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[Experimental] Replace OWLTools with ODK ROBOT plugin #3476

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[Experimental] Replace OWLTools with ODK ROBOT plugin #3476

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c1fbdd9
Remove unused tmp/simple-slim-seed.txt.
gouttegd Feb 7, 2025
b46bab6
Replace most uses of OWLTools to create subsets.
gouttegd Feb 7, 2025
64488ce
Use ROBOT to produce the composite-*-basic.owl products.
gouttegd Feb 7, 2025
2b87599
Fix garbled rule.
gouttegd Feb 7, 2025
41c7fa8
Update calls to ODK plugin.
gouttegd Feb 10, 2025
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168 changes: 86 additions & 82 deletions src/ontology/uberon.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ OWLTOOLS_CAT_DYNAMIC= OWLTOOLS_MEMORY=$(OWLTOOLS_MEMORY) owltools --catalog-xml
DC = http://purl.org/dc/elements/1.1
RELEASE = $(URIBASE)/uberon/releases/$(TODAY)
QELK = --silence-elk
PART_OF = BFO_0000050
PART_OF = BFO:0000050


all: uberon-qc
Expand Down Expand Up @@ -762,13 +762,6 @@ $(REPORTDIR)/bfo-basic-check.txt: uberon-basic.owl $(BRIDGEDIR)/uberon-bridge-to
# SUBSETS & VIEWS
# ----------------------------------------

# Create a seed from the standard (ODK-generated) Uberon seed to which
# we add CL terms. This seed is used by several subsets below.
tmp/simple-slim-seed.txt: $(SRCMERGED) $(SIMPLESEED)
$(ROBOT) query -f csv -i $< --query ../sparql/cl_terms.sparql [email protected] && \
cat [email protected] $(SIMPLESEED) | sort | uniq > $@


# System-specific subsets
# ----------------------------------------

Expand All @@ -788,7 +781,7 @@ TERM_appendicular := UBERON:0002091
TERM_life_cycle_stage := UBERON:0000105

# Subset generation command
SUBSETCMD=$(OWLTOOLS) $< --reasoner-query -r elk -d "$(PART_OF) some $(TERM_ID)" --reasoner-query $(TERM_ID) --make-ontology-from-results $(URIBASE)/uberon/$@ -o $@ 2>&1 > [email protected]
SUBSETCMD=$(ROBOT) odk:subset -i $< -r whelk -a true --query "$(PART_OF) some $(TERM_ID)" --query $(TERM_ID) -o $@

# Source file for all the subsets generated below
subsets/merged-partonomy.owl: uberon.owl
Expand All @@ -797,72 +790,72 @@ subsets/merged-partonomy.owl: uberon.owl
-o $@
.PRECIOUS: subsets/merged-partonomy.owl

subsets/appendicular-minimal.owl: subsets/merged-partonomy.owl
subsets/appendicular-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_appendicular))
$(SUBSETCMD)

subsets/circulatory-minimal.owl: subsets/merged-partonomy.owl
subsets/circulatory-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_circulatory))
$(SUBSETCMD)

subsets/cranial-minimal.owl: subsets/merged-partonomy.owl
subsets/cranial-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_cranial))
$(SUBSETCMD)

subsets/digestive-minimal.owl: subsets/merged-partonomy.owl
subsets/digestive-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_digestive))
$(SUBSETCMD)

subsets/excretory-minimal.owl: subsets/merged-partonomy.owl
subsets/excretory-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_excretory))
$(SUBSETCMD)

subsets/immune-minimal.owl: subsets/merged-partonomy.owl
subsets/immune-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_immune))
$(SUBSETCMD)

subsets/musculoskeletal-minimal.owl: subsets/merged-partonomy.owl
subsets/musculoskeletal-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_musculoskeletal))
$(SUBSETCMD)

subsets/nephron-minimal.owl: subsets/merged-partonomy.owl
subsets/nephron-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_nephron))
$(SUBSETCMD)

subsets/nervous-minimal.owl: subsets/merged-partonomy.owl
subsets/nervous-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_nervous))
$(SUBSETCMD)

subsets/pulmonary-minimal.owl: subsets/merged-partonomy.owl
subsets/pulmonary-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_pulmonary))
$(SUBSETCMD)

subsets/renal-minimal.owl: subsets/merged-partonomy.owl
subsets/renal-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_renal))
$(SUBSETCMD)

subsets/reproductive-minimal.owl: subsets/merged-partonomy.owl
subsets/reproductive-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_reproductive))
$(SUBSETCMD)

subsets/sensory-minimal.owl: subsets/merged-partonomy.owl
subsets/sensory-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_sensory))
$(SUBSETCMD)

subsets/life-stages-minimal.owl: subsets/merged-partonomy.owl
subsets/life-stages-minimal.owl: subsets/merged-partonomy.owl | all_robot_plugins
$(eval TERM_ID := $(TERM_life_cycle_stage))
$(SUBSETCMD)

# TODO: need to add subclass axioms for all intersections
subsets/musculoskeletal-full.obo: uberon.owl
$(OWLTOOLS) $< --reasoner-query -r elk -d -c $(URIBASE)/uberon/$@ \
"$(PART_OF) some UBERON_0002204" \
-o -f obo file://`pwd`/$@ --reasoner-dispose
subsets/musculoskeletal-full.obo: uberon.owl | all_robot_plugins
$(ROBOT) odk:subset -i $< -r whelk --query "$(PART_OF) some UBERON:0002204" \
annotate --ontology-iri $(URIBASE)/uberon/$@ \
--output $@

subsets/vertebrate-head.obo: composite-vertebrate.owl
$(OWLTOOLS) $< --reasoner-query -r elk -d "$(PART_OF) some UBERON_0000033" \
--make-ontology-from-results $(URIBASE)/uberon/$@ \
-o -f obo --no-check $@ --reasoner-dispose 2>&1 > [email protected]
subsets/vertebrate-head.obo: composite-vertebrate.owl | all_robot_plugins
$(ROBOT) odk:subset -i $< -r whelk --query "$(PART_OF) some UBERON:0000033" \
annotate --ontology-iri $(URIBASE)/uberon/$@ \
--output $@


# Life stages subsets
Expand All @@ -872,27 +865,17 @@ subsets/vertebrate-head.obo: composite-vertebrate.owl
subsets/life-stages-mammal.owl: subsets/life-stages-core.owl $(TMPDIR)/mmusdv.owl $(TMPDIR)/hsapdv.owl
$(ROBOT) merge $(foreach input, $^, -i $(input)) -o $@

subsets/life-stages-composite.owl: composite-metazoan.owl
$(ROBOT) query --input $< \
--update $(SPARQLDIR)/inject-life-stages-subset.ru \
--update $(SPARQLDIR)/inject-subset-declaration.ru \
--output [email protected] && mv [email protected] $@ &&\
$(OWLTOOLS) $@ --extract-ontology-subset --fill-gaps --subset life_stage \
-o [email protected] && mv [email protected] $@ && \
$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-o [email protected] && mv [email protected] $@

subsets/life-stages-core.obo: uberon.owl
$(OWLTOOLS) $< --reasoner-query -r elk -l 'life cycle stage' \
--make-ontology-from-results $(URIBASE)/uberon/$@ \
--add-ontology-annotation $(DC)/description "Life cycle stage subset of uberon core (generic stages only)" \
-o -f obo $@ --reasoner-dispose 2>&1 > [email protected]

subsets/life-stages-core.owl: uberon.owl
$(OWLTOOLS) $< --reasoner-query -r elk -l 'life cycle stage' \
--make-ontology-from-results $(URIBASE)/uberon/$@ \
--add-ontology-annotation $(DC)/description "Life cycle stage subset of uberon core (generic stages only)" \
-o file://`pwd`/$@ --reasoner-dispose 2>&1 > [email protected]
subsets/life-stages-composite.owl: composite-metazoan.owl | all_robot_plugins
$(ROBOT) odk:normalize -i $< --subset-decls true --synonym-decls true \
odk:subset --subset life_stage --fill-gaps true \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output $@

subsets/life-stages-core.owl: uberon.owl | all_robot_plugins
$(ROBOT) odk:subset -i $< -r whelk --query "'life cycle stage'" -a true \
annotate --ontology-iri $(URIBASE)/uberon/$@ \
--annotation dc:description "Life cycle stage subset of uberon core (generic stages only)" \
--output $@


# Taxon subsets
Expand Down Expand Up @@ -955,21 +938,29 @@ subsets/%-view.owl subsets/%-tags.ofn: $(POSTPROCESS_SRC) | all_robot_plugins
# ----------------------------------------

# Cumbo subset
subsets/cumbo.owl: uberon-basic.owl
$(OWLTOOLS) $< --extract-ontology-subset --subset cumbo --iri $(URIBASE)/uberon/$@ -o $@
# 1. Extract the list of terms for the subset
$(TMPDIR)/cumbo_subset_terms.txt: uberon-basic.owl
$(ROBOT) filter -i $< --prefix 'uberon: http://purl.obolibrary.org/obo/uberon/core#' \
--select 'oboInOwl:inSubset=uberon:cumbo' \
export --header ID --export $@

# 2. Then extract the subset itself
subsets/cumbo.owl: uberon-basic.owl $(TMPDIR)/cumbo_subset_terms.txt $(KEEPRELATIONS)
$(ROBOT) extract -i $< --method subset \
--term-file $(TMPDIR)/cumbo_subset_terms.txt \
--term-file $(KEEPRELATIONS) \
annotate --ontology-iri $(URIBASE)/uberon/$@ --output $@

# Common anatony subset
common-anatomy.owl: $(ONT).owl
$(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset common_anatomy \
-o [email protected] && mv [email protected] $@ && \
$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-o [email protected] && mv [email protected] $@
common-anatomy.owl: $(ONT).owl | all_robot_plugins
$(ROBOT) odk:subset -i $< --subset common_anatomy --fill-gaps true \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output $@
.PRECIOUS: common-anatomy.owl

subsets/immaterial.obo: uberon.owl
$(OWLTOOLS) $< --reasoner-query -r elk -d UBERON_0000466 \
--make-ontology-from-results $(URIBASE)/uberon/$@ \
-o -f obo $@ --reasoner-dispose 2>&1 > [email protected]
subsets/immaterial.obo: uberon.owl | all_robot_plugins
$(ROBOT) odk:subset -i $< --query UBERON:0000466 \
annotate --ontology-iri $(URIBASE)/uberon/$@ --output $@

%-partview.owl: %.owl
$(OWLTOOLS) $< --remove-subset grouping_class --remove-subset upper_level \
Expand Down Expand Up @@ -1183,25 +1174,38 @@ $(TMPDIR)/mmusdv.owl: $(IMPORTDIR)/local-sslso.owl

# Some special products derived from the products generated above
# ----------------------------------------
BASICRELS = BFO:0000050 RO:0002202 immediate_transformation_of transformation_of

composite-metazoan-basic.owl: composite-metazoan.owl
$(OWLTOOLS) $< --extract-mingraph --remove-axiom-annotations \
--make-subset-by-properties -f $(BASICRELS) \
-o -f obo --no-check [email protected] && \
grep -v '^owl-axioms:' [email protected] > $@ && \
$(ROBOT) annotate -i $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f owl -o [email protected] && \
mv [email protected] $@

composite-vertebrate-basic.owl: composite-vertebrate.owl
$(OWLTOOLS) $< --extract-mingraph --remove-axiom-annotations \
--make-subset-by-properties -f $(BASICRELS) \
-o -f obo --no-check [email protected] && \
grep -v '^owl-axioms:' [email protected] > $@ && \
$(ROBOT) annotate -i $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f owl -o [email protected] && \
mv [email protected] $@

# That ROBOT pipeline *approximately* mimics the following OWLTools commands:
# --mingraph (remove all axioms except SubClassOf, EquivalentClasses, and
# annotation assertions);
# --remove-axiom-annotations (as it says on the can);
# --make-subset-by-properties (remove all object properties except those specified).
# FIXME: get rid of dangling classes
composite-metazoan-basic.owl: composite-metazoan.owl $(KEEPRELATIONS)
$(ROBOT) remove -i $< --select complement --drop-axiom-annotations all \
filter --axioms "subclass equivalent annotation" \
remove --term-file $(KEEPRELATIONS) \
--select complement --select object-properties \
remove --axioms structural-tautologies \
remove --select individuals \
remove --select "owl:deprecated='true'^^xsd:boolean" \
remove --term rdfs:label --select complement --axioms annotation \
--trim false --signature true \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output $@

composite-vertebrate-basic.owl: composite-vertebrate.owl $(KEEPRELATIONS)
$(ROBOT) remove -i $< --select complement --drop-axiom-annotations all \
filter --axioms "subclass equivalent annotation" \
remove --term-file $(KEEPRELATIONS) \
--select complement --select object-properties \
remove --axioms structural-tautologies \
remove --select individuals \
remove --select "owl:deprecated='true'^^xsd:boolean" \
remove --term rdfs:label --select complement --axioms annotation \
--trim false --signature true \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output $@


# Helper commands for composite-* stuff
Expand Down
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