text def fixes using VSAO

obophenotype · Aug 17, 2012 · 728bf8e · 728bf8e
1 parent 65384e9
commit 728bf8e
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Showing 20 changed files with 201 additions and 121 deletions.
diff --git a/Makefile b/Makefile
@@ -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

diff --git a/mod/uberon-bridge-to-aao.obo b/mod/uberon-bridge-to-aao.obo
@@ -1122,6 +1122,12 @@ property_value: IAO:0000589 "vomerine tooth (amphibian)" xsd:string
 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
@@ -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
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (amphibian)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+intersection_of: UBERON:0005944 ! axial skeleton plus cranial skeleton
 intersection_of: part_of NCBITaxon:8292
 
 [Term]

diff --git a/mod/uberon-bridge-to-aao.owl b/mod/uberon-bridge-to-aao.owl
@@ -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"/>

diff --git a/mod/uberon-bridge-to-emapa.obo b/mod/uberon-bridge-to-emapa.obo
@@ -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
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (embryonic mouse)" xsd:string
-is_a: UBERON:0005944 ! axial skeleton
+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
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (embryonic mouse)" xsd:string
-is_a: UBERON:0005944 ! axial skeleton
+is_a: UBERON:0005944 ! axial skeleton plus cranial skeleton
 
 [Term]
 id: EMAPA:18043 ! axial skeleton of skeleton of tail of embryo

diff --git a/mod/uberon-bridge-to-emapa.owl b/mod/uberon-bridge-to-emapa.owl
@@ -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>
 

diff --git a/mod/uberon-bridge-to-fma.obo b/mod/uberon-bridge-to-fma.obo
@@ -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
+property_value: IAO:0000589 "postcranial axial skeleton (post-embryonic human)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+intersection_of: UBERON:0002090 ! postcranial axial skeleton
 intersection_of: part_of NCBITaxon:9606
 
 [Term]

diff --git a/mod/uberon-bridge-to-fma.owl b/mod/uberon-bridge-to-fma.owl
@@ -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"/>

diff --git a/mod/uberon-bridge-to-ma.obo b/mod/uberon-bridge-to-ma.obo
@@ -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
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (post-embryonic mouse)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+intersection_of: UBERON:0005944 ! axial skeleton plus cranial skeleton
 intersection_of: part_of NCBITaxon:10088
 
 [Term]

diff --git a/mod/uberon-bridge-to-ma.owl b/mod/uberon-bridge-to-ma.owl
@@ -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>
 
 

diff --git a/mod/uberon-bridge-to-ncithesaurus.obo b/mod/uberon-bridge-to-ncithesaurus.obo
@@ -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
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (ncithesaurus)" xsd:string
-is_a: UBERON:0005944 ! axial skeleton
+is_a: UBERON:0005944 ! axial skeleton plus cranial skeleton
 
 [Term]
 id: ncithesaurus:Appendicular_Skeleton ! Appendicular Skeleton

diff --git a/mod/uberon-bridge-to-ncithesaurus.owl b/mod/uberon-bridge-to-ncithesaurus.owl
@@ -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>
 

diff --git a/mod/uberon-bridge-to-xao.obo b/mod/uberon-bridge-to-xao.obo
@@ -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
+property_value: IAO:0000589 "axial skeleton plus cranial skeleton (xenopus)" xsd:string
-intersection_of: UBERON:0005944 ! axial skeleton
+intersection_of: UBERON:0005944 ! axial skeleton plus cranial skeleton
 intersection_of: part_of NCBITaxon:8353
 
 [Term]

diff --git a/mod/uberon-bridge-to-xao.owl b/mod/uberon-bridge-to-xao.owl
@@ -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>