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1 parent de71536 commit 047aa5acf03e979147172615f57bce2ac120c47d @cmungall cmungall committed Sep 20, 2012
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2 README-editors.txt
@@ -14,7 +14,7 @@ Workflow:
make uberon-qc
git commit -m 'type message here'
git push
- # check Jenkins
+ # check Jenkins - http://build.berkeleybop.org/job/build-uberon/
Releases:
View
40 mod/uberon-bridge-to-aao.obo
@@ -2827,30 +2827,12 @@ intersection_of: UBERON:0011675 ! perichordal ring
intersection_of: part_of NCBITaxon:8292
[Term]
-id: AAO:0010777 ! perichordal bone
-property_value: IAO:0000589 "perichordal bone (amphibian)" xsd:string
-intersection_of: UBERON:0008909 ! perichordal bone
-intersection_of: part_of NCBITaxon:8292
-
-[Term]
id: AAO:0010445 ! perichondrium
property_value: IAO:0000589 "perichondrium (amphibian)" xsd:string
intersection_of: UBERON:0002222 ! perichondrium
intersection_of: part_of NCBITaxon:8292
[Term]
-id: AAO:0010779 ! perichondral bone
-property_value: IAO:0000589 "perichondral bone (amphibian)" xsd:string
-intersection_of: UBERON:0008913 ! perichondral bone
-intersection_of: part_of NCBITaxon:8292
-
-[Term]
-id: AAO:0010774 ! chondral bone
-property_value: IAO:0000589 "chondral bone (amphibian)" xsd:string
-intersection_of: UBERON:0008911 ! chondral bone
-intersection_of: part_of NCBITaxon:8292
-
-[Term]
id: AAO:0011018 ! basilar papilla
property_value: IAO:0000589 "spiral organ of cochlea (amphibian)" xsd:string
intersection_of: UBERON:0002227 ! spiral organ of cochlea
@@ -3092,8 +3074,26 @@ intersection_of: part_of NCBITaxon:8292
[Term]
id: AAO:0010768 ! replacement bone
-property_value: IAO:0000589 "endochondral bone tissue (amphibian)" xsd:string
-intersection_of: UBERON:0004763 ! endochondral bone tissue
+property_value: IAO:0000589 "replacement bone (amphibian)" xsd:string
+intersection_of: UBERON:0012075 ! replacement bone
+intersection_of: part_of NCBITaxon:8292
+
+[Term]
+id: AAO:0010774 ! chondral bone
+property_value: IAO:0000589 "chondral bone (amphibian)" xsd:string
+intersection_of: UBERON:0008911 ! chondral bone
+intersection_of: part_of NCBITaxon:8292
+
+[Term]
+id: AAO:0010777 ! perichordal bone
+property_value: IAO:0000589 "perichordal bone (amphibian)" xsd:string
+intersection_of: UBERON:0008909 ! perichordal bone
+intersection_of: part_of NCBITaxon:8292
+
+[Term]
+id: AAO:0010779 ! perichondral bone
+property_value: IAO:0000589 "perichondral bone (amphibian)" xsd:string
+intersection_of: UBERON:0008913 ! perichondral bone
intersection_of: part_of NCBITaxon:8292
[Term]
View
16 mod/uberon-bridge-to-aao.owl
@@ -12622,7 +12622,7 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0004763"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0012075"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_8292"/>
@@ -12631,7 +12631,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAO:0010768</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">endochondral bone tissue (amphibian)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">replacement bone (amphibian)</obo:IAO_0000589>
</owl:Class>
@@ -18762,12 +18762,6 @@
- <!-- http://purl.obolibrary.org/obo/UBERON_0004763 -->
-
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004763"/>
-
-
-
<!-- http://purl.obolibrary.org/obo/UBERON_0004765 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004765"/>
@@ -20073,6 +20067,12 @@
<!-- http://purl.obolibrary.org/obo/UBERON_0011879 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0011879"/>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/UBERON_0012075 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0012075"/>
</rdf:RDF>
View
16 mod/uberon-bridge-to-tao.owl
@@ -13532,7 +13532,7 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0004763"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0012075"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_32443"/>
@@ -13541,7 +13541,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TAO:0001637</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">endochondral bone tissue (teleost)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">replacement bone (teleost)</obo:IAO_0000589>
</owl:Class>
@@ -22368,12 +22368,6 @@
- <!-- http://purl.obolibrary.org/obo/UBERON_0004763 -->
-
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004763"/>
-
-
-
<!-- http://purl.obolibrary.org/obo/UBERON_0004765 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004765"/>
@@ -24492,6 +24486,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0012075 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0012075"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_1000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_1000010"/>
View
2 mod/uberon-bridge-to-xao.obo
@@ -2371,7 +2371,7 @@ intersection_of: UBERON:0010522 ! replacement element
intersection_of: part_of NCBITaxon:8353
[Term]
-id: XAO:0004017 ! endochondral elemen
+id: XAO:0004017 ! endochondral element
property_value: IAO:0000589 "endochondral element (xenopus)" xsd:string
intersection_of: UBERON:0010363 ! endochondral element
intersection_of: part_of NCBITaxon:8353
View
40 mod/uberon-bridge-to-zfa.obo
@@ -2977,30 +2977,12 @@ intersection_of: UBERON:0007862 ! perichordal tissue
intersection_of: part_of NCBITaxon:7954
[Term]
-id: ZFA:0001629 ! perichordal bone
-property_value: IAO:0000589 "perichordal bone (zebrafish)" xsd:string
-intersection_of: UBERON:0008909 ! perichordal bone
-intersection_of: part_of NCBITaxon:7954
-
-[Term]
id: ZFA:0001634 ! perichondrium
property_value: IAO:0000589 "perichondrium (zebrafish)" xsd:string
intersection_of: UBERON:0002222 ! perichondrium
intersection_of: part_of NCBITaxon:7954
[Term]
-id: ZFA:0001630 ! perichondral bone
-property_value: IAO:0000589 "perichondral bone (zebrafish)" xsd:string
-intersection_of: UBERON:0008913 ! perichondral bone
-intersection_of: part_of NCBITaxon:7954
-
-[Term]
-id: ZFA:0001693 ! chondral bone
-property_value: IAO:0000589 "chondral bone (zebrafish)" xsd:string
-intersection_of: UBERON:0008911 ! chondral bone
-intersection_of: part_of NCBITaxon:7954
-
-[Term]
id: ZFA:0000538 ! rib
property_value: IAO:0000589 "rib (zebrafish)" xsd:string
intersection_of: UBERON:0002228 ! rib
@@ -3410,8 +3392,26 @@ intersection_of: part_of NCBITaxon:7954
[Term]
id: ZFA:0001628 ! replacement bone
-property_value: IAO:0000589 "endochondral bone tissue (zebrafish)" xsd:string
-intersection_of: UBERON:0004763 ! endochondral bone tissue
+property_value: IAO:0000589 "replacement bone (zebrafish)" xsd:string
+intersection_of: UBERON:0012075 ! replacement bone
+intersection_of: part_of NCBITaxon:7954
+
+[Term]
+id: ZFA:0001693 ! chondral bone
+property_value: IAO:0000589 "chondral bone (zebrafish)" xsd:string
+intersection_of: UBERON:0008911 ! chondral bone
+intersection_of: part_of NCBITaxon:7954
+
+[Term]
+id: ZFA:0001629 ! perichordal bone
+property_value: IAO:0000589 "perichordal bone (zebrafish)" xsd:string
+intersection_of: UBERON:0008909 ! perichordal bone
+intersection_of: part_of NCBITaxon:7954
+
+[Term]
+id: ZFA:0001630 ! perichondral bone
+property_value: IAO:0000589 "perichondral bone (zebrafish)" xsd:string
+intersection_of: UBERON:0008913 ! perichondral bone
intersection_of: part_of NCBITaxon:7954
[Term]
View
16 mod/uberon-bridge-to-zfa.owl
@@ -3674,12 +3674,6 @@
- <!-- http://purl.obolibrary.org/obo/UBERON_0004763 -->
-
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004763"/>
-
-
-
<!-- http://purl.obolibrary.org/obo/UBERON_0004765 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0004765"/>
@@ -5816,6 +5810,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0012075 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0012075"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_1000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_1000010"/>
@@ -19254,7 +19254,7 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0004763"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0012075"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7954"/>
@@ -19263,7 +19263,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ZFA:0001628</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">endochondral bone tissue (zebrafish)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">replacement bone (zebrafish)</obo:IAO_0000589>
</owl:Class>
View
144 uberon-simple.obo
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: 2012-09-20
+data-version: 2012-09-21
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: developmental_classification "developmental_classification"
@@ -56,6 +56,7 @@ property_value: dc-contributor "Carlo Torniai" xsd:string
property_value: dc-contributor "Ceri Van Slyke" xsd:string
property_value: dc-contributor "David Hill" xsd:string
property_value: dc-contributor "David Osumi-Sutherland" xsd:string
+property_value: dc-contributor "Duncan Davidson" xsd:string
property_value: dc-contributor "Frederic Bastian" xsd:string
property_value: dc-contributor "George Gkoutos" xsd:string
property_value: dc-contributor "Hilmar Lapp" xsd:string
@@ -86,6 +87,7 @@ property_value: dc-creator "Melissa Haendel" xsd:string
property_value: dc-creator "Nizar Ibrahim" xsd:string
property_value: dc-creator "Wasila Dahdul" xsd:string
property_value: dc-description "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data." xsd:string
+property_value: dc-publisher http://obofoundry.org xsd:anyURI
property_value: dc-source http://dbpedia.org
property_value: dc-source http://en.wikipedia.org/wiki/
property_value: dc-source http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl
@@ -112,6 +114,7 @@ property_value: dc-source http://purl.obolibrary.org/obo/zfa.owl
property_value: dc-source http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop xsd:anyURI
property_value: dc-source http://wiki.phenotypercn.org/wiki/August_2012_Notes xsd:anyURI
property_value: dc-source http://www.brain-map.org
+property_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl
property_value: dc-source https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit xsd:anyURI
property_value: dc-source https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit xsd:anyURI
property_value: dc-source https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit xsd:anyURI
@@ -132,6 +135,7 @@ property_value: dc-source "ISBN:9780120749034 The laboratory rat" xsd:string
property_value: dc-source "ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte" xsd:string
property_value: dc-source "ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader" xsd:string
property_value: dc-source "ISBN:9780878932504 Developmental Biology" xsd:string
+property_value: dc-source "MESH" xsd:string
property_value: dc-source "PMID:11433360 Placental development: lessons from mouse mutants" xsd:string
property_value: dc-source "PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen" xsd:string
property_value: dc-title "Uber-anatomy ontology" xsd:string
@@ -48564,21 +48568,7 @@ id: UBERON:0002780
name: regional part of forebrain
def: "A regional part of brain that is part of a forebrain [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of forebrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of forebrain" EXACT [OBOL:automatic]
-synonym: "forebrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "forebrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "forebrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "forebrain regional part of brain" EXACT [OBOL:automatic]
synonym: "forebrain segment" EXACT [FMA:61996]
-synonym: "forebrain segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of forebrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of forebrain" EXACT [OBOL:automatic]
synonym: "segment of forebrain" EXACT [NIF_GrossAnatomy:birnlex_1677]
xref: FMA:61996
xref: NIF_GrossAnatomy:birnlex_1677
@@ -48626,64 +48616,7 @@ id: UBERON:0002784
name: regional part of diencephalon
def: "A regional part of brain that is part of a diencephalon [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "between brain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "between brain brain biological structure" EXACT [OBOL:automatic]
-synonym: "between brain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "between brain regional part of brain" EXACT [OBOL:automatic]
-synonym: "between brain segment of brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "diencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "diencephalon segment" EXACT [FMA:62005]
-synonym: "diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "interbrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "interbrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "interbrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "interbrain regional part of brain" EXACT [OBOL:automatic]
-synonym: "interbrain segment of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "mature diencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of between brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of diencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of interbrain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of between brain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of between brain" EXACT [OBOL:automatic]
-synonym: "segment of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of diencephalon" EXACT [NIF_GrossAnatomy:birnlex_1685]
xref: FMA:62005
xref: NIF_GrossAnatomy:birnlex_1685
xref: SCTID:119264001
@@ -48783,22 +48716,8 @@ id: UBERON:0002791
name: regional part of telencephalon
def: "A regional part of brain that is part of a telencephalon [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of telencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of telencephalon" EXACT [OBOL:automatic]
synonym: "segment of telencephalon" EXACT [NIF_GrossAnatomy:birnlex_1700]
-synonym: "telencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "telencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "telencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "telencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "telencephalon segment" EXACT [FMA:62374]
-synonym: "telencephalon segment of brain" EXACT [OBOL:automatic]
xref: FMA:62374
xref: NIF_GrossAnatomy:birnlex_1700
is_a: UBERON:0002780 ! regional part of forebrain
@@ -48825,22 +48744,6 @@ relationship: part_of UBERON:0005462 ! lower back
[Term]
id: UBERON:0002793
name: dorsal longitudinal fasciculus of pons
-def: "A dorsal longitudinal fasciculus that is part of a pons [Obol]." [OBOL:automatic]
-synonym: "bundle of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "bundle of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "dorsal longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "pons bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons of varolius fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
xref: FMA:72492
xref: NIF_GrossAnatomy:birnlex_1707
is_a: UBERON:0003045 ! dorsal longitudinal fasciculus
@@ -78353,26 +78256,20 @@ relationship: develops_from UBERON:0009617 {source="PMC1571569"} ! head paraxial
[Term]
id: UBERON:0004763
name: endochondral bone tissue
-def: "Replacement bone tissue that forms within cartilage[TAO]. Endochondral ossification is the formation of bone by the replacement of cartilage tissue with mineralized bone[GO]. cartilage is present during endochondral ossification. It is also an essential process during the rudimentary formation of long bones, the growth of the length of long bones, and the natural healing of bone fractures[WP]." [GO:0001958, Wikipedia:Endochondral_ossification]
-comment: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
+def: "Replacement bone tissue that forms within cartilage[VSAO, modified]." [GO:0001958, VSAO:0000145, Wikipedia:Endochondral_ossification]
+comment: The text and logical definition of this term was modified from the definition of 'endochondral bone' in ZFA. AO notes: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
subset: uberon_slim
subset: vertebrate_core
-synonym: "replacement bone" BROAD [ZFA:0001628]
-xref: AAO:0010768
xref: MA:0002836
-xref: TAO:0001637
-xref: ZFA:0001628
is_a: UBERON:0002481 ! bone tissue
-is_a: UBERON:0010522 {source="ZFA"} ! replacement element
disjoint_from: UBERON:0004764 ! intramembranous bone tissue
relationship: part_of UBERON:0002513 ! endochondral bone
-property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"}
[Term]
id: UBERON:0004764
name: intramembranous bone tissue
def: "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, Wikipedia:Intramembranous_ossification]
-comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type.
+comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
xref: MA:0002837
is_a: UBERON:0002481 ! bone tissue
relationship: develops_from UBERON:0003104 ! mesenchyme
@@ -109863,38 +109760,38 @@ property_value: external_definition "Intramembranous bone that forms superficial
id: UBERON:0008909
name: perichordal bone
def: "Bone element that is adjacent to the notochord." [VSAO:0000307]
-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
+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
synonym: "perichordal bone" RELATED [ZFA:0001629]
synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629]
xref: AAO:0010777
xref: TAO:0001639
xref: VSAO:0000307
xref: ZFA:0001629
-is_a: UBERON:0001474 ! bone
+is_a: UBERON:0012075 {notes="not in VSAO", source="ZFA"} ! replacement bone
disjoint_from: UBERON:0008913 ! perichondral bone
property_value: external_definition "Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001639", ontology="TAO", source="TAO:wd"}
[Term]
id: UBERON:0008911
name: chondral bone
def: "Replacement bone that forms within or surrounding a cartilaginous skeletal element." [zfin:curator]
-comment: Consider obsoleting
-synonym: "chondral bone" RELATED [ZFA:0001693]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The term was never introduced into VSAO.
xref: AAO:0010774
xref: ZFA:0001693
-is_a: UBERON:0004763 {source="ZFA"} ! endochondral bone tissue
+is_a: UBERON:0012075 {source="ZFA"} ! replacement bone
[Term]
id: UBERON:0008913
name: perichondral bone
def: "Bone element that is located on the surface of a cartilage element." [VSAO:0000308]
+comment: include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
synonym: "perichondral bone" RELATED [ZFA:0001630]
synonym: "perichondral bones" EXACT PLURAL [ZFA:0001630]
xref: AAO:0010779
xref: TAO:0001638
xref: VSAO:0000308
xref: ZFA:0001630
-is_a: UBERON:0001474 {source="VSAO"} ! bone
+is_a: UBERON:0008911 {source="ZFA"} ! chondral bone
relationship: develops_from UBERON:0002222 {source="ZFA"} ! perichondrium
property_value: axiom_lost_from_external_ontology "relationship loss: participates_in perichondral ossification (GO:0036073)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000308", ontology="VSAO"}
property_value: external_definition "Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001638", ontology="TAO", source="TAO:wd"}
@@ -128214,6 +128111,19 @@ relationship: part_of UBERON:0003216 {source="FMA"} ! hard palate
relationship: part_of UBERON:0012072 ! palatal part of dermatocranium
[Term]
+id: UBERON:0012075
+name: replacement bone
+def: "Bone that forms as a replacement of another structural tissue." [ZFA:0001628]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
+synonym: "replacement bones" EXACT PLURAL [ZFA:0001628]
+xref: AAO:0010768
+xref: TAO:0001637
+xref: ZFA:0001628
+is_a: UBERON:0001474 {source="ZFA"} ! bone
+is_a: UBERON:0010522 {source="ZFA"} ! replacement element
+property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"}
+
+[Term]
id: UBERON:1000000
name: chin ventral margin
def: "Subdivision of the head consisting of the area along the lower edge of the chin." [UBERON:EJS]
View
139 uberon-taxmod-amniote.obo
@@ -51645,21 +51645,7 @@ name: regional part of forebrain
namespace: uberon
def: "A regional part of brain that is part of a forebrain [Obol]." [OBOL:automatic]
subset: non_informative ! abstract class brought in to group ontology classes but not informative
-synonym: "anatomical structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of forebrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of forebrain" EXACT [OBOL:automatic]
-synonym: "forebrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "forebrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "forebrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "forebrain regional part of brain" EXACT [OBOL:automatic]
synonym: "forebrain segment" EXACT [FMA:61996]
-synonym: "forebrain segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of forebrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of forebrain" EXACT [OBOL:automatic]
synonym: "segment of forebrain" EXACT [NIF_GrossAnatomy:birnlex_1677]
xref: FMA:61996
xref: NIF_GrossAnatomy:birnlex_1677
@@ -51712,64 +51698,7 @@ name: regional part of diencephalon
namespace: uberon
def: "A regional part of brain that is part of a diencephalon [Obol]." [OBOL:automatic]
subset: non_informative ! abstract class brought in to group ontology classes but not informative
-synonym: "anatomical structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "between brain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "between brain brain biological structure" EXACT [OBOL:automatic]
-synonym: "between brain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "between brain regional part of brain" EXACT [OBOL:automatic]
-synonym: "between brain segment of brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "diencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "diencephalon segment" EXACT [FMA:62005]
-synonym: "diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "interbrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "interbrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "interbrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "interbrain regional part of brain" EXACT [OBOL:automatic]
-synonym: "interbrain segment of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "mature diencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of between brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of diencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of interbrain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of between brain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of between brain" EXACT [OBOL:automatic]
-synonym: "segment of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of diencephalon" EXACT [NIF_GrossAnatomy:birnlex_1685]
xref: FMA:62005
xref: NIF_GrossAnatomy:birnlex_1685
xref: SCTID:119264001
@@ -51880,22 +51809,8 @@ name: regional part of telencephalon
namespace: uberon
def: "A regional part of brain that is part of a telencephalon [Obol]." [OBOL:automatic]
subset: non_informative ! abstract class brought in to group ontology classes but not informative
-synonym: "anatomical structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of telencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of telencephalon" EXACT [OBOL:automatic]
synonym: "segment of telencephalon" EXACT [NIF_GrossAnatomy:birnlex_1700]
-synonym: "telencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "telencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "telencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "telencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "telencephalon segment" EXACT [FMA:62374]
-synonym: "telencephalon segment of brain" EXACT [OBOL:automatic]
xref: FMA:62374
xref: NIF_GrossAnatomy:birnlex_1700
is_a: UBERON:0002780 ! regional part of forebrain
@@ -51926,22 +51841,6 @@ intersection_of: part_of UBERON:0005462 ! lower back
id: UBERON:0002793
name: dorsal longitudinal fasciculus of pons
namespace: uberon
-def: "A dorsal longitudinal fasciculus that is part of a pons [Obol]." [OBOL:automatic]
-synonym: "bundle of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "bundle of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "dorsal longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "pons bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons of varolius fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
xref: FMA:72492
xref: NIF_GrossAnatomy:birnlex_1707
is_a: UBERON:0003045 ! dorsal longitudinal fasciculus
@@ -84196,28 +84095,22 @@ relationship: has_part UBERON:0002418 ! cartilage tissue
id: UBERON:0004763
name: endochondral bone tissue
namespace: uberon
-def: "Replacement bone tissue that forms within cartilage[TAO]. Endochondral ossification is the formation of bone by the replacement of cartilage tissue with mineralized bone[GO]. cartilage is present during endochondral ossification. It is also an essential process during the rudimentary formation of long bones, the growth of the length of long bones, and the natural healing of bone fractures[WP]." [GO:0001958, Wikipedia:Endochondral_ossification]
-comment: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
+def: "Replacement bone tissue that forms within cartilage[VSAO, modified]." [GO:0001958, VSAO:0000145, Wikipedia:Endochondral_ossification]
+comment: The text and logical definition of this term was modified from the definition of 'endochondral bone' in ZFA. AO notes: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
subset: uberon_slim ! Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms
subset: vertebrate_core ! core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO
-synonym: "replacement bone" BROAD [ZFA:0001628]
-xref: AAO:0010768
xref: MA:0002836
-xref: TAO:0001637
-xref: ZFA:0001628
is_a: UBERON:0002481 ! bone tissue
-is_a: UBERON:0010522 ! replacement element
relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue
relationship: part_of UBERON:0002513 ! endochondral bone
disjoint_from: UBERON:0004764 ! intramembranous bone tissue
-property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string
[Term]
id: UBERON:0004764
name: intramembranous bone tissue
namespace: uberon
def: "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, Wikipedia:Intramembranous_ossification]
-comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type.
+comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
xref: MA:0002837
is_a: UBERON:0002481 ! bone tissue
relationship: develops_from UBERON:0003104 ! mesenchyme
@@ -119278,14 +119171,14 @@ id: UBERON:0008909
name: perichordal bone
namespace: uberon
def: "Bone element that is adjacent to the notochord." [VSAO:0000307]
-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
+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
synonym: "perichordal bone" RELATED [ZFA:0001629]
synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629]
xref: AAO:0010777
xref: TAO:0001639
xref: VSAO:0000307
xref: ZFA:0001629
-is_a: UBERON:0001474 ! bone
+is_a: UBERON:0012075 ! replacement bone
relationship: adjacent_to UBERON:0002328 ! notochord
intersection_of: UBERON:0001474 ! bone
intersection_of: adjacent_to UBERON:0002328 ! notochord
@@ -119297,24 +119190,24 @@ id: UBERON:0008911
name: chondral bone
namespace: uberon
def: "Replacement bone that forms within or surrounding a cartilaginous skeletal element." [zfin:curator]
-comment: Consider obsoleting
-synonym: "chondral bone" RELATED [ZFA:0001693]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The term was never introduced into VSAO.
xref: AAO:0010774
xref: ZFA:0001693
-is_a: UBERON:0004763 ! endochondral bone tissue
+is_a: UBERON:0012075 ! replacement bone
[Term]
id: UBERON:0008913
name: perichondral bone
namespace: uberon
def: "Bone element that is located on the surface of a cartilage element." [VSAO:0000308]
+comment: include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
synonym: "perichondral bone" RELATED [ZFA:0001630]
synonym: "perichondral bones" EXACT PLURAL [ZFA:0001630]
xref: AAO:0010779
xref: TAO:0001638
xref: VSAO:0000308
xref: ZFA:0001630
-is_a: UBERON:0001474 ! bone
+is_a: UBERON:0008911 ! chondral bone
relationship: develops_from UBERON:0002222 ! perichondrium
property_value: axiom_lost_from_external_ontology "relationship loss: participates_in perichondral ossification (GO:0036073)[VSAO]" xsd:string
property_value: external_definition "Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]" xsd:string
@@ -140087,6 +139980,20 @@ intersection_of: UBERON:0000075 ! subdivision of skeletal system
intersection_of: subdivision_of UBERON:0003216 ! hard palate
[Term]
+id: UBERON:0012075
+name: replacement bone
+namespace: uberon
+def: "Bone that forms as a replacement of another structural tissue." [ZFA:0001628]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
+synonym: "replacement bones" EXACT PLURAL [ZFA:0001628]
+xref: AAO:0010768
+xref: TAO:0001637
+xref: ZFA:0001628
+is_a: UBERON:0001474 ! bone
+is_a: UBERON:0010522 ! replacement element
+property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string
+
+[Term]
id: UBERON:1000000
name: chin ventral margin
namespace: uberon
View
145 uberon-with-isa.obo
@@ -51967,21 +51967,7 @@ name: regional part of forebrain
namespace: uberon
def: "A regional part of brain that is part of a forebrain [Obol]." [OBOL:automatic]
subset: non_informative ! abstract class brought in to group ontology classes but not informative
-synonym: "anatomical structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of forebrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of forebrain" EXACT [OBOL:automatic]
-synonym: "forebrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "forebrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "forebrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "forebrain regional part of brain" EXACT [OBOL:automatic]
synonym: "forebrain segment" EXACT [FMA:61996]
-synonym: "forebrain segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of forebrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of forebrain" EXACT [OBOL:automatic]
synonym: "segment of forebrain" EXACT [NIF_GrossAnatomy:birnlex_1677]
xref: FMA:61996
xref: NIF_GrossAnatomy:birnlex_1677
@@ -52034,64 +52020,7 @@ name: regional part of diencephalon
namespace: uberon
def: "A regional part of brain that is part of a diencephalon [Obol]." [OBOL:automatic]
subset: non_informative ! abstract class brought in to group ontology classes but not informative
-synonym: "anatomical structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "between brain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "between brain brain biological structure" EXACT [OBOL:automatic]
-synonym: "between brain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "between brain regional part of brain" EXACT [OBOL:automatic]
-synonym: "between brain segment of brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "diencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "diencephalon segment" EXACT [FMA:62005]
-synonym: "diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "interbrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "interbrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "interbrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "interbrain regional part of brain" EXACT [OBOL:automatic]
-synonym: "interbrain segment of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "mature diencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of between brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of diencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of interbrain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of between brain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of between brain" EXACT [OBOL:automatic]
-synonym: "segment of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of diencephalon" EXACT [NIF_GrossAnatomy:birnlex_1685]
xref: FMA:62005
xref: NIF_GrossAnatomy:birnlex_1685
xref: SCTID:119264001
@@ -52202,22 +52131,8 @@ name: regional part of telencephalon
namespace: uberon
def: "A regional part of brain that is part of a telencephalon [Obol]." [OBOL:automatic]
subset: non_informative ! abstract class brought in to group ontology classes but not informative
-synonym: "anatomical structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of telencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of telencephalon" EXACT [OBOL:automatic]
synonym: "segment of telencephalon" EXACT [NIF_GrossAnatomy:birnlex_1700]
-synonym: "telencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "telencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "telencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "telencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "telencephalon segment" EXACT [FMA:62374]
-synonym: "telencephalon segment of brain" EXACT [OBOL:automatic]
xref: FMA:62374
xref: NIF_GrossAnatomy:birnlex_1700
is_a: UBERON:0002780 ! regional part of forebrain
@@ -52248,22 +52163,6 @@ intersection_of: part_of UBERON:0005462 ! lower back
id: UBERON:0002793
name: dorsal longitudinal fasciculus of pons
namespace: uberon
-def: "A dorsal longitudinal fasciculus that is part of a pons [Obol]." [OBOL:automatic]
-synonym: "bundle of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "bundle of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "dorsal longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "pons bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons of varolius fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
xref: FMA:72492
xref: NIF_GrossAnatomy:birnlex_1707
is_a: UBERON:0003045 ! dorsal longitudinal fasciculus
@@ -84726,28 +84625,22 @@ relationship: has_part UBERON:0002418 ! cartilage tissue
id: UBERON:0004763
name: endochondral bone tissue
namespace: uberon
-def: "Replacement bone tissue that forms within cartilage[TAO]. Endochondral ossification is the formation of bone by the replacement of cartilage tissue with mineralized bone[GO]. cartilage is present during endochondral ossification. It is also an essential process during the rudimentary formation of long bones, the growth of the length of long bones, and the natural healing of bone fractures[WP]." [GO:0001958, Wikipedia:Endochondral_ossification]
-comment: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
+def: "Replacement bone tissue that forms within cartilage[VSAO, modified]." [GO:0001958, VSAO:0000145, Wikipedia:Endochondral_ossification]
+comment: The text and logical definition of this term was modified from the definition of 'endochondral bone' in ZFA. AO notes: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
subset: uberon_slim ! Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms
subset: vertebrate_core ! core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO
-synonym: "replacement bone" BROAD [ZFA:0001628]
-xref: AAO:0010768
xref: MA:0002836
-xref: TAO:0001637
-xref: ZFA:0001628
is_a: UBERON:0002481 ! bone tissue
-is_a: UBERON:0010522 ! replacement element
relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue
relationship: part_of UBERON:0002513 ! endochondral bone
disjoint_from: UBERON:0004764 ! intramembranous bone tissue
-property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string
[Term]
id: UBERON:0004764
name: intramembranous bone tissue
namespace: uberon
def: "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, Wikipedia:Intramembranous_ossification]
-comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type.
+comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
xref: MA:0002837
is_a: UBERON:0002481 ! bone tissue
relationship: develops_from UBERON:0003104 ! mesenchyme
@@ -120208,14 +120101,14 @@ id: UBERON:0008909
name: perichordal bone
namespace: uberon
def: "Bone element that is adjacent to the notochord." [VSAO:0000307]
-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
+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
synonym: "perichordal bone" RELATED [ZFA:0001629]
synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629]
xref: AAO:0010777
xref: TAO:0001639
xref: VSAO:0000307
xref: ZFA:0001629
-is_a: UBERON:0001474 ! bone
+is_a: UBERON:0012075 ! replacement bone
relationship: adjacent_to UBERON:0002328 ! notochord
intersection_of: UBERON:0001474 ! bone
intersection_of: adjacent_to UBERON:0002328 ! notochord
@@ -120227,24 +120120,24 @@ id: UBERON:0008911
name: chondral bone
namespace: uberon
def: "Replacement bone that forms within or surrounding a cartilaginous skeletal element." [zfin:curator]
-comment: Consider obsoleting
-synonym: "chondral bone" RELATED [ZFA:0001693]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The term was never introduced into VSAO.
xref: AAO:0010774
xref: ZFA:0001693
-is_a: UBERON:0004763 ! endochondral bone tissue
+is_a: UBERON:0012075 ! replacement bone
[Term]
id: UBERON:0008913
name: perichondral bone
namespace: uberon
def: "Bone element that is located on the surface of a cartilage element." [VSAO:0000308]
+comment: include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
synonym: "perichondral bone" RELATED [ZFA:0001630]
synonym: "perichondral bones" EXACT PLURAL [ZFA:0001630]
xref: AAO:0010779
xref: TAO:0001638
xref: VSAO:0000308
xref: ZFA:0001630
-is_a: UBERON:0001474 ! bone
+is_a: UBERON:0008911 ! chondral bone
relationship: develops_from UBERON:0002222 ! perichondrium
property_value: axiom_lost_from_external_ontology "relationship loss: participates_in perichondral ossification (GO:0036073)[VSAO]" xsd:string
property_value: external_definition "Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]" xsd:string
@@ -141585,6 +141478,20 @@ intersection_of: UBERON:0000075 ! subdivision of skeletal system
intersection_of: subdivision_of UBERON:0003216 ! hard palate
[Term]
+id: UBERON:0012075
+name: replacement bone
+namespace: uberon
+def: "Bone that forms as a replacement of another structural tissue." [ZFA:0001628]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
+synonym: "replacement bones" EXACT PLURAL [ZFA:0001628]
+xref: AAO:0010768
+xref: TAO:0001637
+xref: ZFA:0001628
+is_a: UBERON:0001474 ! bone
+is_a: UBERON:0010522 ! replacement element
+property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string
+
+[Term]
id: UBERON:1000000
name: chin ventral margin
namespace: uberon
@@ -145351,7 +145258,7 @@ is_a: UBERON:0005414 ! zone of polarizing activity
[Term]
id: AAO:0010768
-is_a: UBERON:0004763 ! endochondral bone tissue
+is_a: UBERON:0012075 ! replacement bone
[Term]
id: AAO:0010769
@@ -237732,7 +237639,7 @@ is_a: UBERON:0004767 ! vomerine tooth
[Term]
id: TAO:0001637
-is_a: UBERON:0004763 ! endochondral bone tissue
+is_a: UBERON:0012075 ! replacement bone
[Term]
id: TAO:0001638
@@ -249478,7 +249385,7 @@ is_a: UBERON:0001359 ! cerebrospinal fluid
[Term]
id: ZFA:0001628
-is_a: UBERON:0004763 ! endochondral bone tissue
+is_a: UBERON:0012075 ! replacement bone
[Term]
id: ZFA:0001629
View
144 uberon.obo
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: 2012-09-20
+data-version: 2012-09-21
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: developmental_classification "developmental_classification"
@@ -56,6 +56,7 @@ property_value: dc-contributor "Carlo Torniai" xsd:string
property_value: dc-contributor "Ceri Van Slyke" xsd:string
property_value: dc-contributor "David Hill" xsd:string
property_value: dc-contributor "David Osumi-Sutherland" xsd:string
+property_value: dc-contributor "Duncan Davidson" xsd:string
property_value: dc-contributor "Frederic Bastian" xsd:string
property_value: dc-contributor "George Gkoutos" xsd:string
property_value: dc-contributor "Hilmar Lapp" xsd:string
@@ -86,6 +87,7 @@ property_value: dc-creator "Melissa Haendel" xsd:string
property_value: dc-creator "Nizar Ibrahim" xsd:string
property_value: dc-creator "Wasila Dahdul" xsd:string
property_value: dc-description "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data." xsd:string
+property_value: dc-publisher http://obofoundry.org xsd:anyURI
property_value: dc-source http://dbpedia.org
property_value: dc-source http://en.wikipedia.org/wiki/
property_value: dc-source http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl
@@ -112,6 +114,7 @@ property_value: dc-source http://purl.obolibrary.org/obo/zfa.owl
property_value: dc-source http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop xsd:anyURI
property_value: dc-source http://wiki.phenotypercn.org/wiki/August_2012_Notes xsd:anyURI
property_value: dc-source http://www.brain-map.org
+property_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl
property_value: dc-source https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit xsd:anyURI
property_value: dc-source https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit xsd:anyURI
property_value: dc-source https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit xsd:anyURI
@@ -132,6 +135,7 @@ property_value: dc-source "ISBN:9780120749034 The laboratory rat" xsd:string
property_value: dc-source "ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte" xsd:string
property_value: dc-source "ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader" xsd:string
property_value: dc-source "ISBN:9780878932504 Developmental Biology" xsd:string
+property_value: dc-source "MESH" xsd:string
property_value: dc-source "PMID:11433360 Placental development: lessons from mouse mutants" xsd:string
property_value: dc-source "PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen" xsd:string
property_value: dc-title "Uber-anatomy ontology" xsd:string
@@ -50650,21 +50654,7 @@ id: UBERON:0002780
name: regional part of forebrain
def: "A regional part of brain that is part of a forebrain [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of forebrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of forebrain" EXACT [OBOL:automatic]
-synonym: "forebrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "forebrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "forebrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "forebrain regional part of brain" EXACT [OBOL:automatic]
synonym: "forebrain segment" EXACT [FMA:61996]
-synonym: "forebrain segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of forebrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of forebrain" EXACT [OBOL:automatic]
synonym: "segment of forebrain" EXACT [NIF_GrossAnatomy:birnlex_1677]
xref: FMA:61996
xref: NIF_GrossAnatomy:birnlex_1677
@@ -50714,64 +50704,7 @@ id: UBERON:0002784
name: regional part of diencephalon
def: "A regional part of brain that is part of a diencephalon [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "between brain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "between brain brain biological structure" EXACT [OBOL:automatic]
-synonym: "between brain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "between brain regional part of brain" EXACT [OBOL:automatic]
-synonym: "between brain segment of brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "diencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "diencephalon segment" EXACT [FMA:62005]
-synonym: "diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "interbrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "interbrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "interbrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "interbrain regional part of brain" EXACT [OBOL:automatic]
-synonym: "interbrain segment of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "mature diencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of between brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of diencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of interbrain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of between brain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of between brain" EXACT [OBOL:automatic]
-synonym: "segment of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of diencephalon" EXACT [NIF_GrossAnatomy:birnlex_1685]
xref: FMA:62005
xref: NIF_GrossAnatomy:birnlex_1685
xref: SCTID:119264001
@@ -50878,22 +50811,8 @@ id: UBERON:0002791
name: regional part of telencephalon
def: "A regional part of brain that is part of a telencephalon [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of telencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of telencephalon" EXACT [OBOL:automatic]
synonym: "segment of telencephalon" EXACT [NIF_GrossAnatomy:birnlex_1700]
-synonym: "telencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "telencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "telencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "telencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "telencephalon segment" EXACT [FMA:62374]
-synonym: "telencephalon segment of brain" EXACT [OBOL:automatic]
xref: FMA:62374
xref: NIF_GrossAnatomy:birnlex_1700
is_a: UBERON:0002780 ! regional part of forebrain
@@ -50924,22 +50843,6 @@ relationship: part_of UBERON:0005462 ! lower back
[Term]
id: UBERON:0002793
name: dorsal longitudinal fasciculus of pons
-def: "A dorsal longitudinal fasciculus that is part of a pons [Obol]." [OBOL:automatic]
-synonym: "bundle of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "bundle of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "dorsal longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "pons bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons of varolius fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
xref: FMA:72492
xref: NIF_GrossAnatomy:birnlex_1707
is_a: UBERON:0003045 ! dorsal longitudinal fasciculus
@@ -82657,27 +82560,21 @@ relationship: has_part UBERON:0002418 ! cartilage tissue
[Term]
id: UBERON:0004763
name: endochondral bone tissue
-def: "Replacement bone tissue that forms within cartilage[TAO]. Endochondral ossification is the formation of bone by the replacement of cartilage tissue with mineralized bone[GO]. cartilage is present during endochondral ossification. It is also an essential process during the rudimentary formation of long bones, the growth of the length of long bones, and the natural healing of bone fractures[WP]." [GO:0001958, Wikipedia:Endochondral_ossification]
-comment: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
+def: "Replacement bone tissue that forms within cartilage[VSAO, modified]." [GO:0001958, VSAO:0000145, Wikipedia:Endochondral_ossification]
+comment: The text and logical definition of this term was modified from the definition of 'endochondral bone' in ZFA. AO notes: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
subset: uberon_slim
subset: vertebrate_core
-synonym: "replacement bone" BROAD [ZFA:0001628]
-xref: AAO:0010768
xref: MA:0002836
-xref: TAO:0001637
-xref: ZFA:0001628
is_a: UBERON:0002481 ! bone tissue
-is_a: UBERON:0010522 {source="ZFA"} ! replacement element
disjoint_from: UBERON:0004764 ! intramembranous bone tissue
relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue
relationship: part_of UBERON:0002513 ! endochondral bone
-property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"}
[Term]
id: UBERON:0004764
name: intramembranous bone tissue
def: "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, Wikipedia:Intramembranous_ossification]
-comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type.
+comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
xref: MA:0002837
is_a: UBERON:0002481 ! bone tissue
relationship: develops_from UBERON:0003104 ! mesenchyme
@@ -116959,14 +116856,14 @@ property_value: external_definition "Intramembranous bone that forms superficial
id: UBERON:0008909
name: perichordal bone
def: "Bone element that is adjacent to the notochord." [VSAO:0000307]
-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
+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
synonym: "perichordal bone" RELATED [ZFA:0001629]
synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629]
xref: AAO:0010777
xref: TAO:0001639
xref: VSAO:0000307
xref: ZFA:0001629
-is_a: UBERON:0001474 ! bone
+is_a: UBERON:0012075 {notes="not in VSAO", source="ZFA"} ! replacement bone
relationship: adjacent_to UBERON:0002328
intersection_of: UBERON:0001474 ! bone
intersection_of: adjacent_to UBERON:0002328 ! notochord
@@ -116978,23 +116875,23 @@ property_value: external_definition "Replacement bone that forms within the conn
id: UBERON:0008911
name: chondral bone
def: "Replacement bone that forms within or surrounding a cartilaginous skeletal element." [zfin:curator]
-comment: Consider obsoleting
-synonym: "chondral bone" RELATED [ZFA:0001693]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The term was never introduced into VSAO.
xref: AAO:0010774
xref: ZFA:0001693
-is_a: UBERON:0004763 {source="ZFA"} ! endochondral bone tissue
+is_a: UBERON:0012075 {source="ZFA"} ! replacement bone
[Term]
id: UBERON:0008913
name: perichondral bone
def: "Bone element that is located on the surface of a cartilage element." [VSAO:0000308]
+comment: include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
synonym: "perichondral bone" RELATED [ZFA:0001630]
synonym: "perichondral bones" EXACT PLURAL [ZFA:0001630]
xref: AAO:0010779
xref: TAO:0001638
xref: VSAO:0000308
xref: ZFA:0001630
-is_a: UBERON:0001474 {source="VSAO"} ! bone
+is_a: UBERON:0008911 {source="ZFA"} ! chondral bone
relationship: develops_from UBERON:0002222 {source="ZFA"} ! perichondrium
property_value: axiom_lost_from_external_ontology "relationship loss: participates_in perichondral ossification (GO:0036073)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000308", ontology="VSAO"}
property_value: external_definition "Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001638", ontology="TAO", source="TAO:wd"}
@@ -137469,6 +137366,19 @@ relationship: part_of UBERON:0012072 ! palatal part of dermatocranium
relationship: subdivision_of UBERON:0003216 ! hard palate
[Term]
+id: UBERON:0012075
+name: replacement bone
+def: "Bone that forms as a replacement of another structural tissue." [ZFA:0001628]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
+synonym: "replacement bones" EXACT PLURAL [ZFA:0001628]
+xref: AAO:0010768
+xref: TAO:0001637
+xref: ZFA:0001628
+is_a: UBERON:0001474 {source="ZFA"} ! bone
+is_a: UBERON:0010522 {source="ZFA"} ! replacement element
+property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"}
+
+[Term]
id: UBERON:1000000
name: chin ventral margin
def: "Subdivision of the head consisting of the area along the lower edge of the chin." [UBERON:EJS]
View
145 uberon_edit-implied.obo
@@ -55,6 +55,7 @@ property_value: dc-contributor "Carlo Torniai" xsd:string
property_value: dc-contributor "Ceri Van Slyke" xsd:string
property_value: dc-contributor "David Hill" xsd:string
property_value: dc-contributor "David Osumi-Sutherland" xsd:string
+property_value: dc-contributor "Duncan Davidson" xsd:string
property_value: dc-contributor "Frederic Bastian" xsd:string
property_value: dc-contributor "George Gkoutos" xsd:string
property_value: dc-contributor "Hilmar Lapp" xsd:string
@@ -85,6 +86,7 @@ property_value: dc-creator "Melissa Haendel" xsd:string
property_value: dc-creator "Nizar Ibrahim" xsd:string
property_value: dc-creator "Wasila Dahdul" xsd:string
property_value: dc-description "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data." xsd:string
+property_value: dc-publisher http://obofoundry.org xsd:anyURI
property_value: dc-source http://dbpedia.org
property_value: dc-source http://en.wikipedia.org/wiki/
property_value: dc-source http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl
@@ -111,6 +113,7 @@ property_value: dc-source http://purl.obolibrary.org/obo/zfa.owl
property_value: dc-source http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop xsd:anyURI
property_value: dc-source http://wiki.phenotypercn.org/wiki/August_2012_Notes xsd:anyURI
property_value: dc-source http://www.brain-map.org
+property_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl
property_value: dc-source https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit xsd:anyURI
property_value: dc-source https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit xsd:anyURI
property_value: dc-source https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit xsd:anyURI
@@ -131,6 +134,7 @@ property_value: dc-source "ISBN:9780120749034 The laboratory rat" xsd:string
property_value: dc-source "ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte" xsd:string
property_value: dc-source "ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader" xsd:string
property_value: dc-source "ISBN:9780878932504 Developmental Biology" xsd:string
+property_value: dc-source "MESH" xsd:string
property_value: dc-source "PMID:11433360 Placental development: lessons from mouse mutants" xsd:string
property_value: dc-source "PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen" xsd:string
property_value: dc-title "Uber-anatomy ontology" xsd:string
@@ -46286,7 +46290,6 @@ is_obsolete: true
consider: EFO:0000950
consider: MAT:0000277
consider: MIAA:0000277
-consider: VSAO:0000170
consider: ZFA:0001123
[Term]
@@ -50677,21 +50680,7 @@ id: UBERON:0002780
name: regional part of forebrain
def: "A regional part of brain that is part of a forebrain [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of forebrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of forebrain" EXACT [OBOL:automatic]
-synonym: "forebrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "forebrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "forebrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "forebrain regional part of brain" EXACT [OBOL:automatic]
synonym: "forebrain segment" EXACT [FMA:61996]
-synonym: "forebrain segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of forebrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of forebrain" EXACT [OBOL:automatic]
synonym: "segment of forebrain" EXACT [NIF_GrossAnatomy:birnlex_1677]
xref: FMA:61996
xref: NIF_GrossAnatomy:birnlex_1677
@@ -50740,64 +50729,7 @@ id: UBERON:0002784
name: regional part of diencephalon
def: "A regional part of brain that is part of a diencephalon [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "between brain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "between brain brain biological structure" EXACT [OBOL:automatic]
-synonym: "between brain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "between brain regional part of brain" EXACT [OBOL:automatic]
-synonym: "between brain segment of brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "diencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "diencephalon segment" EXACT [FMA:62005]
-synonym: "diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "interbrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "interbrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "interbrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "interbrain regional part of brain" EXACT [OBOL:automatic]
-synonym: "interbrain segment of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "mature diencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of between brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of diencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of interbrain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of between brain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of between brain" EXACT [OBOL:automatic]
-synonym: "segment of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of diencephalon" EXACT [NIF_GrossAnatomy:birnlex_1685]
xref: FMA:62005
xref: NIF_GrossAnatomy:birnlex_1685
xref: SCTID:119264001
@@ -50901,22 +50833,8 @@ id: UBERON:0002791
name: regional part of telencephalon
def: "A regional part of brain that is part of a telencephalon [Obol]." [OBOL:automatic]
subset: non_informative
-synonym: "anatomical structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of telencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of telencephalon" EXACT [OBOL:automatic]
synonym: "segment of telencephalon" EXACT [NIF_GrossAnatomy:birnlex_1700]
-synonym: "telencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "telencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "telencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "telencephalon regional part of brain" EXACT [OBOL:automatic]
synonym: "telencephalon segment" EXACT [FMA:62374]
-synonym: "telencephalon segment of brain" EXACT [OBOL:automatic]
xref: FMA:62374
xref: NIF_GrossAnatomy:birnlex_1700
is_a: UBERON:0002780 ! regional part of forebrain
@@ -50945,22 +50863,6 @@ relationship: part_of UBERON:0005462 ! lower back
[Term]
id: UBERON:0002793
name: dorsal longitudinal fasciculus of pons
-def: "A dorsal longitudinal fasciculus that is part of a pons [Obol]." [OBOL:automatic]
-synonym: "bundle of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "bundle of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "dorsal longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "pons bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons of varolius fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
xref: FMA:72492
xref: NIF_GrossAnatomy:birnlex_1707
is_a: UBERON:0003045 ! dorsal longitudinal fasciculus
@@ -81807,7 +81709,6 @@ property_value: external_definition "Sliver of bone that invest part of or all t
property_value: external_definition "The cartilaginous autopalatine forms from the anterior palatoquadrate arch. The first sign of ossification is visible at the anterior tip where it articulates with the maxilla (7.6 mm). In adults there are three processes at the anterior portion of the palatine: a ventromedial process, which forms the socket of the small ball- and- socket joint with the preethmoid; a dorsomedial process, which is connected by a short ligament to the ethmoid; and a lateral process, which extends toward the first infraorbital. Possession of a dorsomedial process, which abuts the ethmoid, is a unique feature shared by Cypriniformes (Fink and Fink, 1981). The palatine has two components, the autopalatine (derived from pars autopalatine) and the dermal component having teeth, the dermopalatine Arratia & Schultze 1990. The element in cypriniforms is only the cartilage part, so that it is more correct to name it autopalatine and not as palatine in general that it implies a fusion of elements (as in perciforms).[ZFA]" xsd:string {date_retrieved="2012-08-08", external_class="ZFA:0000620", ontology="ZFA", source="ZFIN:curator"}
is_obsolete: true
consider: AAO:0000372
-consider: TAO:0000620
consider: ZFA:0000620
[Term]
@@ -82034,30 +81935,24 @@ relationship: has_part UBERON:0002418 ! cartilage tissue
[Term]
id: UBERON:0004763
name: endochondral bone tissue
-def: "Replacement bone tissue that forms within cartilage[TAO]. Endochondral ossification is the formation of bone by the replacement of cartilage tissue with mineralized bone[GO]. cartilage is present during endochondral ossification. It is also an essential process during the rudimentary formation of long bones, the growth of the length of long bones, and the natural healing of bone fractures[WP]." [GO:0001958, Wikipedia:Endochondral_ossification]
-comment: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
+def: "Replacement bone tissue that forms within cartilage[VSAO, modified]." [GO:0001958, VSAO:0000145, Wikipedia:Endochondral_ossification]
+comment: The text and logical definition of this term was modified from the definition of 'endochondral bone' in ZFA. AO notes: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
subset: uberon_slim
subset: vertebrate_core
-synonym: "replacement bone" BROAD [ZFA:0001628]
-xref: AAO:0010768
xref: MA:0002836
-xref: TAO:0001637
-xref: ZFA:0001628
is_a: UBERON:0002481 ! bone tissue
-is_a: UBERON:0010522 {source="ZFA"} ! replacement element
intersection_of: UBERON:0002481 ! bone tissue
intersection_of: output_of GO:0001958
disjoint_from: UBERON:0004764 ! intramembranous bone tissue
relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue
relationship: output_of GO:0001958
relationship: part_of UBERON:0002513 ! endochondral bone
-property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"}
[Term]
id: UBERON:0004764
name: intramembranous bone tissue
def: "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, Wikipedia:Intramembranous_ossification]
-comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type.
+comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
xref: MA:0002837
is_a: UBERON:0002481 ! bone tissue
intersection_of: UBERON:0002481 ! bone tissue
@@ -115585,14 +115480,14 @@ property_value: external_definition "Intramembranous bone that forms superficial
id: UBERON:0008909
name: perichordal bone
def: "Bone element that is adjacent to the notochord." [VSAO:0000307]
-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
+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
synonym: "perichordal bone" RELATED [ZFA:0001629]
synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629]
xref: AAO:0010777
xref: TAO:0001639
xref: VSAO:0000307
xref: ZFA:0001629
-is_a: UBERON:0001474 ! bone
+is_a: UBERON:0012075 {notes="not in VSAO", source="ZFA"} ! replacement bone
intersection_of: UBERON:0001474 ! bone
intersection_of: adjacent_to UBERON:0002328 ! notochord
disjoint_from: UBERON:0008913 ! perichondral bone
@@ -115603,23 +115498,23 @@ property_value: external_definition "Replacement bone that forms within the conn
id: UBERON:0008911
name: chondral bone
def: "Replacement bone that forms within or surrounding a cartilaginous skeletal element." [zfin:curator]
-comment: Consider obsoleting
-synonym: "chondral bone" RELATED [ZFA:0001693]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The term was never introduced into VSAO.
xref: AAO:0010774
xref: ZFA:0001693
-is_a: UBERON:0004763 {source="ZFA"} ! endochondral bone tissue
+is_a: UBERON:0012075 {source="ZFA"} ! replacement bone
[Term]
id: UBERON:0008913
name: perichondral bone
def: "Bone element that is located on the surface of a cartilage element." [VSAO:0000308]
+comment: include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
synonym: "perichondral bone" RELATED [ZFA:0001630]
synonym: "perichondral bones" EXACT PLURAL [ZFA:0001630]
xref: AAO:0010779
xref: TAO:0001638
xref: VSAO:0000308
xref: ZFA:0001630
-is_a: UBERON:0001474 {source="VSAO"} ! bone
+is_a: UBERON:0008911 {source="ZFA"} ! chondral bone
relationship: develops_from UBERON:0002222 {source="ZFA"} ! perichondrium
property_value: axiom_lost_from_external_ontology "relationship loss: participates_in perichondral ossification (GO:0036073)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000308", ontology="VSAO"}
property_value: external_definition "Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001638", ontology="TAO", source="TAO:wd"}
@@ -132195,7 +132090,6 @@ name: obsolete proteinaceous extracellular matrix
comment: obsoleted as it was already present in GO
is_obsolete: true
consider: GO:0005578
-consider: VSAO:0000021
[Term]
id: UBERON:0011587
@@ -135567,6 +135461,19 @@ relationship: part_of UBERON:0012072 ! palatal part of dermatocranium
relationship: subdivision_of UBERON:0003216 ! hard palate
[Term]
+id: UBERON:0012075
+name: replacement bone
+def: "Bone that forms as a replacement of another structural tissue." [ZFA:0001628]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
+synonym: "replacement bones" EXACT PLURAL [ZFA:0001628]
+xref: AAO:0010768
+xref: TAO:0001637
+xref: ZFA:0001628
+is_a: UBERON:0001474 {source="ZFA"} ! bone
+is_a: UBERON:0010522 {source="ZFA"} ! replacement element
+property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"}
+
+[Term]
id: UBERON:1000000
name: chin ventral margin
def: "Subdivision of the head consisting of the area along the lower edge of the chin." [UBERON:EJS]
View
215 uberon_edit.obo
@@ -61,6 +61,7 @@ property_value: dc-source http://purl.obolibrary.org/obo/xao.owl
property_value: dc-source http://purl.obolibrary.org/obo/caro.owl
property_value: dc-source http://purl.obolibrary.org/obo/aeo.owl
property_value: dc-source http://purl.obolibrary.org/obo/bila.owl
+property_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl
property_value: dc-source http://en.wikipedia.org/wiki/
property_value: dc-source http://dbpedia.org
property_value: dc-source http://palaeos.com
@@ -69,6 +70,7 @@ property_value: dc-source http://purl.obolibrary.org/obo/go.owl
property_value: dc-source http://purl.obolibrary.org/obo/cl.owl
property_value: dc-source http://purl.obolibrary.org/obo/aba.owl
property_value: dc-source http://www.brain-map.org
+property_value: dc-source "MESH" xsd:string
property_value: dc-source "ISBN10:0073040584 Vertebrates, Kardong" xsd:string
property_value: dc-source "ISBN:9780878932504 Developmental Biology" xsd:string
property_value: dc-source "ISBN10:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos" xsd:string
@@ -57043,22 +57045,6 @@ relationship: part_of UBERON:0007862 {source="AAO"} ! perichordal tissue
xref: AAO:0000738 ! perichordal ring
[Term]
-id: UBERON:0008909
-name: perichordal bone
-def: "Bone element that is adjacent to the notochord." [VSAO:0000307]
-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
-intersection_of: UBERON:0001474 ! bone
-intersection_of: adjacent_to UBERON:0002328 ! notochord
-synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629]
-synonym: "perichordal bone" RELATED [ZFA:0001629]
-disjoint_from: UBERON:0008913 ! perichondral bone
-xref: TAO:0001639 ! perichordal bone
-xref: AAO:0010777 ! perichordal bone
-xref: ZFA:0001629 ! perichordal bone
-xref: VSAO:0000307 ! perichordal bone
-property_value: external_definition "Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001639", date_retrieved="2012-08-14", source="TAO:wd"}
-
-[Term]
id: UBERON:0002222
name: perichondrium
def: "Fibrous connective tissue that surrounds cartilage." [Wikipedia:Perichondrium, VSAO:0000036]
@@ -57080,20 +57066,6 @@ xref: XAO:0004049 ! perichondrium
xref: MA:0003008 ! perichondrium
property_value: external_definition "Portion of connective tissue which surrounds cartilage.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001643", date_retrieved="2012-08-14", source="TAO:wd"}
-[Term]
-id: UBERON:0008913 ! perichondral bone
-name: perichondral bone
-def: "Bone element that is located on the surface of a cartilage element." [VSAO:0000308]
-synonym: "perichondral bones" EXACT PLURAL [ZFA:0001630]
-synonym: "perichondral bone" RELATED [ZFA:0001630]
-xref: TAO:0001638 ! perichondral bone
-is_a: UBERON:0001474 {source="VSAO"} ! bone
-relationship: develops_from UBERON:0002222 {source="ZFA"} ! perichondrium
-xref: ZFA:0001630 ! perichondral bone
-xref: AAO:0010779 ! perichondral bone
-xref: VSAO:0000308 ! perichondral bone
-property_value: external_definition "Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001638", date_retrieved="2012-08-14", source="TAO:wd"}
-property_value: axiom_lost_from_external_ontology "relationship loss: participates_in perichondral ossification (GO:0036073)[VSAO]" xsd:string {ontology="VSAO", external_class="VSAO:0000308", date_retrieved="2012-08-14"}
[Term]
id: UBERON:0008304
@@ -57112,16 +57084,6 @@ relationship: part_of UBERON:0002222 {source="BTO"} ! perichondrium
xref: BTO:0005091 ! outer fibrous layer of perichondrium
[Term]
-id: UBERON:0008911
-name: chondral bone
-def: "Replacement bone that forms within or surrounding a cartilaginous skeletal element." [zfin:curator]
-comment: Consider obsoleting
-synonym: "chondral bone" RELATED [ZFA:0001693]
-is_a: UBERON:0004763 {source="ZFA"} ! endochondral bone tissue
-xref: ZFA:0001693 ! chondral bone
-xref: AAO:0010774 ! chondral bone
-
-[Term]
id: UBERON:0002224
name: thoracic cavity
def: "Body cavity subdivision which is enclosed by the thoracic wall and the diaphragm[FMA]." [Wikipedia:Thoracic_cavity, FMA:7565]
@@ -65124,33 +65086,83 @@ synonym: "endochondral replacement element" EXACT [VSAO:0000139]
is_a: UBERON:0004765 {source="VSAO"} ! skeletal element
xref: VSAO:0000139 ! endochondral element
xref: ZFA:0005620 ! endochondral element
-xref: XAO:0004017 ! endochondral elemen
+xref: XAO:0004017 ! endochondral element
+
+[Term]
+id: UBERON:0012075
+name: replacement bone
+def: "Bone that forms as a replacement of another structural tissue." [ZFA:0001628]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
+synonym: "replacement bones" EXACT PLURAL [ZFA:0001628]
+xref: ZFA:0001628 ! replacement bone
+xref: AAO:0010768 ! replacement bone
+xref: TAO:0001637 ! replacement bone
+is_a: UBERON:0001474 {source="ZFA"} ! bone
+is_a: UBERON:0010522 {source="ZFA"} ! replacement element
+property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001637", date_retrieved="2012-08-14", source="TAO:wd"}
+
+[Term]
+id: UBERON:0008911
+name: chondral bone
+def: "Replacement bone that forms within or surrounding a cartilaginous skeletal element." [zfin:curator]
+comment: This class was introduced to be consistent with the ZFA hierarchy. The term was never introduced into VSAO.
+is_a: UBERON:0012075 {source="ZFA"} ! replacement bone
+xref: ZFA:0001693 ! chondral bone
+xref: AAO:0010774 ! chondral bone
+
+[Term]
+id: UBERON:0008909
+name: perichordal bone
+def: "Bone element that is adjacent to the notochord." [VSAO:0000307]
+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
+is_a: UBERON:0012075 {source="ZFA", notes="not in VSAO"} ! replacement bone
+intersection_of: UBERON:0001474 ! bone
+intersection_of: adjacent_to UBERON:0002328 ! notochord
+synonym: "perichordal bones" EXACT PLURAL [ZFA:0001629]
+synonym: "perichordal bone" RELATED [ZFA:0001629]
+disjoint_from: UBERON:0008913 ! perichondral bone
+xref: TAO:0001639 ! perichordal bone
+xref: AAO:0010777 ! perichordal bone
+xref: ZFA:0001629 ! perichordal bone
+xref: VSAO:0000307 ! perichordal bone
+property_value: external_definition "Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001639", date_retrieved="2012-08-14", source="TAO:wd"}
+
+[Term]
+id: UBERON:0008913 ! perichondral bone
+name: perichondral bone
+def: "Bone element that is located on the surface of a cartilage element." [VSAO:0000308]
+comment: include the subtyping under 'replacement bone', for consistency with ZFA, but VSAO does not include this intermediate class
+synonym: "perichondral bones" EXACT PLURAL [ZFA:0001630]
+synonym: "perichondral bone" RELATED [ZFA:0001630]
+xref: TAO:0001638 ! perichondral bone
+is_a: UBERON:0008911 {source="ZFA"} ! chondral bone
+is_a: UBERON:0001474 {source="VSAO", notes="redunant but higher confidence than more specific placement"} ! bone
+relationship: develops_from UBERON:0002222 {source="ZFA"} ! perichondrium
+xref: ZFA:0001630 ! perichondral bone
+xref: AAO:0010779 ! perichondral bone
+xref: VSAO:0000308 ! perichondral bone
+property_value: external_definition "Replacement bone that forms within the connective tissue surrounding cartilage.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001638", date_retrieved="2012-08-14", source="TAO:wd"}
+property_value: axiom_lost_from_external_ontology "relationship loss: participates_in perichondral ossification (GO:0036073)[VSAO]" xsd:string {ontology="VSAO", external_class="VSAO:0000308", date_retrieved="2012-08-14"}
[Term]
id: UBERON:0004763
name: endochondral bone tissue
-def: "Replacement bone tissue that forms within cartilage[TAO]. Endochondral ossification is the formation of bone by the replacement of cartilage tissue with mineralized bone[GO]. cartilage is present during endochondral ossification. It is also an essential process during the rudimentary formation of long bones, the growth of the length of long bones, and the natural healing of bone fractures[WP]." [Wikipedia:Endochondral_ossification, GO:0001958]
-comment: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
+def: "Replacement bone tissue that forms within cartilage[VSAO, modified]." [Wikipedia:Endochondral_ossification, GO:0001958, VSAO:0000145]
+comment: The text and logical definition of this term was modified from the definition of 'endochondral bone' in ZFA. AO notes: note the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type
subset: uberon_slim
subset: vertebrate_core
-synonym: "replacement bone" BROAD [ZFA:0001628]
xref: MA:0002836 ! endochondral bone
-is_a: UBERON:0010522 {source="ZFA"} ! replacement element
intersection_of: UBERON:0002481 ! bone tissue
intersection_of: output_of GO:0001958 ! endochondral ossification
-disjoint_from: UBERON:0004764 ! intramembranous bone tissue
relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue
relationship: part_of UBERON:0002513 ! endochondral bone
-xref: ZFA:0001628 ! replacement bone
-xref: AAO:0010768 ! replacement bone
-xref: TAO:0001637 ! replacement bone
-property_value: external_definition "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0001637", date_retrieved="2012-08-14", source="TAO:wd"}
+disjoint_from: UBERON:0004764 ! intramembranous bone tissue
[Term]
id: UBERON:0004764
name: intramembranous bone tissue
def: "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [Wikipedia:Intramembranous_ossification, GO:0001957]
-comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type.
+comment: note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)
xref: MA:0002837 ! intramembranous bone
intersection_of: UBERON:0002481 ! bone tissue
intersection_of: output_of GO:0001957 ! intramembranous ossification
@@ -70500,20 +70512,6 @@ subset: non_informative
def: "A regional part of brain that is part of a forebrain [Obol]." [OBOL:automatic]
synonym: "forebrain segment" EXACT [FMA:61996]
synonym: "segment of forebrain" EXACT [NIF_GrossAnatomy:birnlex_1677]
-synonym: "forebrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "forebrain regional part of brain" EXACT [OBOL:automatic]
-synonym: "forebrain segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of forebrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of forebrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of forebrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of forebrain" EXACT [OBOL:automatic]
-synonym: "forebrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "forebrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "forebrain brain biological structure" EXACT [OBOL:automatic]
xref: FMA:61996 ! Segment of forebrain
xref: NIF_GrossAnatomy:birnlex_1677 ! Regional part of forebrain
intersection_of: UBERON:0000481 ! multi-tissue structure
@@ -70532,63 +70530,6 @@ name: regional part of diencephalon
subset: non_informative
def: "A regional part of brain that is part of a diencephalon [Obol]." [OBOL:automatic]
synonym: "diencephalon segment" EXACT [FMA:62005]
-synonym: "segment of diencephalon" EXACT [NIF_GrossAnatomy:birnlex_1685]
-synonym: "between brain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "between brain regional part of brain" EXACT [OBOL:automatic]
-synonym: "between brain segment of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "diencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "interbrain neuraxis segment" EXACT [OBOL:automatic]
-synonym: "interbrain regional part of brain" EXACT [OBOL:automatic]
-synonym: "interbrain segment of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "mature diencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of between brain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of diencephalon" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of interbrain" EXACT [OBOL:automatic]
-synonym: "neuraxis segment of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of between brain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "regional part of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of between brain" EXACT [OBOL:automatic]
-synonym: "segment of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "segment of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "between brain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "between brain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "between brain brain biological structure" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of between brain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of diencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of interbrain" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of between brain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of diencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of interbrain" EXACT [OBOL:automatic]
-synonym: "brain biological structure of mature diencephalon" EXACT [OBOL:automatic]
-synonym: "diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "diencephalon brain biological structure" EXACT [OBOL:automatic]
-synonym: "interbrain anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain biological structure of brain" EXACT [OBOL:automatic]
-synonym: "interbrain brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "interbrain brain biological structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "mature diencephalon brain biological structure" EXACT [OBOL:automatic]
xref: FMA:62005 ! Segment of diencephalon
xref: NIF_GrossAnatomy:birnlex_1685 ! Regional part of diencephalon
is_a: UBERON:0002780 ! regional part of forebrain
@@ -70707,20 +70648,6 @@ subset: non_informative
def: "A regional part of brain that is part of a telencephalon [Obol]." [OBOL:automatic]
synonym: "segment of telencephalon" EXACT [NIF_GrossAnatomy:birnlex_1700]
synonym: "telencephalon segment" EXACT [FMA:62374]
-synonym: "neuraxis segment of telencephalon" EXACT [OBOL:automatic]
-synonym: "regional part of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "segment of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "telencephalon neuraxis segment" EXACT [OBOL:automatic]
-synonym: "telencephalon regional part of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon segment of brain" EXACT [OBOL:automatic]
-synonym: "anatomical structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "biological structure of brain of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain anatomical structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "brain biological structure of telencephalon" EXACT [OBOL:automatic]
-synonym: "telencephalon anatomical structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon biological structure of brain" EXACT [OBOL:automatic]
-synonym: "telencephalon brain anatomical structure" EXACT [OBOL:automatic]
-synonym: "telencephalon brain biological structure" EXACT [OBOL:automatic]
xref: FMA:62374 ! Segment of telencephalon
xref: NIF_GrossAnatomy:birnlex_1700 ! Regional part of telencephalon
is_a: UBERON:0002780 ! regional part of forebrain
@@ -70730,22 +70657,6 @@ intersection_of: part_of UBERON:0001893 ! telencephalon
[Term]
id: UBERON:0002793
name: dorsal longitudinal fasciculus of pons
-def: "A dorsal longitudinal fasciculus that is part of a pons [Obol]." [OBOL:automatic]
-synonym: "bundle of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "bundle of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "dorsal longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons" EXACT [OBOL:automatic]
-synonym: "fasciculus of Schutz of pons of varolius" EXACT [OBOL:automatic]
-synonym: "pons bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius bundle of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius dorsal longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons of varolius fasciculus of Schutz" EXACT [OBOL:automatic]
-synonym: "pons of varolius posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "pons posterior longitudinal fasciculus" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons" EXACT [OBOL:automatic]
-synonym: "posterior longitudinal fasciculus of pons of varolius" EXACT [OBOL:automatic]
xref: FMA:72492 ! Dorsal longitudinal fasciculus of pons
xref: NIF_GrossAnatomy:birnlex_1707 ! Dorsal longitudinal fasciculus of pons
is_a: UBERON:0003045 ! dorsal longitudinal fasciculus

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