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1 parent 22e13b9 commit bab7bb7cf3885360451f29a981faeb1040d43007 @cmungall cmungall committed May 5, 2012
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@@ -10,8 +10,8 @@ all: adult_mouse_xp.obo po_anatomy_xp.obo zebrafish_anatomy_xp.obo worm_anatomy_
# General release management
# ----------------------------------------
uberon_edit.owl: uberon_edit.obo
-# obolib-obo2owl -x -xm GCI --allow-dangling -o $@ $<
- obolib-obo2owl --allow-dangling -o $@ $<
+ obolib-obo2owl -x -xm INPLACE --allow-dangling -o $@ $<
+# obolib-obo2owl --allow-dangling -o $@ $<
.PRECIOUS: uberon_edit.owl
# ----------------------------------------
@@ -32,7 +32,7 @@ oort-min: clear-r
ontology-release-runner --no-subsets --skip-format owx --outdir r/ --prefix $(OBO)/UBERON_ --prefix $(OBO)/CL_ --reasoner elk --asserted --expand-xrefs --re-mireot --allow-overwrite uberon_edit.obo $(OBO)/cl.owl pr-core.obo $(OBO)/go.owl CHEBI.obo $(OBO)/pato.owl $(OBO)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl
oort: clear-r
- ontology-release-runner --outdir r/ --prefix $(OBO)/UBERON_ --reasoner hermit --asserted --simple --expand-xrefs --re-mireot --allow-overwrite uberon_edit.obo $(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 --expand-macros-inplace --outdir r/ --prefix $(OBO)/UBERON_ --reasoner elk --asserted --simple --expand-xrefs --re-mireot --allow-overwrite uberon_edit.obo $(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
@@ -140,12 +140,15 @@ multi_closure-ontol_db.pro: merged.obo
efo_anat.obo:
blip -r efo ontol-subset -query "subclassRT(ID,'EFO:0000635')" -to obo > $@.tmp && mv $@.tmp $@
+# note that this is now partly hand-edited
emapaa.obo:
blip-ddb -debug index -r emapa -consult fix_emapa.pro -goal ix,rewrite io-convert -to obo -o $@
-ehdaaa.obo:
- blip-ddb -debug index -r ehdaa -consult fix_emapa.pro -goal ix,rewrite io-convert -to obo -o $@
+emapaa-inferred.obo: emapaa.obo
+ owltools $< uberon.owl mod/uberon-bridge-to-emapa.owl --merge-support-ontologies --run-reasoner -r elk --assert-implied -o -f obo $@
+emapaa-remainder.obo: emapaa-inferred.obo
+ obo-grep.pl -r 'id: (EMAPA|part_of)' $< > $@
sao.obo:
blip -r sao -u ontol_manifest_metadata_from_sao io-convert -to obo -o $@
@@ -928,7 +931,7 @@ mod/bridges:
cd mod && ../make-bridge-ontologies-from-xrefs.pl ../uberon_edit.obo
RELDIR=trunk
-release: mod/bridges all_taxmods
+release:
cp uberon_edit.owl $(RELDIR)/core.owl ;\
cp uberon_edit.obo $(RELDIR)/core.obo ;\
cp uberon.{obo,owl} $(RELDIR) ;\
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