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Updated makefile for new cl-basic and cl-simple
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| Original file line number | Diff line number | Diff line change |
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@@ -20,3 +20,85 @@ imports/ncbitaxon_import.owl: | |
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| object_properties.txt: $(SRC) | ||
| $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/object-properties-in-signature.sparql $@ | ||
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| $(ONT)-simple.obo: $(ONT)-simple.owl | ||
| $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo &&\ | ||
| grep -v ^owl-axioms $@.tmp.obo > $@.tmp &&\ | ||
| cat $@.tmp | perl -0777 -e '$$_ = <>; s/^name[:].*?\nname[:]/name:/g; print' | perl -0777 -e '$$_ = <>; s/def[:].*?\ndef[:]/def:/g; print' > $@ | ||
| rm -f $@.tmp.obo $@.tmp | ||
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| simple_seed.txt: $(SRC) #$(ONTOLOGYTERMS) #prepare_patterns | ||
| $(ROBOT) query --use-graphs false -f csv -i $< --query ../sparql/object-properties.sparql $@.tmp &&\ | ||
| cat $@.tmp $(ONTOLOGYTERMS) | sort | uniq > $@ &&\ | ||
| echo "http://www.geneontology.org/formats/oboInOwl#SubsetProperty" >> $@ &&\ | ||
| echo "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty" >> $@ | ||
| #rm -f [email protected] | ||
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| non_native_classes.txt: $(SRC) | ||
| $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/non-native-classes.sparql $@.tmp &&\ | ||
| cat $@.tmp | sort | uniq > $@ | ||
| rm -f $@.tmp | ||
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| $(ONT)-simple.owl: $(SRC) $(OTHER_SRC) simple_seed.txt non_native_classes.txt $(ONTOLOGYTERMS) | ||
| $(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) --collapse-import-closure true \ | ||
| reason --reasoner ELK \ | ||
| relax \ | ||
| remove --axioms equivalent \ | ||
| relax \ | ||
| filter --term-file simple_seed.txt --trim true --select "annotations ontology anonymous parents object-properties self" --preserve-structure false \ | ||
| remove --term-file non_native_classes.txt --preserve-structure false \ | ||
| reduce -r ELK \ | ||
| annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@ | ||
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| # TODO add back: remove --term-file non_native_classes.txt \ | ||
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| $(ONT).obo: $(ONT)-basic.owl | ||
| $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo | ||
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| $(PATTERNDIR)/dosdp-patterns: .FORCE | ||
| echo "WARNING WARNING Skipped until fixed: delete from cl.Makefile" | ||
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| $(ONT)-basic.owl: $(SRC) $(OTHER_SRC) $(ONTOLOGYTERMS) $(KEEPRELATIONS) simple_seed.txt non_native_classes.txt | ||
| $(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) --collapse-import-closure true \ | ||
| reason --reasoner ELK \ | ||
| relax \ | ||
| remove --axioms equivalent \ | ||
| relax \ | ||
| filter --term-file simple_seed.txt --trim true --select "annotations ontology anonymous parents object-properties self" --preserve-structure false \ | ||
| remove --term-file non_native_classes.txt --preserve-structure false \ | ||
| remove --term-file $(KEEPRELATIONS) --select complement --select object-properties --trim true \ | ||
| reduce -r ELK \ | ||
| annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@ | ||
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| oort: $(SRC) | ||
| ontology-release-runner --reasoner elk $< --no-subsets --allow-equivalent-pairs --simple --relaxed --asserted --allow-overwrite --outdir oort | ||
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| KEEPRS=part_of develops_from | ||
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| $(ONT)-basic.owl: $(ONT)-simple.owl | ||
| owltools $< --make-subset-by-properties $(KEEPRS) -o -f owl $@ | ||
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| $(ONT)-simple.owl: oort | ||
| cp oort/$@ $@ | ||
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| $(ONT)-basic.obo: $(ONT)-simple.obo | ||
| owltools $< --make-subset-by-properties $(KEEPRS) -o -f obo $@ | ||
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| $(ONT)-simple.obo: oort | ||
| cp oort/$@ $@ | ||
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| # TODO add BACK remove --term-file $(KEEPRELATIONS) --select complement --select object-properties --trim true \ | ||
| # TODO add BACK remove --term-file non_native_classes.txt \ | ||
| # remove --term-file $(KEEPRELATIONS) --select complement --select object-properties --trim true \ | ||
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| fail_seed_by_entity_type_cl: | ||
| robot query --use-graphs false -f csv -i cl-edit.owl --query ../sparql/object-properties.sparql $@.tmp &&\ | ||
| cat $@.tmp | sort | uniq > $@.txt && rm -f $@.tmp | ||
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| works_seed_by_entity_type_cl: | ||
| robot query --use-graphs false -f csv -i cl-edit.owl --query ../sparql/object-properties-in-signature.sparql $@.tmp &&\ | ||
| cat $@.tmp | sort | uniq > $@.txt && rm -f $@.tmp | ||
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