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1 parent 7e142f9 commit 266c92239f4ff8ce8106bddeb06a2049ffa5bac2 @cmungall cmungall committed Aug 27, 2011
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@@ -10,6 +10,7 @@ all: adult_mouse_xp.obo po_anatomy_xp.obo fly_anatomy_xp.obo zebrafish_anatomy_x
uberon_edit.owl: uberon_edit.obo
obolib-obo2owl --allow-dangling -o $@ $<
+.PRECIOUS: uberon_edit.owl
%.owl: %.obo
obolib-obo2owl --to RDF -o file://`pwd`/$@ $<
@@ -301,10 +302,10 @@ uberon-isa-to-%.obo: uberon.obo
obo-grep.pl -r '^id: $*' $< > $@
# note: use cell.obo for now; TODO: need to take care of duplicate defs in MIREOTs...
-uberon-with-extmod.owl: uberon_edit.obo
+merged.owl: uberon_edit.obo
owltools $< ncbi_taxon_slim.obo GO.obo CHEBI.obo cell.obo PATO.obo PRO.obo --mcat -o file://`pwd`/$@
-.PRECIOUS: uberon-with-extmod.owl
-uberon-with-extmod.obo: uberon-with-extmod.owl
+.PRECIOUS: uberon-merged.owl
+merged.obo: uberon-merged.owl
obolib-owl2obo -o $@ $<
mod/bridges:
@@ -331,23 +332,25 @@ mod-%.obo: mod1-%.obo
# blip -table_pred ontol_db:bf_parentRT/2 -i $< -r fma_simple -r mouse_anatomy -r zebrafish_anatomy -r fly_anatomy -r xenopus_anatomy ontol-query -query "entity_xref(_,X),bf_parentRT(X,ID),entity_label(ID,_)" -to obo > $@.tmp && mv $@.tmp $@
#.PRECIOUS: %-extmod.obo
+# TODO: use Oort
%-simple.obo: %.obo
grep -v ^intersection_of $< | perl -ne 'print unless (/^relationship: (\S+)/ && ($$1 ne "part_of" && $$1 ne "develops_from"))' > $@
-%-bridge.obo: %-with-isa.obo
- obo-filter-tags.pl -t id -t is_a $< | obo-grep.pl --neg -r 'id: UBERON' - | obo-grep.pl -r Term - > $@
+# TODO: use Oort
+#%-bridge.obo: %-with-isa.obo
+# obo-filter-tags.pl -t id -t is_a $< | obo-grep.pl --neg -r 'id: UBERON' - | obo-grep.pl -r Term - > $@
-%-merged.obo: %.obo %-mireot.obo %-bridge.obo
- obo2obo -o $@ $< $*-mireot.obo $*-bridge.obo
+#%-merged.obo: %.obo %-mireot.obo %-bridge.obo
+# obo2obo -o $@ $< $*-mireot.obo $*-bridge.obo
%_all.obo: %_links_obo.obo
obo2obo -o $@ $< $*_obo.obo part_of.obo
uberon_edit-implied.obo: uberon_edit.obo
obo2obo -allowdangling -o -saveimpliedlinks -allowdangling $@ $<
-uberon_edit-mireot-implied.obo: uberon_edit-mireot.obo
- obo2obo -o -saveimpliedlinks $@ $<
+#uberon_edit-mireot-implied.obo: uberon_edit-mireot.obo
+# obo2obo -o -saveimpliedlinks $@ $<
uberon.obo: uberon_edit-implied.obo
obo-filter-external.pl --xp2rel $< | egrep -v '^(domain|range):' > $@.tmp && obo-add-data-version.pl $@.tmp > $@
@@ -393,12 +396,11 @@ caro-usage-%.txt:
%-to-caro.obo:
obo-promote-dbxref-to-relationship.pl --minimal --idspace CARO --relation is_a $*.obo > $@.tmp && mv $@.tmp $@
+# OBO-Format Hacking
%-cmt.obo: %.obo
obo-add-comments.pl -t xref -t intersection_of uberon_edit.obo animal_gross_anatomy/*/*.obo ../cell_type/cell.obo ../caro/caro.obo MIAA.obo animal_gross_anatomy/*/*/*.obo ~/cvs/fma-conversion/fma2/fma2.obo gemina_anatomy.obo birnlex_anatomy.obo NIF-GrossAnatomy.obo hao.obo HOG.obo efo_anat.obo $< > $@
-uberon_ext.pro:
- blip -debug anatomy -r zebrafish_anatomy -r xenopus_anatomy -r uberon -u query_anatomy -i zfa-xao-aln.tbl findall extend_ontology/0 > $@
-
+# Induction of links from sources
links-uberon-fma.txt:
blip -debug anatomy -r fma_simple -r uberonp -u query_obo -table_pred parent_by_xref/4 findall "parent_by_xref_nr(uberon,_,_,_)" -label > $@.tmp && cut -f3-8 $@.tmp | sort -u > $@
@@ -469,18 +471,15 @@ align-uberon-%.obo:
obol -goal "consult('ignore_word_adult.pro')" -u onto_grep -r $* -i uberon_edit.obo onto-exact-align -ont2 uberon -exclude_xref_strict -exclude_xref -disp 'allow(related)' -disp 'allow(narrow)' -disp 'allow(broad)' -disp 'format(obo)' > $@.tmp && mv $@.tmp $@
.PRECIOUS: align-uberon-%.obo
-
+# get synonyms from sources
syns-uberon-%.obo:
blip -r $* -r uberon -i fetchsyns.pro -goal write_syns,halt > $@
-merge-uberon-%.obo: align-uberon-%.obo
- obo-merge-tags.pl -t xref uberon_edit.obo $< > $@
+#uberon-go-defs.txt:
+# blip -r go $(GO_XP_ARGS) -u ontol_db findall "belongs(X,uberon),differentium(Y,_,X),def(Y,D),belongs(Y,biological_process),(\+ def(X,_) ; def(X,'.'))" -select "td(X,Y,D)" -label > $@.tmp && sort -u $@.tmp > $@
-uberon-go-defs.txt:
- blip -r go $(GO_XP_ARGS) -u ontol_db findall "belongs(X,uberon),differentium(Y,_,X),def(Y,D),belongs(Y,biological_process),(\+ def(X,_) ; def(X,'.'))" -select "td(X,Y,D)" -label > $@.tmp && sort -u $@.tmp > $@
-
-%-syns.obo: %.obo
- obol -debug obol -i $< -u obol_anat_xpgen obol-generate-synonyms -query "id_idspace(ID,'UBERON'),genus(ID,_)" > $@.tmp && mv $@.tmp $@
+#%-syns.obo: %.obo
+# obol -debug obol -i $< -u obol_anat_xpgen obol-generate-synonyms -query "id_idspace(ID,'UBERON'),genus(ID,_)" > $@.tmp && mv $@.tmp $@
%-defs.obo: %.obo
obol -debug obol -r pato -i $< -u obol_anat_xpgen obol-generate-textdefs -idspace UBERON > $@.tmp && mv $@.tmp $@
@@ -561,14 +560,8 @@ newterms-zebrafish-fly.obo:
newterms-hao-fly.obo:
obol -u onto_grep onto-3-way-align -r fly_anatomy -r hao -r uberon -ont1 fly_anatomy.ontology -ont2 HAO -ont3 uberon > $@
-newterms-zebrafish-ehdaa.obo:
- obol -u onto_grep onto-3-way-align -r ehdaa -r zebrafish_anatomy -r uberon -ont1 human-dev-anat-abstract -ont2 zebrafish_anatomy -ont3 uberon > $@
-
-newterms-fma-ehdaa.obo:
- obol -u onto_grep onto-3-way-align -r ehdaa -r fma -i fma3-latin.obo -r uberon -ont1 human-dev-anat-abstract -ont2 fma -ont3 uberon > $@
-
newterms-fma-ehdaa2.obo:
- obol -debug index -u onto_grep onto-3-way-align -r ehdaa2 -r fma -i fma3-latin.obo -r uberonp -ont1 abstract_anatomy -ont2 fma -ont3 uberon > $@
+ obol -debug index -u onto_grep onto-3-way-align -r ehdaa2 -r fma -i fma3-latin.obo -r uberonp -ont1 'http://www.xspan.org/obo.owl#' -ont2 fma -ont3 uberon > $@
newterms-fma-emapa.obo:
obol -u onto_grep onto-3-way-align -r emapaa -r fma -i fma3-latin.obo -r uberonp -ont1 abstract_anatomy -ont2 fma -ont3 uberon > $@
@@ -1082,8 +1075,10 @@ uberon-taxmod-%.obo: uberon-taxmod-%.ids
# ----------------------------------------
RELDIR=$(HOME)/cvs/obo-svn/ontologies/UBERON
release: mod/bridges uberon-taxmods
+ cp uberon_edit.owl $(RELDIR)/core.owl ;\
+ cp uberon_edit.obo $(RELDIR)/core.obo ;\
cp uberon.{obo,owl} $(RELDIR) ;\
- cp uberon-with-extmod.{obo,owl} $(RELDIR)/mod ;\
+ cp merged.{obo,owl} $(RELDIR)/mod ;\
cp uberon-taxmod-*.{obo,owl} $(RELDIR)/mod ;\
cp mod/*.{obo,owl} $(RELDIR)/mod ;\
cp uberon-simple*.{obo,owl} $(RELDIR)/subsets ;\
@@ -2127,7 +2127,7 @@ intersection_of: part_of NCBITaxon:8292
[Term]
id: AAO:0000060 ! cartilage
-intersection_of: UBERON:0002418 ! cartilage
+intersection_of: UBERON:0002418 ! cartilage tissue
intersection_of: part_of NCBITaxon:8292
[Term]
@@ -3473,6 +3473,14 @@ id: EHDAA:547 ! primitive groove
is_a: UBERON:0004056 ! primitive groove
[Term]
+id: EHDAA:4786 ! lateral nasal process
+is_a: UBERON:0004067 ! lateral nasal prominence
+
+[Term]
+id: EHDAA:4792 ! medial nasal process
+is_a: UBERON:0004068 ! medial nasal prominence
+
+[Term]
id: EHDAA:5871 ! mandibular process
is_a: UBERON:0005867 ! mandibular prominence
@@ -4312,6 +4312,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA_4786 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA_4786">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004067"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA:4786</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA_4790 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA_4790">
@@ -4321,6 +4330,15 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA_4792 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA_4792">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004068"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA:4792</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA_4796 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA_4796">
@@ -2126,7 +2126,7 @@ is_a: UBERON:0007812 ! post-anal tail
[Term]
id: EHDAA2:0003087 ! cartilage
-is_a: UBERON:0002418 ! cartilage
+is_a: UBERON:0002418 ! cartilage tissue
[Term]
id: EHDAA2:0000997 ! liver
@@ -3117,6 +3117,14 @@ id: EHDAA2:0001944 ! sulcus limitans
is_a: UBERON:0005478 ! sulcus limitans
[Term]
+id: EHDAA2:0000916 ! lateral nasal process
+is_a: UBERON:0004067 ! lateral nasal prominence
+
+[Term]
+id: EHDAA2:0001076 ! medial nasal process
+is_a: UBERON:0004068 ! medial nasal prominence
+
+[Term]
id: EHDAA2:0001061 ! mandibular process
is_a: UBERON:0005867 ! mandibular prominence
@@ -3409,6 +3417,18 @@ id: EHDAA2:0001078 ! medial nasal process ectoderm
is_a: UBERON:0005233 ! medial-nasal process ectoderm
[Term]
+id: EHDAA2:0001077 ! medial nasal process mesenchyme
+is_a: UBERON:0009204 ! medial nasal process mesenchyme
+
+[Term]
+id: EHDAA2:0000917 ! lateral nasal process mesenchyme
+is_a: UBERON:0009205 ! lateral nasal process mesenchyme
+
+[Term]
+id: EHDAA2:0000918 ! lateral nasal process surface ectoderm
+is_a: UBERON:0009206 ! lateral nasal process surface ectoderm
+
+[Term]
id: EHDAA2:0001309 ! optic eminence ectoderm
is_a: UBERON:0005234 ! optic eminence ectoderm
@@ -3607,6 +3607,33 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0000916 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0000916">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004067"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0000916</oboInOwl:id>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0000917 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0000917">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009205"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0000917</oboInOwl:id>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0000918 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0000918">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009206"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0000918</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0000919 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0000919">
@@ -4399,6 +4426,24 @@
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0001076 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0001076">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004068"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0001076</oboInOwl:id>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/EHDAA2_0001077 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0001077">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009204"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2:0001077</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EHDAA2_0001078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EHDAA2_0001078">
@@ -5725,6 +5725,10 @@ id: EMAPA:17557 ! basal plate of lateral wall of medulla oblongata
is_a: UBERON:0004064 ! basal plate
[Term]
+id: EMAPA:16805 ! latero-nasal process
+is_a: UBERON:0004067 ! lateral nasal prominence
+
+[Term]
id: EMAPA:16808 ! medial-nasal process
is_a: UBERON:0004068 ! medial nasal prominence
@@ -6549,6 +6553,18 @@ id: EMAPA:16809 ! ectoderm of medial-nasal process
is_a: UBERON:0005233 ! medial-nasal process ectoderm
[Term]
+id: EMAPA:16810 ! mesenchyme
+is_a: UBERON:0009204 ! medial nasal process mesenchyme
+
+[Term]
+id: EMAPA:16807 ! mesenchyme of latero-nasal process
+is_a: UBERON:0009205 ! lateral nasal process mesenchyme
+
+[Term]
+id: EMAPA:16806 ! ectoderm of latero-nasal process
+is_a: UBERON:0009206 ! lateral nasal process surface ectoderm
+
+[Term]
id: EMAPA:16323 ! ectoderm of optic eminence
is_a: UBERON:0005234 ! optic eminence ectoderm
@@ -3430,6 +3430,33 @@
+ <!-- http://purl.obolibrary.org/obo/EMAPA_16805 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EMAPA_16805">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004067"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMAPA:16805</oboInOwl:id>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/EMAPA_16806 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EMAPA_16806">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009206"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMAPA:16806</oboInOwl:id>
+ </owl:Class>
+
+
+
+ <!-- http://purl.obolibrary.org/obo/EMAPA_16807 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EMAPA_16807">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009205"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMAPA:16807</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EMAPA_16808 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EMAPA_16808">
@@ -3448,6 +3475,15 @@
+ <!-- http://purl.obolibrary.org/obo/EMAPA_16810 -->
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/EMAPA_16810">
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0009204"/>
+ <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMAPA:16810</oboInOwl:id>
+ </owl:Class>
+
+
+
<!-- http://purl.obolibrary.org/obo/EMAPA_16811 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EMAPA_16811">
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