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NT: lateral malleolus; NTs for some fused tarsals and carpals, incl. …
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…centrocarpal. fixes 154, 155
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@cmungall
cmungall committed Nov 20, 2012
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6 changes: 6 additions & 0 deletions mod/uberon-bridge-to-fma.obo
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Expand Up @@ -20287,6 +20287,12 @@ property_value: IAO:0000589 "distal epiphysis of fibula (post-embryonic human)"
intersection_of: UBERON:0004410 ! distal epiphysis of fibula intersection_of: UBERON:0004410 ! distal epiphysis of fibula
intersection_of: part_of NCBITaxon:9606 intersection_of: part_of NCBITaxon:9606


[Term]
id: FMA:35502 ! lateral malleolus
property_value: IAO:0000589 "lateral malleolus of fibula (post-embryonic human)" xsd:string
intersection_of: UBERON:0012291 ! lateral malleolus of fibula
intersection_of: part_of NCBITaxon:9606

[Term] [Term]
id: FMA:23362 ! Proximal epiphysis of humerus id: FMA:23362 ! Proximal epiphysis of humerus
property_value: IAO:0000589 "proximal epiphysis of humerus (post-embryonic human)" xsd:string property_value: IAO:0000589 "proximal epiphysis of humerus (post-embryonic human)" xsd:string
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26 changes: 26 additions & 0 deletions mod/uberon-bridge-to-fma.owl
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Expand Up @@ -26938,6 +26938,26 @@






<!-- http://purl.obolibrary.org/obo/FMA_35502 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/FMA_35502">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0012291"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:35502</oboInOwl:id>
<obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">lateral malleolus of fibula (post-embryonic human)</obo:IAO_0000589>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/FMA_37018 --> <!-- http://purl.obolibrary.org/obo/FMA_37018 -->


<owl:Class rdf:about="http://purl.obolibrary.org/obo/FMA_37018"> <owl:Class rdf:about="http://purl.obolibrary.org/obo/FMA_37018">
Expand Down Expand Up @@ -114998,6 +115018,12 @@






<!-- http://purl.obolibrary.org/obo/UBERON_0012291 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0012291"/>



<!-- http://purl.obolibrary.org/obo/UBERON_1000019 --> <!-- http://purl.obolibrary.org/obo/UBERON_1000019 -->


<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_1000019"/> <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_1000019"/>
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42 changes: 38 additions & 4 deletions uberon-simple.obo
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@@ -1,6 +1,6 @@
format-version: 1.2 format-version: 1.2
data-version: 2012-11-21 data-version: 2012-11-21
data-version: 2012-11-19 data-version: 2012-11-20
subsetdef: cyclostome_subset "cyclostome structures" subsetdef: cyclostome_subset "cyclostome structures"
subsetdef: defined_by_ordinal_series "classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology" subsetdef: defined_by_ordinal_series "classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology"
subsetdef: developmental_classification "developmental_classification" subsetdef: developmental_classification "developmental_classification"
Expand Down Expand Up @@ -27559,6 +27559,7 @@ relationship: part_of UBERON:0005334 ! oral lamina propria
id: UBERON:0001831 id: UBERON:0001831
name: parotid gland name: parotid gland
def: "The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]." [Wikipedia:Parotid_gland] def: "The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]." [Wikipedia:Parotid_gland]
comment: The mouse parotid, exorbital lacrimal gland and exocrine pancreas have similar histological appearances[ISBN10:0123813611]
subset: uberon_slim subset: uberon_slim
synonym: "glandula parotidea" RELATED LATIN [Wikipedia:Parotid_gland] synonym: "glandula parotidea" RELATED LATIN [Wikipedia:Parotid_gland]
synonym: "parotid" EXACT [] synonym: "parotid" EXACT []
Expand Down Expand Up @@ -27589,7 +27590,7 @@ property_value: homology_notes "The most common oral glands in mammals are the s
id: UBERON:0001832 id: UBERON:0001832
name: sublingual gland name: sublingual gland
def: "The sublingual glands are salivary glands in the mouth. They lie anterior to the submandibular gland under the tongue, beneath the mucous membrane of the floor of the mouth. They are drained by 8-20 excretory ducts called the ducts of Rivinus. The largest duct, the sublingual duct (of Bartholin) joins the submandibular duct to drain through the sublingual caruncle. The sublingual gland consists mostly of Mucous acini capped with serous demilunes and is therefore categorized as a mixed gland. Most of the remaining small sublingual ducts open separately into the mouth on an elevated crest of mucous membrane, the sublingual fold, caused by the gland and on either side of the frenulum linguae. The chorda tympani nerve is secretomotor to the sublingual glands. [WP,unvetted]." [Wikipedia:Sublingual_gland] def: "The sublingual glands are salivary glands in the mouth. They lie anterior to the submandibular gland under the tongue, beneath the mucous membrane of the floor of the mouth. They are drained by 8-20 excretory ducts called the ducts of Rivinus. The largest duct, the sublingual duct (of Bartholin) joins the submandibular duct to drain through the sublingual caruncle. The sublingual gland consists mostly of Mucous acini capped with serous demilunes and is therefore categorized as a mixed gland. Most of the remaining small sublingual ducts open separately into the mouth on an elevated crest of mucous membrane, the sublingual fold, caused by the gland and on either side of the frenulum linguae. The chorda tympani nerve is secretomotor to the sublingual glands. [WP,unvetted]." [Wikipedia:Sublingual_gland]
comment: This class was created automatically from a combination of ontologies comment: Single lobed in mouse; largest acini of the 3 rodent salivary glands. In human and mouse, secretions are predominantly mucinous[ISBN10:0123813611]
subset: uberon_slim subset: uberon_slim
synonym: "ductus sublingualis" EXACT [] synonym: "ductus sublingualis" EXACT []
synonym: "glandula sublingualis" RELATED LATIN [Wikipedia:Sublingual_gland] synonym: "glandula sublingualis" RELATED LATIN [Wikipedia:Sublingual_gland]
Expand Down Expand Up @@ -123850,7 +123851,7 @@ relationship: part_of UBERON:0003823 ! hindlimb zeugopod
[Term] [Term]
id: UBERON:0011113 id: UBERON:0011113
name: inferior tibiofibular joint name: inferior tibiofibular joint
def: "The inferior tibiofibular articulation (tibiofibular syndesmosis) is formed by the rough, convex surface of the medial side of the lower end of the fibula, and a rough concave surface on the lateral side of the tibia. Below, to the extent of about 4 mm. these surfaces are smooth, and covered with cartilage, which is continuous with that of the ankle-joint. The ligaments are: Anterior ligament of the lateral malleolus Posterior ligament of the lateral malleolus Inferior transverse ligament of the tibiofibular syndesmosis Interosseous ligament" [Wikipedia:Inferior_tibiofibular_articulation] def: "The inferior tibiofibular articulation (tibiofibular syndesmosis) is formed by the rough, convex surface of the medial side of the lower end of the fibula, and a rough concave surface on the lateral side of the tibia. Below, to the extent of about 4 mm. these surfaces are smooth, and covered with cartilage, which is continuous with that of the ankle-joint. The ligaments are: Anterior ligament of the lateral malleolus, Posterior ligament of the lateral malleolus, Inferior transverse ligament of the tibiofibular syndesmosis, Interosseous ligament" [Wikipedia:Inferior_tibiofibular_articulation]
synonym: "distal tibiofibular joint" EXACT [FMA:10465] synonym: "distal tibiofibular joint" EXACT [FMA:10465]
synonym: "inferior tibiofibular articulation" RELATED [Wikipedia:Inferior_tibiofibular_articulation] synonym: "inferior tibiofibular articulation" RELATED [Wikipedia:Inferior_tibiofibular_articulation]
synonym: "syndesmosis tibiofibularis" EXACT LATIN [FMA:TA] synonym: "syndesmosis tibiofibularis" EXACT LATIN [FMA:TA]
Expand Down Expand Up @@ -130254,7 +130255,8 @@ id: UBERON:0012131
name: centrale name: centrale
def: "Endochondral bone located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE]." [PHENOSCAPE:AMAO] def: "Endochondral bone located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE]." [PHENOSCAPE:AMAO]
comment: Usage notes: This term corresponds both to the navicular bone in the pes and the similar central carpals in the manus. AO notes: the FMA term is under 'general anatomical term'. comment: Usage notes: This term corresponds both to the navicular bone in the pes and the similar central carpals in the manus. AO notes: the FMA term is under 'general anatomical term'.
synonym: "os centrale" EXACT [] synonym: "central mesopodium bone" EXACT []
synonym: "os centrale" EXACT [FMA:77232]
xref: FMA:77232 xref: FMA:77232
is_a: UBERON:0003656 ! mesopodium bone is_a: UBERON:0003656 ! mesopodium bone
relationship: part_of UBERON:0009878 ! mesopodium skeleton relationship: part_of UBERON:0009878 ! mesopodium skeleton
Expand Down Expand Up @@ -131164,6 +131166,38 @@ relationship: develops_from UBERON:0009479 {source="EHDAA2"} ! ectoderm of bucco
relationship: part_of UBERON:0005356 ! Rathke's pouch relationship: part_of UBERON:0005356 ! Rathke's pouch
relationship: part_of UBERON:0011642 {source="EHDAA2"} ! oral epithelium from ectoderm relationship: part_of UBERON:0011642 {source="EHDAA2"} ! oral epithelium from ectoderm


[Term]
id: UBERON:0012288
name: centroquartal bone
def: "A tarsal bone that is formed from the fusion of the central and 4th tarsal bones." [UBERON:skansa]
is_a: UBERON:0001447 ! tarsal bone

[Term]
id: UBERON:0012289
name: fused tarsals 2 and 3
def: "A tarsal bone that is formed from the fusion of the 2nd and 3rd tarsal bones." [UBERON:skansa]
is_a: UBERON:0001447 ! tarsal bone

[Term]
id: UBERON:0012290
name: fused carpals 2 and 3
def: "A carpal bone that is formed from the fusion of the 2nd and 3rd carpal bones." [UBERON:skansa]
is_a: UBERON:0001435 ! carpal bone

[Term]
id: UBERON:0012291
name: lateral malleolus of fibula
synonym: "distal extremity of fibula" RELATED [Wikipedia:Malleolus#Lateral_malleolus]
synonym: "external malleolus of fibula" RELATED [Wikipedia:Malleolus#Lateral_malleolus]
synonym: "fibular malleolus" RELATED []
synonym: "lateral malleolus" BROAD [FMA:35502]
xref: FMA:35502
xref: SCTID:361795009
is_a: UBERON:0004120 ! mesoderm-derived structure
is_a: UBERON:0005055 ! zone of long bone
relationship: part_of UBERON:0004410 ! distal epiphysis of fibula
property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulats with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", seeAlso="UBERON:0004410", source="UBERON:skansa"}

[Term] [Term]
id: UBERON:1000000 id: UBERON:1000000
name: chin ventral margin name: chin ventral margin
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44 changes: 41 additions & 3 deletions uberon-taxmod-amniote.obo
View file
Expand Up @@ -29416,6 +29416,7 @@ id: UBERON:0001831
name: parotid gland name: parotid gland
namespace: uberon namespace: uberon
def: "The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]." [Wikipedia:Parotid_gland] def: "The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]." [Wikipedia:Parotid_gland]
comment: The mouse parotid, exorbital lacrimal gland and exocrine pancreas have similar histological appearances[ISBN10:0123813611]
subset: uberon_slim ! Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms subset: uberon_slim ! Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms
synonym: "glandula parotidea" RELATED LATIN [Wikipedia:Parotid_gland] synonym: "glandula parotidea" RELATED LATIN [Wikipedia:Parotid_gland]
synonym: "parotid" EXACT [] synonym: "parotid" EXACT []
Expand Down Expand Up @@ -29448,7 +29449,7 @@ id: UBERON:0001832
name: sublingual gland name: sublingual gland
namespace: uberon namespace: uberon
def: "The sublingual glands are salivary glands in the mouth. They lie anterior to the submandibular gland under the tongue, beneath the mucous membrane of the floor of the mouth. They are drained by 8-20 excretory ducts called the ducts of Rivinus. The largest duct, the sublingual duct (of Bartholin) joins the submandibular duct to drain through the sublingual caruncle. The sublingual gland consists mostly of Mucous acini capped with serous demilunes and is therefore categorized as a mixed gland. Most of the remaining small sublingual ducts open separately into the mouth on an elevated crest of mucous membrane, the sublingual fold, caused by the gland and on either side of the frenulum linguae. The chorda tympani nerve is secretomotor to the sublingual glands. [WP,unvetted]." [Wikipedia:Sublingual_gland] def: "The sublingual glands are salivary glands in the mouth. They lie anterior to the submandibular gland under the tongue, beneath the mucous membrane of the floor of the mouth. They are drained by 8-20 excretory ducts called the ducts of Rivinus. The largest duct, the sublingual duct (of Bartholin) joins the submandibular duct to drain through the sublingual caruncle. The sublingual gland consists mostly of Mucous acini capped with serous demilunes and is therefore categorized as a mixed gland. Most of the remaining small sublingual ducts open separately into the mouth on an elevated crest of mucous membrane, the sublingual fold, caused by the gland and on either side of the frenulum linguae. The chorda tympani nerve is secretomotor to the sublingual glands. [WP,unvetted]." [Wikipedia:Sublingual_gland]
comment: This class was created automatically from a combination of ontologies comment: Single lobed in mouse; largest acini of the 3 rodent salivary glands. In human and mouse, secretions are predominantly mucinous[ISBN10:0123813611]
subset: uberon_slim ! Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms subset: uberon_slim ! Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms
synonym: "Rivinus gland" RELATED [BTO:0001315] synonym: "Rivinus gland" RELATED [BTO:0001315]
synonym: "Rivinus' gland" EXACT [] synonym: "Rivinus' gland" EXACT []
Expand Down Expand Up @@ -134952,7 +134953,7 @@ intersection_of: part_of UBERON:0003823 ! hindlimb zeugopod
id: UBERON:0011113 id: UBERON:0011113
name: inferior tibiofibular joint name: inferior tibiofibular joint
namespace: uberon namespace: uberon
def: "The inferior tibiofibular articulation (tibiofibular syndesmosis) is formed by the rough, convex surface of the medial side of the lower end of the fibula, and a rough concave surface on the lateral side of the tibia. Below, to the extent of about 4 mm. these surfaces are smooth, and covered with cartilage, which is continuous with that of the ankle-joint. The ligaments are: Anterior ligament of the lateral malleolus Posterior ligament of the lateral malleolus Inferior transverse ligament of the tibiofibular syndesmosis Interosseous ligament" [Wikipedia:Inferior_tibiofibular_articulation] def: "The inferior tibiofibular articulation (tibiofibular syndesmosis) is formed by the rough, convex surface of the medial side of the lower end of the fibula, and a rough concave surface on the lateral side of the tibia. Below, to the extent of about 4 mm. these surfaces are smooth, and covered with cartilage, which is continuous with that of the ankle-joint. The ligaments are: Anterior ligament of the lateral malleolus, Posterior ligament of the lateral malleolus, Inferior transverse ligament of the tibiofibular syndesmosis, Interosseous ligament" [Wikipedia:Inferior_tibiofibular_articulation]
synonym: "distal tibiofibular joint" EXACT [FMA:10465] synonym: "distal tibiofibular joint" EXACT [FMA:10465]
synonym: "inferior tibiofibular articulation" RELATED [Wikipedia:Inferior_tibiofibular_articulation] synonym: "inferior tibiofibular articulation" RELATED [Wikipedia:Inferior_tibiofibular_articulation]
synonym: "syndesmosis tibiofibularis" EXACT LATIN [FMA:TA] synonym: "syndesmosis tibiofibularis" EXACT LATIN [FMA:TA]
Expand Down Expand Up @@ -142405,7 +142406,8 @@ name: centrale
namespace: uberon namespace: uberon
def: "Endochondral bone located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE]." [PHENOSCAPE:AMAO] def: "Endochondral bone located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE]." [PHENOSCAPE:AMAO]
comment: Usage notes: This term corresponds both to the navicular bone in the pes and the similar central carpals in the manus. AO notes: the FMA term is under 'general anatomical term'. comment: Usage notes: This term corresponds both to the navicular bone in the pes and the similar central carpals in the manus. AO notes: the FMA term is under 'general anatomical term'.
synonym: "os centrale" EXACT [] synonym: "central mesopodium bone" EXACT []
synonym: "os centrale" EXACT [FMA:77232]
xref: FMA:77232 xref: FMA:77232
is_a: UBERON:0003656 ! mesopodium bone is_a: UBERON:0003656 ! mesopodium bone
relationship: part_of UBERON:0009878 ! mesopodium skeleton relationship: part_of UBERON:0009878 ! mesopodium skeleton
Expand Down Expand Up @@ -143458,6 +143460,42 @@ relationship: part_of UBERON:0011642 ! oral epithelium from ectoderm
intersection_of: UBERON:0007499 ! epithelial sac intersection_of: UBERON:0007499 ! epithelial sac
intersection_of: part_of UBERON:0005356 ! Rathke's pouch intersection_of: part_of UBERON:0005356 ! Rathke's pouch


[Term]
id: UBERON:0012288
name: centroquartal bone
namespace: uberon
def: "A tarsal bone that is formed from the fusion of the central and 4th tarsal bones." [UBERON:skansa]
is_a: UBERON:0001447 ! tarsal bone

[Term]
id: UBERON:0012289
name: fused tarsals 2 and 3
namespace: uberon
def: "A tarsal bone that is formed from the fusion of the 2nd and 3rd tarsal bones." [UBERON:skansa]
is_a: UBERON:0001447 ! tarsal bone

[Term]
id: UBERON:0012290
name: fused carpals 2 and 3
namespace: uberon
def: "A carpal bone that is formed from the fusion of the 2nd and 3rd carpal bones." [UBERON:skansa]
is_a: UBERON:0001435 ! carpal bone

[Term]
id: UBERON:0012291
name: lateral malleolus of fibula
namespace: uberon
synonym: "distal extremity of fibula" RELATED [Wikipedia:Malleolus#Lateral_malleolus]
synonym: "external malleolus of fibula" RELATED [Wikipedia:Malleolus#Lateral_malleolus]
synonym: "fibular malleolus" RELATED []
synonym: "lateral malleolus" BROAD [FMA:35502]
xref: FMA:35502
xref: SCTID:361795009
is_a: UBERON:0004120 ! mesoderm-derived structure
is_a: UBERON:0005055 ! zone of long bone
relationship: part_of UBERON:0004410 ! distal epiphysis of fibula
property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulats with the lateral side of the distal tibia." xsd:string

[Term] [Term]
id: UBERON:1000000 id: UBERON:1000000
name: chin ventral margin name: chin ventral margin
Expand Down

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