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1 parent c3e3fa3 commit c7e104b4c50e6865c81dbb81a41314fddeb38f9e @cmungall cmungall committed Sep 6, 2012
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@@ -9,34 +9,34 @@ all: uberon-qc
# ----------------------------------------
IMPORTS= $(OBO)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
-uberon_edit-NI.owl: uberon_edit.obo
- obolib-obo2owl -x -xm INPLACE --allow-dangling -o $@ $<
-uberon_edit.owl: uberon_edit-NI.owl
+# edit owl file has
+# * macros
+# * imports to ncbitax
+uberon_edit.owl: uberon_edit-XM.owl
owltools $< --add-imports-declarations $(IMPORTS) // -o -f functional file://`pwd`/$@
.PRECIOUS: uberon_edit.owl
+uberon_edit-XM.owl: uberon_edit.obo
+ obolib-obo2owl -x -xm INPLACE --allow-dangling -o $@ $<
+
+external-disjoints.owl: external-disjoints.obo
+ obolib-obo2owl --allow-dangling -o $@ $<
-uberon_edit-ndd.obo: uberon_edit.obo
- ./util/remove-dangling-disjoint.pl $< > $@
-uberon_edit-ndd.owl: uberon_edit-ndd.obo
- owltools $< -o -f functional file://`pwd`/$@
+#uberon_edit-ndd.obo: uberon_edit.obo
+# ./util/remove-dangling-disjoint.pl $< > $@
+#uberon_edit-ndd.owl: uberon_edit-ndd.obo
+# owltools $< -o -f functional file://`pwd`/$@
# owltools $< --add-imports-declarations $(IMPORTS) // -o -f functional file://`pwd`/$@
-%-noimports.obo: %.obo
- grep -v ^import: $< > $@
+#%-noimports.obo: %.obo
+# grep -v ^import: $< > $@
# REPLACEME
# step 1 - use noimports
# step 2 - with imports, --add-support-from-imports
# todo: fix chemosensory organ problem...
# todo: fix relation IDs
-uberon_edit-implied.obo: uberon_edit-ndd.owl
+uberon_edit-implied.obo: uberon_edit.obo
ontology-release-runner --catalog-xml $(CATALOG) --add-support-from-imports --no-subsets --skip-format owx --outdir r/ --reasoner elk --asserted --allow-overwrite $< && cp r/uberon.obo $@
-##OLD:
-##uberon_edit-implied.obo: uberon_edit-noimports.obo
-## obo2obo -allowdangling -o -saveimpliedlinks -allowdangling $@ $<
-
-#uberon_edit-mireot-implied.obo: uberon_edit-mireot.obo
-# obo2obo -o -saveimpliedlinks $@ $<
# TODO: use by Oort
uberon.obo: uberon_edit-implied.obo
@@ -54,13 +54,12 @@ uberon.obo: uberon_edit-implied.obo
#uberon-merged.owl: uberon_edit.obo pr-core.obo
# ontology-release-runner --outdir . --prefix $(OBO)/UBERON_ --prefix $(OBO)/CL_ --reasoner elk --simple --no-subsets --re-mireot --allow-overwrite uberon_edit.obo -b cl-core.obo pr-core.obo GO.obo CHEBI.obo PATO.obo $(OBO)/ncbitaxon/subsets/taxslim.owl
-clear-r:
- (test -f r/staging/.lock && rm r/staging/.lock) || echo
-# NEW
+#clear-r:
+# (test -f r/staging/.lock && rm r/staging/.lock) || echo
# taxon checks (TODO: SWITCH TO THIS)
-uberon_edit-plus-tax-equivs.owl: uberon_edit.owl
- owltools --catalog-xml $(CATALOG) $< mod/uberon-bridge-to-*.owl --merge-support-ontologies --translate-disjoint-to-equivalent -o -f functional file://`pwd`/$@
+uberon_edit-plus-tax-equivs.owl: uberon_edit.owl external-disjoints.obo
+ owltools --catalog-xml $(CATALOG) $< external-disjoints.obo mod/uberon-bridge-to-*.owl --merge-support-ontologies --translate-disjoint-to-equivalent -o -f functional file://`pwd`/$@
.PRECIOUS: uberon_edit-plus-tax-equivs.owl
new-taxcheck.txt: uberon_edit-plus-tax-equivs.owl
owltools --catalog-xml $(CATALOG) $< --run-reasoner -r elk -u > $@
@@ -69,29 +68,27 @@ new-taxcheck-%.txt: uberon_edit.owl
#oort-taxcheck: uberon_edit-plus-tax-equivs.owl clear-r
# ontology-release-runner --catalog-xml $(CATALOG) --no-subsets --skip-format owx --outdir r/ --reasoner elk --allow-overwrite $<
-oort-min: uberon_edit-noimports.obo clear-r
- ontology-release-runner --catalog-xml $(CATALOG) --no-subsets --skip-format owx --outdir r/ --prefix $(OBO)/UBERON_ --prefix $(OBO)/CL_ --reasoner elk --asserted --expand-xrefs --re-mireot --allow-overwrite $< $(OBO)/cl.owl pr-core.obo $(OBO)/go.owl CHEBI.obo $(OBO)/pato.owl $(OBO)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
+#oort-min: uberon_edit-noimports.obo clear-r
+# ontology-release-runner --catalog-xml $(CATALOG) --no-subsets --skip-format owx --outdir r/ --prefix $(OBO)/UBERON_ --prefix $(OBO)/CL_ --reasoner elk --asserted --expand-xrefs --re-mireot --allow-overwrite $< $(OBO)/cl.owl pr-core.obo $(OBO)/go.owl CHEBI.obo $(OBO)/pato.owl $(OBO)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
-oort: uberon_edit-noimports.obo clear-r
- ontology-release-runner --catalog-xml $(CATALOG) --expand-macros-inplace --outdir r/ --prefix $(OBO)/UBERON_ --reasoner elk --asserted --simple --expand-xrefs --re-mireot --allow-overwrite $< $(OBO)/cl.owl pr-core.obo $(OBO)/go.owl CHEBI.obo $(OBO)/pato.owl $(OBO)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
+#oort: uberon_edit.obo clear-r
+# ontology-release-runner --catalog-xml $(CATALOG) --expand-macros-inplace --outdir r/ --prefix $(OBO)/UBERON_ --reasoner elk --asserted --simple --expand-xrefs --re-mireot --allow-overwrite $< $(OBO)/cl.owl pr-core.obo $(OBO)/go.owl CHEBI.obo $(OBO)/pato.owl $(OBO)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
# ontology-release-runner --outdir r/ --enforceEL --reasoner jcel --asserted --simple --expand-xrefs --re-mireot --allow-overwrite uberon_edit.obo cl-core.obo pr-core.obo GO.obo CHEBI.obo PATO.obo
# ontology-release-runner -outdir stagedir -reasoner jcel --asserted --simple --expand-xrefs --re-mireot --expand-macros --allow-overwrite uberon_edit.obo cl-core.obo pr-core.obo
# TODO - expand macros
%.owl: %.obo
obolib-obo2owl -o $@ $<
-# roundtrip
-%-rt.obo: %.owl
- obolib-owl2obo -o $@ $<
-
-%.owlcheck: %.obo
- obolib-obo2owl --allow-dangling -o $@ $< && obolib-owl2obo -o $@-rt.obo $@
+#%.owlcheck: %.obo
+# obolib-obo2owl --allow-dangling -o $@ $< && obolib-owl2obo -o $@-rt.obo $@
# check for dangling classes
+# TODO: add to Oort
%-orphans: %.obo
obo-grep.pl --neg -r "(is_a|intersection_of|is_obsolete):" $< | obo-grep.pl -r Term - | obo-grep.pl --neg -r "id: UBERON:(0001062|0000000)" - | obo-grep.pl -r Term - > $@.tmp && obo-skip-header.pl $@.tmp > $@
+# TODO: add to Oort
%-xp-check: %.obo
obo-check-xps.pl $< >& $@ || echo "problems"
@@ -101,9 +98,11 @@ oort: uberon_edit-noimports.obo clear-r
%-el.owl: %.owl
makeElWithoutReasoning.sh -i `pwd`/$< -o `pwd`/$@
+# simplified CHEBI - we only want to follow SubClassOf in closure
CHEBI.obo: $(HOME)/cvs/obo/ontology/chemical/chebi.obo
perl -ne 'print unless /^relationship/' $< | grep -v ^xref > $@
+# See: http://douroucouli.wordpress.com/2012/07/03/45/
depictions.owl: uberon_edit.obo
./util/mk-image-ont.pl $< > $@
@@ -115,6 +114,7 @@ QC_FILES = uberon_edit.owl\
uberon-obscheck.txt\
uberon-orphans\
uberon-synclash\
+ external-disjoints.owl\
mod/bridges\
new-taxcheck.txt\
uberon_edit-cycles\
@@ -293,7 +293,7 @@ uberon-isa-to-%.obo: uberon.obo
#merged.owl: uberon_edit-implied.obo cl-core.obo ncbi_taxon_slim.obo
# owltools $< cl-core.obo --merge-support-ontologies ncbi_taxon_slim.obo GO.obo CHEBI.obo PATO.obo pr-core.obo --mcat --prefix http://purl.obolibrary.org/obo/UBERON_ --prefix http://purl.obolibrary.org/obo/CL_ -n 'http://purl.obolibrary.org/obo/uberon/merged.owl' -o file://`pwd`/$@
# NOTE!!! currently merged is not pre-reasoned...
-merged.owl: uberon_edit-ndd.owl cl-core.obo ncbi_taxon_slim.obo
+merged.owl: uberon_edit.obo cl-core.obo ncbi_taxon_slim.obo
owltools $< cl-core.obo --merge-support-ontologies ncbi_taxon_slim.obo GO.obo CHEBI.obo PATO.obo pr-core.obo --mcat --prefix http://purl.obolibrary.org/obo/UBERON_ --prefix http://purl.obolibrary.org/obo/CL_ -n 'http://purl.obolibrary.org/obo/uberon/merged.owl' -o file://`pwd`/$@
.PRECIOUS: merged.owl
merged.obo: merged.owl
@@ -1079,6 +1079,7 @@ release:
cp uberon-simple.obo $(RELDIR)/basic.obo ;\
cp uberon-simple.owl $(RELDIR)/basic.owl ;\
cp mod/*.{obo,owl} $(RELDIR)/bridge/ ;\
+ cp external-disjoints.{obo,owl} $(RELDIR)/bridge/ ;\
cp uberon-taxmod-amniote.obo $(RELDIR)/subsets/amniote-basic.obo ;\
cp uberon-taxmod-amniote.owl $(RELDIR)/subsets/amniote-basic.owl ;\
cp uberon-taxmod-aves.obo $(RELDIR)/subsets/aves-basic.obo ;\
View
@@ -43967,8 +43967,7 @@ namespace: abstract_anatomy
relationship: ends_at TS26 ! TS26 (E18)
relationship: part_of EMAPA:17529 ! vibrissa
relationship: starts_at TS24 ! TS24 (E16)
-intersection_of: UBERON:0003199 ! follicle
-intersection_of: part_of EMAPA:17529 ! vibrissa
+relationship: part_of EMAPA:17529 ! vibrissa
[Term]
id: EMAPA:26759
View
@@ -536,3 +536,10 @@ id: UBERON:0011245 ! infra-orbital canal of maxilla
disjoint_from: ZFA:0005392 ! infraorbital sensory canal
disjoint_from: TAO:0001811 ! infraorbital sensory canal
+[Term]
+id: UBERON:0000950 ! gracilis
+disjoint_from: FBbt:00003277 ! salivary pump muscle 13
+
+[Term]
+id: UBERON:0000964 ! cornea
+disjoint_from: FBbt:00004191 ! cornea
View
@@ -23,6 +23,7 @@ anatomy(geisha).
anatomy(vsao).
anatomy(vhog).
anatomy(galen).
+anatomy(rad).
allow_dangling(ceph).
allow_dangling(uberon_edit).
@@ -2665,13 +2665,13 @@ intersection_of: UBERON:0002103 ! hindlimb
intersection_of: part_of NCBITaxon:8292
[Term]
-id: AAO:0000199 ! fore propodium
+id: AAO:0000887 ! hind propodium
property_value: IAO:0000589 "hindlimb stylopod (amphibian)" xsd:string
intersection_of: UBERON:0000376 ! hindlimb stylopod
intersection_of: part_of NCBITaxon:8292
[Term]
-id: AAO:0000887 ! hind propodium
+id: AAO:0000199 ! fore propodium
property_value: IAO:0000589 "forelimb stylopod (amphibian)" xsd:string
intersection_of: UBERON:0003822 ! forelimb stylopod
intersection_of: part_of NCBITaxon:8292
@@ -3001,6 +3001,12 @@ intersection_of: UBERON:0002384 ! connective tissue
intersection_of: part_of NCBITaxon:8292
[Term]
+id: AAO:0000121 ! dense connective tissue
+property_value: IAO:0000589 "dense connective tissue (amphibian)" xsd:string
+intersection_of: UBERON:0011823 ! dense connective tissue
+intersection_of: part_of NCBITaxon:8292
+
+[Term]
id: AAO:0000857 ! fore digit
property_value: IAO:0000589 "hand digit (amphibian)" xsd:string
intersection_of: UBERON:0002389 ! hand digit
@@ -4699,6 +4705,12 @@ intersection_of: UBERON:0010880 ! gular fold
intersection_of: part_of NCBITaxon:8292
[Term]
+id: AAO:0010530 ! mesorchium
+property_value: IAO:0000589 "mesorchium (amphibian)" xsd:string
+intersection_of: UBERON:0011879 ! mesorchium
+intersection_of: part_of NCBITaxon:8292
+
+[Term]
id: AAO:ENTITY
name: AAO entity
intersection_of: UBERON:0001062 ! anatomical entity
@@ -830,6 +830,26 @@
+ <!-- http://purl.obolibrary.org/obo/AAO_0000121 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/AAO_0000121">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0011823"/>
+ <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:0000121</oboInOwl:id>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dense connective tissue (amphibian)</obo:IAO_0000589>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/AAO_0000124 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/AAO_0000124">
@@ -1256,7 +1276,7 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000376"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0003822"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_8292"/>
@@ -1265,7 +1285,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAO:0000199</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hindlimb stylopod (amphibian)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">forelimb stylopod (amphibian)</obo:IAO_0000589>
</owl:Class>
@@ -5198,7 +5218,7 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0003822"/>
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000376"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_8292"/>
@@ -5207,7 +5227,7 @@
</owl:Class>
</owl:equivalentClass>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAO:0000887</oboInOwl:id>
- <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">forelimb stylopod (amphibian)</obo:IAO_0000589>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hindlimb stylopod (amphibian)</obo:IAO_0000589>
</owl:Class>
@@ -10942,6 +10962,26 @@
+ <!-- http://purl.obolibrary.org/obo/AAO_0010530 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/AAO_0010530">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0011879"/>
+ <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:0010530</oboInOwl:id>
+ <obo:IAO_0000589 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mesorchium (amphibian)</obo:IAO_0000589>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/AAO_0010531 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/AAO_0010531">
@@ -20019,6 +20059,18 @@
<!-- http://purl.obolibrary.org/obo/UBERON_0011773 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0011773"/>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/UBERON_0011823 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0011823"/>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/UBERON_0011879 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0011879"/>
</rdf:RDF>
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