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text def fixes using VSAO

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1 parent 65384e9 commit 728bf8eca20ffac8c707c2fcb6dfb6221968815c @cmungall cmungall committed Aug 17, 2012
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@@ -1032,7 +1032,9 @@ fake.obo:
aao-fixed.obo: phenoscape-vocab/AAO_cjm.obo
obo-map-ids.pl --use-xref --regex-filter 'CL:' $< | grep -v ^develops_from > $@
-tao-fixed.obo: $(TAO_SRC)
+tao-isaM.obo: $(TAO_SRC)
+ obo-merge-tags.pl -t is_a $< phenoscape-vocab/tao-scratchdir/tao-isa-from-zfa.obo > $@
+tao-fixed.obo: tao-isaM.obo
obo-map-ids.pl --ignore-tag alt_id --use-xref --regex-filter 'CL:' $< $< | perl -npe 's/OBO_REL://' | obo-grep.pl -r 'id: TAO' - > $@
psc-merged.obo: $(TAO) fake.obo
obo2obo -o $@ $(MSAOS) fake.obo
@@ -1053,7 +1055,7 @@ phenoscape-vocab/phenoscape-anatomy.obo: psc-merged-u.obo merged-dates.txt
# copy this manually to phenoscape-vocab/edit/ (but only before the switch!)
phenoscape-ext.owl: phenoscape-vocab/phenoscape-anatomy.obo
- obo-grep.pl --neg -r 'id: (UBERON|CL)' $< | ./util/pa-to-uberon-ids.pl | obo-sed.pl -r 'is_obsolete:.*true' 's/name: /name: obsolete /' - > $@.obo && owltools $@.obo --add-imports-declarations $(OBO)/uberon/merged.owl -o -f functional file://`pwd`/$@.tmp && egrep -v '^Declaration.*UBERON_0' $@.tmp > $@
+ obo-grep.pl --neg -r 'id: (UBERON|CL)' $< | ./util/pa-to-uberon-ids.pl | obo-grep.pl -r 'id: UBERON' - | obo-sed.pl -r 'is_obsolete:.*true' 's/name: /name: obsolete /' - > $@.obo && owltools $@.obo --add-imports-declarations $(OBO)/uberon/merged.owl -o -f functional file://`pwd`/$@.tmp && egrep -v '^Declaration.*UBERON_0' $@.tmp > $@
# ----------------------------------------
# RELEASE
@@ -1123,6 +1123,12 @@ intersection_of: UBERON:0004767 ! vomerine tooth
intersection_of: part_of NCBITaxon:8292
[Term]
+id: AAO:0000287 ! maxillary teeth
+property_value: IAO:0000589 "maxillary tooth (amphibian)" xsd:string
+intersection_of: UBERON:0011593 ! maxillary tooth
+intersection_of: part_of NCBITaxon:8292
+
+[Term]
id: AAO:0000125 ! dentary tooth
property_value: IAO:0000589 "dentary tooth (amphibian)" xsd:string
intersection_of: UBERON:0011594 ! dentary tooth
@@ -2600,8 +2606,8 @@ intersection_of: part_of NCBITaxon:8292
[Term]
id: AAO:0000963 ! axial skeleton
-property_value: IAO:0000589 "axial skeleton (amphibian)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (amphibian)" xsd:string
+intersection_of: UBERON:0005944 ! axial skeleton plus cranial skeleton
intersection_of: part_of NCBITaxon:8292
[Term]
@@ -2011,6 +2011,26 @@
+ <!-- http://purl.obolibrary.org/obo/AAO_0000287 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/AAO_0000287">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0011593"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
+ <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_8292"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAO:0000287</oboInOwl:id>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">maxillary tooth (amphibian)</obo:IAO_0000589>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/AAO_0000289 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/AAO_0000289">
@@ -5888,7 +5908,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAO:0000963</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton (amphibian)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton plus cranial skeleton (amphibian)</obo:IAO_0000589>
</owl:Class>
@@ -19895,6 +19915,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0011593 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0011593"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0011594 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0011594"/>
@@ -4207,13 +4207,13 @@ is_a: UBERON:0002137 ! aortic valve
[Term]
id: EMAPA:18043 ! axial skeleton of skeleton of tail of embryo
-property_value: IAO:0000589 "axial skeleton (embryonic mouse)" xsd:string
-is_a: UBERON:0005944 ! axial skeleton
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (embryonic mouse)" xsd:string
+is_a: UBERON:0005944 ! axial skeleton plus cranial skeleton
[Term]
id: EMAPA:17214 ! axial skeleton of skeleton of embryo
-property_value: IAO:0000589 "axial skeleton (embryonic mouse)" xsd:string
-is_a: UBERON:0005944 ! axial skeleton
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (embryonic mouse)" xsd:string
+is_a: UBERON:0005944 ! axial skeleton plus cranial skeleton
[Term]
id: EMAPA:18043 ! axial skeleton of skeleton of tail of embryo
@@ -6790,7 +6790,7 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002090"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0005944"/>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMAPA:17214</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton (embryonic mouse)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton plus cranial skeleton (embryonic mouse)</obo:IAO_0000589>
<obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">postcranial axial skeleton (embryonic mouse)</obo:IAO_0000589>
</owl:Class>
@@ -12002,7 +12002,7 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002090"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0005944"/>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMAPA:18043</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton (embryonic mouse)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton plus cranial skeleton (embryonic mouse)</obo:IAO_0000589>
<obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">postcranial axial skeleton (embryonic mouse)</obo:IAO_0000589>
</owl:Class>
@@ -11048,8 +11048,8 @@ intersection_of: part_of NCBITaxon:9606
[Term]
id: FMA:71221 ! Axial skeleton
-property_value: IAO:0000589 "axial skeleton (post-embryonic human)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+property_value: IAO:0000589 "postcranial axial skeleton (post-embryonic human)" xsd:string
+intersection_of: UBERON:0002090 ! postcranial axial skeleton
intersection_of: part_of NCBITaxon:9606
[Term]
@@ -61429,7 +61429,7 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0005944"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0002090"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
@@ -61438,7 +61438,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:71221</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton (post-embryonic human)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">postcranial axial skeleton (post-embryonic human)</obo:IAO_0000589>
</owl:Class>
@@ -93939,6 +93939,12 @@
+ <!-- http://purl.obolibrary.org/obo/UBERON_0002090 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002090"/>
+
+
+
<!-- http://purl.obolibrary.org/obo/UBERON_0002091 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002091"/>
@@ -104787,12 +104793,6 @@
- <!-- http://purl.obolibrary.org/obo/UBERON_0005944 -->
-
- <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0005944"/>
-
-
-
<!-- http://purl.obolibrary.org/obo/UBERON_0005946 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0005946"/>
@@ -8150,8 +8150,8 @@ intersection_of: part_of NCBITaxon:10088
[Term]
id: MA:0000308 ! axial skeleton
-property_value: IAO:0000589 "axial skeleton (post-embryonic mouse)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (post-embryonic mouse)" xsd:string
+intersection_of: UBERON:0005944 ! axial skeleton plus cranial skeleton
intersection_of: part_of NCBITaxon:10088
[Term]
@@ -6106,7 +6106,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MA:0000308</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton (post-embryonic mouse)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton plus cranial skeleton (post-embryonic mouse)</obo:IAO_0000589>
</owl:Class>
@@ -6162,8 +6162,8 @@ is_a: UBERON:0002137 ! aortic valve
[Term]
id: ncithesaurus:Axial_Skeleton ! Axial Skeleton
-property_value: IAO:0000589 "axial skeleton (ncithesaurus)" xsd:string
-is_a: UBERON:0005944 ! axial skeleton
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (ncithesaurus)" xsd:string
+is_a: UBERON:0005944 ! axial skeleton plus cranial skeleton
[Term]
id: ncithesaurus:Appendicular_Skeleton ! Appendicular Skeleton
@@ -17976,7 +17976,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ncithesaurus#_Axial_Skeleton">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0005944"/>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton (ncithesaurus)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton plus cranial skeleton (ncithesaurus)</obo:IAO_0000589>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncithesaurus:Axial_Skeleton</oboInOwl:id>
</owl:Class>
@@ -1988,8 +1988,8 @@ intersection_of: part_of NCBITaxon:8353
[Term]
id: XAO:0004011 ! axial skeleton
-property_value: IAO:0000589 "axial skeleton (xenopus)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (xenopus)" xsd:string
+intersection_of: UBERON:0005944 ! axial skeleton plus cranial skeleton
intersection_of: part_of NCBITaxon:8353
[Term]
@@ -12506,7 +12506,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XAO:0004011</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton (xenopus)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">axial skeleton plus cranial skeleton (xenopus)</obo:IAO_0000589>
</owl:Class>
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