diff --git a/src/ontology/Makefile b/src/ontology/Makefile index bbb3f2403..79b91ad7d 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern. FORMATS = $(sort owl obo json owl) FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) -RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy ) +RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy ) # ---------------------------------------- # Top-level targets @@ -129,7 +129,7 @@ all_imports: $(IMPORT_FILES) # ---------------------------------------- -SUBSETS = appendicular-minimal circulatory-minimal cranial-minimal cumbo digestive-minimal excretory-minimal human-view immune-minimal life-stages-composite life-stages-core life-stages-minimal merged-partonomy metazoan-view mouse-view musculoskeletal-minimal nephron-minimal nervous-minimal pulmonary-minimal renal-minimal reproductive-minimal sensory-minimal xenopus-view amniote-basic euarchontoglires-basic +SUBSETS = appendicular-minimal circulatory-minimal cranial-minimal cumbo digestive-minimal excretory-minimal human-view immune-minimal life-stages-composite life-stages-core life-stages-minimal merged-partonomy mouse-view musculoskeletal-minimal nephron-minimal nervous-minimal pulmonary-minimal renal-minimal reproductive-minimal sensory-minimal xenopus-view amniote-basic euarchontoglires-basic SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS)) SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f))) @@ -701,12 +701,6 @@ $(ONT)-basic.json: $(ONT)-basic.owl $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ convert --check false -f json -o $@.tmp.json &&\ mv $@.tmp.json $@ -basic.obo: basic.owl - $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo -basic.json: basic.owl - $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ - convert --check false -f json -o $@.tmp.json &&\ - mv $@.tmp.json $@ collected-metazoan.obo: collected-metazoan.owl $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo collected-metazoan.json: collected-metazoan.owl @@ -814,9 +808,6 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION reduce -r ELK \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ -basic.owl: - echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false - collected-metazoan.owl: echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml index a9161761c..88eb27f8e 100644 --- a/src/ontology/uberon-odk.yaml +++ b/src/ontology/uberon-odk.yaml @@ -20,7 +20,6 @@ release_artefacts: - full - simple - basic - - custom-basic - custom-collected-metazoan - custom-composite-metazoan - custom-composite-metazoan-basic @@ -89,7 +88,6 @@ subset_group: - id: life-stages-core - id: life-stages-minimal - id: merged-partonomy - - id: metazoan-view - id: mouse-view - id: musculoskeletal-minimal - id: nephron-minimal diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index de7bd68cf..7f377d609 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -69,7 +69,7 @@ update_dynamic_catalog: # This target is invoked as part of the automated CI workflow. # To include a specific check/report in the CI workflow, add it # to the pre-requisites here. -test: $(REPORTDIR)/basic-allcycles \ +test: $(REPORTDIR)/uberon-basic-allcycles \ $(REPORTDIR)/bfo-check.txt \ $(REPORTDIR)/taxon-constraint-check.txt \ $(REPORTDIR)/uberon-edit-xp-check \ @@ -91,7 +91,7 @@ uberon-qc: checks \ quick-bridge-checks \ bridge-checks \ extra-full-bridge-checks \ - $(REPORTDIR)/basic-allcycles \ + $(REPORTDIR)/uberon-basic-allcycles \ $(REPORTDIR)/basic-orphans \ $(REPORTDIR)/composite-metazoan-dv.txt \ $(REPORTDIR)/taxon-constraint-check.txt \ @@ -670,9 +670,6 @@ src-cycles: $(REPORTDIR)/%-allcycles: %.owl $(OWLTOOLS) --no-debug $< --list-cycles -f > $@ -$(REPORTDIR)/basic-allcycles: basic.owl - $(OWLTOOLS) --no-debug $< --list-cycles -f > $@ - # Other checks # ---------------------------------------- @@ -818,7 +815,7 @@ $(REPORTDIR)/bfo-check.txt: $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl reason -r ELK --equivalent-classes-allowed asserted-only > $@ # Similar to above, but with the basic product and without RO -$(REPORTDIR)/bfo-basic-check.txt: basic.owl $(BRIDGEDIR)/uberon-bridge-to-bfo.owl +$(REPORTDIR)/bfo-basic-check.txt: uberon-basic.owl $(BRIDGEDIR)/uberon-bridge-to-bfo.owl $(ROBOT) merge -i $< -i $(BRIDGEDIR)/uberon-bridge-to-bfo.owl \ -I $(URIBASE)/bfo.owl \ reason -r ELK > $@ @@ -1003,16 +1000,8 @@ $(TMPDIR)/uberon-taxmod-%.owl: uberon.owl # Other subsets # ---------------------------------------- -# Basic subset -# FIXME: https://github.com/obophenotype/uberon/issues/3013 -basic.owl: uberon-basic.owl - $(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@ - -basic.obo: basic.owl - $(MAKEOBO) - # Cumbo subset -subsets/cumbo.owl: basic.owl +subsets/cumbo.owl: uberon-basic.owl $(OWLTOOLS) $< --extract-ontology-subset --subset cumbo --iri $(URIBASE)/uberon/$@ -o $@ subsets/cumbo.obo: subsets/cumbo.owl @@ -1031,9 +1020,6 @@ subsets/immaterial.obo: uberon.owl --make-ontology-from-results $(URIBASE)/uberon/$@ \ -o -f obo $@ --reasoner-dispose 2>&1 > $@.LOG -subsets/metazoan-view.owl: basic.owl - cp $< $@ - # The first step is a simple "merge+reason", but it still requires # Owltools because ROBOT has no equivalent to the -x option to simply # ignore unsatisfiable classes without erroring out. @@ -1651,7 +1637,7 @@ normalise_release_serialisation_ofn: sh ../scripts/normalisation/norm_ofn.sh ../../src/ontology/subsets/xenopus-view.owl normalise_release_serialisation_rdfmxml: - sh ../scripts/normalisation/norm_rdfxml.sh ../../basic.owl + sh ../scripts/normalisation/norm_rdfxml.sh ../../uberon-basic.owl sh ../scripts/normalisation/norm_rdfxml.sh ../../uberon-base.owl sh ../scripts/normalisation/norm_rdfxml.sh ../../src/ontology/imports/caro_import.owl src/ontology/imports/fbbt_import.owl sh ../scripts/normalisation/norm_rdfxml.sh ../../src/ontology/subsets/amniote-basic.owl