis
xref: ZFA:0005488 ! mandibular symphysis
xref: FMA:75779 ! Mandibular symphysis
xref: MA:0001490 ! symphysis menti
is_a: UBERON:0002216 {source="FMA"} ! symphysis
intersection_of: UBERON:0002213 ! cartilaginous joint
intersection_of: connects UBERON:0004742 {cardinality="2"} ! dentary
relationship: connects UBERON:0004742 {notes="connects adjacent mandibles"} ! dentary
relationship: part_of UBERON:0001710 ! lower jaw region
xref: TAO:0001851 ! mandibular symphysis
synonym: "symphysis mandibulae" RELATED LATIN [Wikipedia:Symphysis_menti]
xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png
property_value: external_definition "Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001851", date_retrieved="2012-08-14", source="TAO:wd"}
synonym: "dentary symphysis" EXACT [TAO:0001851]
synonym: "inter-dentary joint" EXACT [TAO:0001851]
synonym: "inter-mandibular joint" EXACT [TAO:0001851]

[Term]
id: UBERON:0004745
name: parasphenoid
def: "Long, unpaired median dermal bone that runs almost the entire length of the cranium. Contacts the prevomer anteriorly, and the prootic and basioccipital posteriorly. Anteriorly the parasphenoid is a long, thin bone that widens abruptly at the point of contact with the prootic." [ZFA:0000561]
synonym: "keilbein" RELATED [AAO:0000385]
synonym: "os parasphenoidale" RELATED [AAO:0000385]
synonym: "os sphenoideum" RELATED [AAO:0000385]
synonym: "parabasale" RELATED [AAO:0000385]
xref: AAO:0000385 ! parasphenoid
xref: ZFA:0000561 ! parasphenoid
is_a: UBERON:0002514 ! intramembranous bone
relationship: part_of UBERON:0003111 {source="ZFA"} ! sphenoid region
relationship: part_of UBERON:0003112 {source="ZFA"} ! olfactory region
relationship: part_of UBERON:0003113 {source="Kardong", notes="palatal series"} ! dermatocranium
relationship: overlaps UBERON:0001697 {source="ZFA-modified"} ! orbit
relationship: part_of UBERON:0001703 {source="ZFA"} ! neurocranium
xref: TAO:0000561 ! parasphenoid
property_value: external_definition "Azygous, dermal bone of intramembranous origin that underlies the ventral surface of the braincase in anurans and salamanders. In caecilians, the parasphenoid and other bones are fused to form the Os basale.[AAO]" xsd:string {ontology="AAO", external_class="AAO:0000385", date_retrieved="2012-06-20", source="AAO:LAP"}
property_value: axiom_lost_from_external_ontology "relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]" xsd:string {ontology="AAO", external_class="AAO:0000385", date_retrieved="2012-06-20"}
property_value: external_definition "Dermal bone that forms part of the base of the skull and the lateral walls of the braincase through its ascending processes. It may articulate with the vomer anteriorly, the prootics and exoccipitals laterally, and the basioccipital posteriorly. The parasphenoid is an elongate median bone.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000561", date_retrieved="2012-08-14", source="TAO:GA_TG"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps parasphenoid-basioccipital joint (TAO:0001832)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000561", date_retrieved="2012-08-14"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps parasphenoid-pterosphenoid joint (TAO:0002217)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000561", date_retrieved="2012-08-14"}

[Term]
id: UBERON:0006844
name: cusp of tooth
def: "Acellular anatomical structure that is a natural outgrowth, prominence, or point that is part of the surface of a tooth." [ZFA:0005434]
subset: vertebrate_core
synonym: "tooth cusp" EXACT [FMA:56481]
synonym: "cusp" BROAD []
xref: ZFA:0005434 ! tooth cusp
xref: FMA:56481 ! Cusp of tooth
is_a: UBERON:0000476 ! acellular anatomical structure
relationship: part_of UBERON:0003675 ! tooth crown
xref: SCTID:362107000 ! Entire cusp of tooth
xref: ncithesaurus:Tooth_Cusp ! tooth cusp
xref: TAO:0001973 ! tooth cusp
property_value: external_definition "Anatomical structure that is a natural outgrowth, prominence, or point that is part of the surface of a tooth.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001973", date_retrieved="2012-08-14", source="TAO:wd"}

[Term]
id: UBERON:0004865
name: teleost parietal bone
def: "Paired dermal bone that covers the hind part of the cranium, overlapping the dorsal edge of the sphenotic, pterotic, epiotic and the anterior edge of the supraoccipital. The parietal are overlapped anteriorly by the frontal." [ZFA:0000486]
synonym: "frontal bone" NARROW [FMA:52734]
synonym: "parietal bone" NARROW SENSU [TAO:0000486]
synonym: "post parietal" RELATED [ZFA:0000486]
synonym: "teleost parietal" EXACT []
xref: TAO:0000486 ! parietal bone
xref: ZFA:0000486 ! parietal bone
xref: VHOG:0001327 ! interparietal bone
is_a: UBERON:0002514 ! intramembranous bone
relationship: part_of UBERON:0003110 {source="ZFA"} ! otic region
relationship: part_of UBERON:0003113 {source="ZFA"} ! dermatocranium
relationship: part_of UBERON:0001703 {source="ZFA"} ! neurocranium
relationship: part_of UBERON:0004339 {source="PMID:11523816"} ! vault of skull
property_value: external_definition "Dermal bone that covers the otic region and may articulate with its antimere medially, with the frontal bone anteriorly, the pterotic laterally, the supraoccipital medio-posteriorly, and the epiotic and extrascapula latero-posteriorly. The parietal is a paired bone.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000486", date_retrieved="2012-08-14", source="TAO:GA_TG"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps posttemporal-parietal joint (TAO:0002059)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000486", date_retrieved="2012-08-14"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps inter-parietal joint (TAO:0005245)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000486", date_retrieved="2012-08-14"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps frontal-parietal joint (TAO:0005255)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000486", date_retrieved="2012-08-14"}
property_value: axiom_lost_from_external_ontology "relationship loss: overlaps supraoccipital-parietal joint (TAO:0005264)[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000486", date_retrieved="2012-08-14"}
synonym: "parietals" RELATED PLURAL [TAO:0000486]
cmungall commented 12 years ago

Following changes were made. Note that for some parts, e.g. skull more work needs to be done.

mellybelly commented 12 years ago

Wasila or Alex and Melissa to review and finalize these soon.