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Makefile
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OBOBASE= http://purl.obolibrary.org/obo
URIBASE= http://purl.obolibrary.org/obo
VERSION= $(TODAY)
ANNOTATION_PROPERTIES= rdfs:label IAO:0000115 IAO:0000116 IAO:0100001 owl:deprecated
ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output [email protected] && mv [email protected] $@
OBO=http://purl.obolibrary.org/obo
OIO=http://www.geneontology.org/formats/oboInOwl\#
RDFS=http://www.w3.org/2000/01/rdf-schema#
SKOS=http://www.w3.org/2004/02/skos/core\#
EFO=http://www.ebi.ac.uk/efo
ONT=mondo
ONTURI=$(OBO)/$(ONT)
ONTBASE=$(OBO)/$(ONT)
MIRRORDIR=mirror
IMPORTDIR=imports
SRC=$(ONT)-edit.obo
#RELEASEDIR=../../target/
CATALOG=catalog-v001.xml
ROBOT= robot --catalog $(CATALOG)
OWLTOOLS= owltools
USECAT= --use-catalog
SPARQLDIR = ../sparql
PATTERNDIR = ../patterns
TMPDIR = tmp
CONSTRUCTS= embedded-definition
INCLUDES_OWL = $(patsubst %,include-%.owl,$(CONSTRUCTS))
ISODATE:=`date +%Y-%m-%d`
TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
FMTS = obo owl json
obo-filter-axiom-header = grep -v ^owl-axioms:
OWL2OBO = $(ROBOT) convert -i $< -o [email protected] && grep -v ^owl-axioms: [email protected] > $@
PV_CC0 = http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/
# In converting to obo format, everything is assumed to have an OBO prefix.
# This perl corrects this.
# Longer term we need to eliminate passing through obo and/or fix the owlapi implementation to respect prefixes
FIX_URI_EXPR = 's@$(OBO)/EFO_@http://www.ebi.ac.uk/efo/EFO_@g; s@$(OBO)/UMLS_@http://linkedlifedata.com/resource/umls/id/@g'
# EFO uses different properties. The following command can be used on owltools
EFO2OBO_OPTS = --rename-entity $(EFO)/definition $(OBO)/IAO_0000115 \
--rename-entity $(EFO)/reason_for_obsolescence $(RDFS)comment \
--rename-entity $(EFO)/alternative_term $(OIO)hasExactSynonym\
--rename-entity $(OBO)/ECO_0000218 $(OIO)source
# EFO uses different prefixes in xrefs. We replace these with the following perl
# intended to be used within a perl -npe loop.
# In future we should use a more robust translation
EFO2OBO_PERL = 's@NCIt:@NCIT:@; s@MSH:@MESH:@; s@SNOMEDCT:@SCTID:@;'
OBOGREPL=../scripts/obo-grepl.pl
OBOGREP=../scripts/obo-grep.pl
ADDTOTBD=../scripts/add-to-tbd.pl
# ----------------------------------------
# Top-level targets
# ----------------------------------------
.PHONY: .FORCE
all: test all_artefacts mappings
echo "release finished"
# ----------------------------------------
# Artefacts
# ----------------------------------------
IMPORTS = uberon cl go pato envo ro hp mf ncbitaxon chebi ncit hgnc foodon so ecto omo chr hsapdv nbo maxo mfomd ncbigene
IMPORT_ROOTS = $(IMPORTDIR)/merged_import
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
IMPORT_FILES = $(IMPORT_OWL_FILES)
.PHONY: all_imports
all_imports: $(IMPORT_FILES)
COMPONENTS = mondo-tags
COMPONENT_FILES = $(foreach n, $(COMPONENTS), components/$(n).owl)
SUBSETS = mondo-rare
SUBSET_ROOTS = $(patsubst %, subsets/%, $(SUBSETS))
SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(n).owl $(n).obo $(n).json $(n)_nodes.tsv $(n)_edges.tsv)
REPORTS = basic-report class-count-by-prefix edges xrefs obsoletes obsoletion-candidates synonyms class-stats root-classes superclass-count
REPORT_ARGS = $(foreach V,$(REPORTS),-s $(SPARQLDIR)/reports/$V.sparql reports/$V.tmp.tsv)
MAIN_REPORT_FILES = $(foreach V, $(REPORTS), reports/$V.tsv)
ADDITIONAL_REPORT_FILES = reports/semantic-xref-pairs.tsv
#ADDITIONAL_REPORT_FILES = reports/release/mondo-obo-report.yaml reports/release/mondo-owl-report.yaml reports/release/semantic-xref-pairs.tsv
REPORT_FILES = $(MAIN_REPORT_FILES) $(ADDITIONAL_REPORT_FILES)
MAIN_PRODUCTS = $(ONT) $(ONT)-base $(ONT)-simple
MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(n).owl $(n).obo $(n).json) $(ONT)_nodes.tsv $(ONT)_edges.tsv
EQUIVALENTS_FILES=imports/equivalencies
EQUIVALENTS = $(foreach n, $(EQUIVALENTS_FILES), $(n).owl $(n).obo $(n).json)
ARTEFACTS = \
$(IMPORT_FILES) \
$(MAIN_FILES) \
$(EQUIVALENTS) \
$(REPORT_FILES) \
$(COMPONENT_FILES) \
$(SUBSET_FILES)
REPORT_FILES_RELEASE = reports/mondo_release_diff_changed_terms.tsv \
reports/mondo_release_diff_new_terms.tsv \
reports/mondo_obsoletioncandidates.tsv
ASSETS = $(MAIN_FILES) $(SUBSET_FILES) $(EQUIVALENTS) \
../../README.md \
$(REPORT_FILES_RELEASE)
list_main_files:
echo $(MAIN_FILES)
list_artefacts:
echo $(ARTEFACTS)
du -sh $(ARTEFACTS)
%-DU:
@test -f $* && du -sh $* || echo "MISSING" $*
all_artefacts: all_reports $(ARTEFACTS)
all_release_reports: $(REPORT_FILES_RELEASE)
# ----------------------------------------
# Tests
# ----------------------------------------
#all: test all_imports all_reports all_equivalencies all_subsets imports/equivalencies.obo $(ONT).owl $(ONT).obo $(ONT).json pre/$(ONT).owl pre/$(ONT).obo pre/$(ONT).json extid/$(ONT).owl extid/$(ONT).obo extid/$(ONT).json $(ONT)-merged.owl
#TODO: roundtrip.obo seems unnecessary check.
test: sparql_test_edit roundtrip.obo debug.owl debug_inference_check.owl mondo-edit.owl sparql_test_main_obo test_nomerge
test: reports/robot-report-mondo-tags-reasoned.owl.tsv
# ----------------------------------------
# Staging releases
# ----------------------------------------
#prepare_release: $(ARTEFACTS)
# $(MAKE) mappings -B
# rsync -R $^ ../..
# note: only reports, imports
prepare_release_direct:
rsync -R $(ARTEFACTS) ../..
all_includes: $(INCLUDES_OWL)
#OSF_UPLOAD = $(HOME)/repos/osf-cli/venv/bin/osf -p 2qk53 upload
#osf_upload: prepare_release osf_upload_direct
#osf_upload_direct:
# cd ../.. && $(OSF_UPLOAD) -f -r target/ current/ && $(OSF_UPLOAD) -f -r target/ releases/$(ISODATE)
list_assets:
ls -alt $(ASSETS)
echo $(GHVERSION)
check_version_set:
@test $(GHVERSION)
# REMEMBER TO COMMIT/PUSH
# e.g. make deploy_release GHVERSION=v2018-10-26
# this will create the GH repo. Use --no-create if repo already created.
deploy_release: deploy_assets_direct
#deploy_assets_current see https://github.com/OBOFoundry/purl.obolibrary.org/pull/723
# deploys to a versioned released
deploy_assets_direct:
@test $(GHVERSION)
ls -alt $(ASSETS)
gh release create $(GHVERSION) --notes "TBD." --title "$(GHVERSION)" --draft $(ASSETS)
# ../utils/make-release-assets.py -c $(RELEASE_ASSETS_OPTS) --release $(GHVERSION) $(ASSETS)
# deploys to https://github.com/monarch-initiative/mondo/releases/tag/current
#deploy_assets_current:
# ls -alt $(ASSETS)
# ../utils/make-release-assets.py -c -f --release current $(ASSETS)
# ----------------------------------------
# Main release targets
# ----------------------------------------
ANN = annotate -V $(ONTURI)/releases/`date +%Y-%m-%d`/[email protected]
# the GITHUB_ACTION flag should be set to true to skip computationally intensive actions in the pipeline that are not necessary for QC, see filtered.obo
# Use sparingly
GITHUB_ACTION = false
filtered.obo: $(SRC)
perl -ne 'print unless (m@^xref: (Orphanet|OMIM|OMIMPS|DOID|EFO|NCIT|SCTID|MESH|UMLS|ICD10CM|icd11.foundation):@ && !(m@(obsoleteEquivalent|equivalentObsolete|equivalentTo|relatedTo|mondoIsNarrowerThanSource|directSiblingOf|mondoIsBroaderThanSource)@i))' $< | grep -v '^property_value: excluded_subClassOf' | egrep -v '^synonym: .*EXCLUDE' | egrep -v 'relationship: disease_has_basis_in_dysfunction_of (hgnc|HGNC|NCBIGene):' > [email protected] && mv [email protected] $@
perl -ne 'print if !(/^xref: (Orphanet|OMIM|OMIMPS|DOID):/ && !(/(obsoleteEquivalent|equivalentObsolete|equivalentTo|obsoleteEquivalentObsolete)/i))' $@ > [email protected] && mv [email protected] $@
if [ $(GITHUB_ACTION) = false ]; then $(ROBOT) query -i $@ --use-graphs false \
--update ../sparql/update/delete-axiom-annotations.ru \
--update ../sparql/update/delete-axiom-annotations-by-prefix.ru \
--update ../sparql/update/inject-cross-species-analog.ru \
remove --term-file config/remove-annotations-before-release.txt \
convert -f obo --check false -o [email protected] && mv [email protected] $@; fi
#egrep -v 'MONDO:(subClassOf|superClassOf|relatedTo)' $< > $@
skos.ttl: filtered.obo
../utils/mk-skos.pl $< > $@
# this appears to be problematic. not all declarations are restored on a save.
#REMOVE_DECLARATIONS = --remove-axioms -t Declaration
REMOVE_DECLARATIONS=
# necessary to remove stray declarations induced by obo2owl;
# we remove declaration axioms for ALL classes;
# all necessary ones are implicitly added back when converting back to OWL
# see: https://github.com/owlcs/owlapi/pull/761
filtered.owl: filtered.obo skos.ttl
owltools --use-catalog $< $(REMOVE_DECLARATIONS) skos.ttl --merge-support-ontologies -o $@
# perform reasoning on source
# PREVIOUS: SKIP FOR NOW: assume pre-asserted, but run reasoner to check
# note: $(ROBOT) will protect redundant annotated axioms
reasoned.owl: filtered.owl
$(ROBOT) reason -T true -x true -X true -i $< -r ELK relax reduce -p false -r ELK \
remove --term MONDO:0700097 --term OGMS:0000031 $(ANN) -o $@
#test: reasoned-plus-equivalents.owl
# merged = reasoned + equivalencies
reasoned-plus-equivalents.owl: reasoned.owl imports/equivalencies.owl
owltools --use-catalog $^ --merge-support-ontologies -o $@
#$(ROBOT) reason -i $@ --equivalent-classes-allowed asserted-only -o $(TMPDIR)/$@_test_equivalents.owl
# PRE-RELEASES: MONDO IDs primary
#
# by default we use Elk to perform a reason-relax-reduce chain
# after that we annotate the ontology with the release versionInfo
$(ONT).owl: reasoned.owl
$(ROBOT) merge -i $< annotate -V $(ONTURI)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@
$(ONT).obo: $(ONT).owl
$(ROBOT) annotate -i $< \
-V $(ONTURI)/releases/`date +%Y-%m-%d`/$(ONT).owl \
--ontology-iri $(OBO)/$(ONT).owl \
convert --check false -f obo -o [email protected] &&\
grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT).json: $(ONT).owl
$(ROBOT) convert --input $< --check false -f json -o [email protected] &&\
mv [email protected] $@
$(ONT)_nodes.tsv $(ONT)_edges.tsv: $(ONT).json
kgx transform --input-format obojson --output-format tsv --output $(ONT) $< && test -f $(ONT)_nodes.tsv
ONTOLOGYTERMS=$(TMPDIR)/mondo_classes.txt
$(ONTOLOGYTERMS): reasoned.owl
$(ROBOT) query -f csv -i $< --query ../sparql/signature/mondo-classes.sparql $@
SIMPLESEED=$(TMPDIR)/simple_seed.txt
$(SIMPLESEED): reasoned.owl $(ONTOLOGYTERMS)
$(ROBOT) query -f csv -i $< --query ../sparql/signature/simple-seed.sparql [email protected] &&\
cat [email protected] $(ONTOLOGYTERMS) | sort | uniq > $@ &&\
echo "http://www.geneontology.org/formats/oboInOwl#SubsetProperty" >> $@ &&\
echo "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty" >> $@
# foo-simple: (edit->reason,relax,reduce,drop imports, drop every axiom which contains an entity outside the "namespaces of interest")
# drop every axiom: filter --term-file keep_terms.txt --trim true
# remove --select imports --trim false
# NOTE FOR FUTURE: this is slightly different from the usual simple as it completely removes all
# Object properties from the ontology (remove --select object-properties).
$(ONT)-simple.owl: reasoned.owl $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
$(ROBOT) merge --input $< \
reason --equivalent-classes-allowed none --exclude-tautologies true --annotate-inferred-axioms true \
relax \
remove --axioms equivalent \
remove --select object-properties \
relax \
filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
reduce \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@
$(ONT)-simple.obo: $(ONT)-simple.owl
$(OWL2OBO)
$(ONT)-simple.json: $(ONT)-simple.owl
$(ROBOT) convert -i $< -o [email protected] && mv [email protected] $@
#$(ONT)-atomic.owl: $(ONT).owl
# owltools --use-catalog $< --remove-imports-declarations --set-ontology-id $(OBO)/$(ONT)/$@ -o [email protected] && mv [email protected] $@
# Component module.
# we remove imports and merge in additional assertions
# note: typically component is not pre-reasoned, but this is compex for mondo.
OTHER_SRC=imports/axioms.owl #components/mondo-tags.owl
# The --select "<http://purl.obolibrary.org/obo/BFO_*>" is due to a bug with the reason -x option
# Which is supposed to exclude external namespaces from reason, but does not. My guess:
# BFO namespace was needed for Object Properties.
$(ONT)-base.owl: reasoned.owl $(OTHER_SRC)
$(ROBOT) remove --input $< --select imports --trim false \
merge $(patsubst %, -i %, $(OTHER_SRC)) \
remove --select "<http://purl.obolibrary.org/obo/BFO_*>" --select classes \
annotate --annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
--ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ \
--output [email protected] && mv [email protected] $@
$(ONT)-base.obo: $(ONT)-base.owl
$(OWL2OBO)
$(ONT)-base.json: $(ONT)-base.owl
$(ROBOT) convert -i $< -o [email protected] && mv [email protected] $@
#pre/$(ONT).%: $(ONT).%
# $(ROBOT) annotate -i $< -V $(ONTURI)/pre/$(ONT).owl -o $@
#pre/$(ONT).json: $(ONT).owl
# $(ROBOT) annotate -i $< -V $(ONTURI)/pre/$(ONT).owl -o $@
# CURRENT RELEASES: map back to clique leaders
#extid/mondo.owl: mondo.owl
# owltools --use-catalog $< --reasoner elk --merge-equivalence-sets -s NCIT 20 -s Orphanet 10 -s OMIM 8 -s EFO 6 -s DOID 5 -s MESH 4 -s MONDO 1 --remove-dangling -o $@
#extid/mondo.obo: extid/mondo.owl
# owltools --use-catalog $< --remove-imports-declarations --remove-dangling -o -f obo --no-check [email protected] && $(obo-filter-axiom-header) [email protected] > $@
#$(ONT)-basic.owl: $(ONT).owl
# owltools --use-catalog $< --remove-imports-declarations --remove-dangling -o $@
#$(ONT)-basic.obo: $(ONT)-basic.owl
# owltools --use-catalog $< -o -f obo $(ONT).obo.tmp && mv $(ONT).obo.tmp $@
%.json: %.owl
$(ROBOT) convert --input $< --check false -f json -o [email protected] &&\
mv [email protected] $@
# ensure that inference including equivalencies does not result in merging any classes in MONDO.
# if this fails, the resolution is to look for two MONDO classes with equivalence to the same external class
test_nomerge: mondo.owl
owltools --log-error --use-catalog $< --reasoner elk --merge-equivalence-sets -P MONDO -s MONDO 100 --remove-dangling -o $@
# ----------------------------------------
# Inference comparison
# ----------------------------------------
filtered-nr.obo: filtered.owl
$(ROBOT) relax -i $< reduce -p false -r ELK annotate -O $(OBO)/mondo/$@ -o [email protected] && owltools --use-catalog [email protected] --remove-axiom-annotations -o -f obo --no-check [email protected] && grep -v ^owl-axioms [email protected] | obo-grep.pl -r MONDO: - > $@
filtered-nr-reasoned.obo: filtered.owl
$(ROBOT) relax -i $< reduce -p false -r ELK reason -r ELK annotate -O $(OBO)/mondo/$@ -o [email protected] && owltools --use-catalog [email protected] --remove-axiom-annotations -o -f obo --no-check [email protected] && grep -v ^owl-axioms [email protected] | obo-grep.pl -r MONDO: - > $@
reports/reasoner-diff.obo: filtered-nr.obo filtered-nr-reasoned.obo
obo-simple-diff.pl -l $^ > $@
# ----------------------------------------
# CC-0 MINIMAL
# ----------------------------------------
all_subsets: $(SUBSET_FILES)
RARE_SUBSET_PRESERVED_RELATIONS=RO:0004003 RO:0000053
tmp/rare-subset-pre.owl: #$(SRC)
$(ROBOT) merge -i $(SRC) reason relax materialize $(patsubst %, --term %, $(RARE_SUBSET_PRESERVED_RELATIONS)) -o $@
# This gets us all the rare disease classes:
tmp/rare-seed-classes.txt: tmp/rare-subset-pre.owl
$(ROBOT) merge -i $< query --query ../sparql/signature/rare-subset.sparql $@
.PRECIOUS: tmp/rare-seed-classes.txt
# This gets us all the rare disease classes:
tmp/rare-seed-parents.txt: tmp/rare-subset-pre.owl
$(ROBOT) merge -i $< query --query ../sparql/signature/rare-subset-parents.sparql $@
.PRECIOUS: tmp/rare-seed-parents.txt
# This gets us all the entities linked to the rare disease classes
# Make sure you add the relationships you want to add to ../sparql/signature/rare-subset-related-entity.sparql
# AND config/rare_subset_relations.txt
tmp/rare-seed-entities.txt: tmp/rare-subset-pre.owl tmp/rare-seed-classes.txt
$(ROBOT) merge -i $< filter -T tmp/rare-seed-classes.txt --trim false query --query ../sparql/signature/rare-subset-related-entity.sparql $@
.PRECIOUS: tmp/rare-seed-entities.txt
# This merges thes seed together into one file (including rare disease classes _and_ related entities.)
tmp/rare-seed.txt: tmp/rare-seed-entities.txt tmp/rare-seed-classes.txt config/rare_subset_relations.txt tmp/rare-seed-parents.txt
cat $^ | sort | uniq > $@
.PRECIOUS: tmp/rare-seed.txt
subsets/mondo-rare.owl: $(ONT)-base.owl $(TMPDIR)/hgnc_import.owl tmp/rare-seed.txt | $(SUBSETDIR)
$(ROBOT) merge -i $< -i $(TMPDIR)/hgnc_import.owl extract --method subset -T tmp/rare-seed.txt --output $@ &&\
$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o [email protected] && mv [email protected] $@
.PRECIOUS: $(SUBSETDIR)/mondo-rare.owl
subsets/%.json: subsets/%.owl
$(ROBOT) convert -i $< -o $@
subsets/%_nodes.tsv subsets/%_edges.tsv: subsets/%.json
kgx transform --input-format obojson --output-format tsv --output subsets/$* $< && test -f subsets/$*_nodes.tsv
subsets/%.obo: subsets/%.owl
$(ROBOT) convert -i $< -o [email protected] && grep -v ^owl-axioms: [email protected] > $@ && rm [email protected]
rare_subset:
$(MAKE) IMP=false MIR=false COMP=false subsets/mondo-rare.owl subsets/mondo-rare.json subsets/mondo-rare.obo
# ----------------------------------------
# DOSDP Modules
# ----------------------------------------
all_mods: modules/disease_by_location.owl
modules/%.tsv: modules/%.csv
csv2tsv.py $< $@
modules/%.owl: modules/%.tsv
dosdp-tools --obo-prefixes --ontology=../ontology/mondo-edit.obo --template=../patterns/$*.yaml --outfile=$@ generate --infile=$<
###### BEGIN PARTIAL ODK MIGRATION ##############
$(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR):
mkdir -p $@
# ----------------------------------------
# Import modules
# ----------------------------------------
# Most ontologies are modularly constructed using portions of other ontologies
# These live in the imports/ folder
# This pattern uses ROBOT to generate an import module
# Should be able to drop this if robot can just take a big messy list of terms as input.
$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt
if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi
ALL_TERMS_COMBINED = $(patsubst %, $(IMPORTDIR)/%_terms_combined.txt, $(IMPORTS))
$(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi
$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
remove --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove --select "<http://www.informatics.jax.org/marker/MGI:*>" remove --select "<http://purl.obolibrary.org/obo/OBI_*>" remove --select "<http://purl.obolibrary.org/obo/CARO_*>" remove --select "<http://purl.obolibrary.org/obo/RnorDv_*>" remove --select "<http://purl.obolibrary.org/obo/PR_*>" remove --select "<http://purl.obolibrary.org/obo/PCO_*>" remove --select "<http://purl.obolibrary.org/obo/ExO_*>" remove --select "<http://purl.obolibrary.org/obo/FAO_*>" remove --select "<http://purl.obolibrary.org/obo/UPHENO_*>" remove --select "<http://purl.obolibrary.org/obo/COB_*>" remove --select "<http://purl.obolibrary.org/obo/MPATH_*>" remove --select "<http://purl.obolibrary.org/obo/PO_*>" remove --select "<http://purl.obolibrary.org/obo/ENVO_01001055*>" \
extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select "annotation-properties" \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi
$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi
.PRECIOUS: $(IMPORTDIR)/%_import.owl
.PHONY: refresh-imports
refresh-imports:
$(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B
.PHONY: no-mirror-refresh-imports
no-mirror-refresh-imports:
$(MAKE) IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B
.PHONY: refresh-imports-excluding-large
refresh-imports-excluding-large:
$(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B
.PHONY: refresh-%
refresh-%:
$(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B
.PHONY: no-mirror-refresh-%
no-mirror-refresh-%:
$(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B
# ----------------------------------------
# Mirroring upstream ontologies
# ----------------------------------------
IMP=true # Global parameter to bypass import generation
MIR=true # Global parameter to bypass mirror generation
IMP_LARGE=true # Global parameter to bypass handling of large imports
## ONTOLOGY: uberon
.PHONY: mirror-uberon
.PRECIOUS: $(MIRRORDIR)/uberon.owl
mirror-uberon: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uberon.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri http://purl.obolibrary.org/obo/UBERON_ --base-iri http://purl.obolibrary.org/obo/UBPROP_ --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: cl
.PHONY: mirror-cl
.PRECIOUS: $(MIRRORDIR)/cl.owl
mirror-cl: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/CL --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: go
.PHONY: mirror-go
.PRECIOUS: $(MIRRORDIR)/go.owl
mirror-go: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/go.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/GO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: pato
.PHONY: mirror-pato
.PRECIOUS: $(MIRRORDIR)/pato.owl
mirror-pato: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/PATO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: envo
.PHONY: mirror-envo
.PRECIOUS: $(MIRRORDIR)/envo.owl
mirror-envo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/envo.owl --create-dirs -o $(MIRRORDIR)/envo.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/envo.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/ENVO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: ro
.PHONY: mirror-ro
.PRECIOUS: $(MIRRORDIR)/ro.owl
mirror-ro: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: hp
.PHONY: mirror-hp
.PRECIOUS: $(MIRRORDIR)/hp.owl
mirror-hp: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/hp.owl --create-dirs -o $(MIRRORDIR)/hp.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/hp.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/HP --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: mf
.PHONY: mirror-mf
.PRECIOUS: $(MIRRORDIR)/mf.owl
mirror-mf: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/mf.owl --create-dirs -o $(MIRRORDIR)/mf.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/mf.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/MF --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: ncbitaxon
.PHONY: mirror-ncbitaxon
.PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl
mirror-ncbitaxon: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri http://purl.obolibrary.org/obo/NCBITaxon_ --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: chebi
.PHONY: mirror-chebi
.PRECIOUS: $(MIRRORDIR)/chebi.owl
mirror-chebi: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/CHEBI --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: ncit
.PHONY: mirror-ncit
.PRECIOUS: $(MIRRORDIR)/ncit.owl
mirror-ncit: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ncit.owl --create-dirs -o $(MIRRORDIR)/ncit.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/ncit.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/NCIT --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: hgnc
.PHONY: mirror-hgnc
.PRECIOUS: $(MIRRORDIR)/hgnc.owl
mirror-hgnc: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/hgnc.owl --create-dirs -o $(MIRRORDIR)/hgnc.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/hgnc.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: foodon
.PHONY: mirror-foodon
.PRECIOUS: $(MIRRORDIR)/foodon.owl
mirror-foodon: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/foodon.owl --create-dirs -o $(MIRRORDIR)/foodon.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/foodon.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/FOODON --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: so
.PHONY: mirror-so
.PRECIOUS: $(MIRRORDIR)/so.owl
mirror-so: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/so.owl --create-dirs -o $(MIRRORDIR)/so.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/so.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/SO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: ecto
.PHONY: mirror-ecto
.PRECIOUS: $(MIRRORDIR)/ecto.owl
mirror-ecto: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ecto.owl --create-dirs -o $(MIRRORDIR)/ecto.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/ecto.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/ECTO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: omo
.PHONY: mirror-omo
.PRECIOUS: $(MIRRORDIR)/omo.owl
mirror-omo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: chr
.PHONY: mirror-chr
.PRECIOUS: $(MIRRORDIR)/chr.owl
mirror-chr: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr-base.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: hsapdv
.PHONY: mirror-hsapdv
.PRECIOUS: $(MIRRORDIR)/hsapdv.owl
mirror-hsapdv: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/hsapdv.owl --create-dirs -o $(MIRRORDIR)/hsapdv.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/hsapdv.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri http://purl.obolibrary.org/obo/HsapDv_ --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: nbo
.PHONY: mirror-nbo
.PRECIOUS: $(MIRRORDIR)/nbo.owl
mirror-nbo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/nbo.owl --create-dirs -o $(MIRRORDIR)/nbo.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/nbo.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/NBO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: maxo
.PHONY: mirror-maxo
.PRECIOUS: $(MIRRORDIR)/maxo.owl
mirror-maxo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/maxo.owl --create-dirs -o $(MIRRORDIR)/maxo.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/maxo.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/MAXO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: mfomd
.PHONY: mirror-mfomd
.PRECIOUS: $(MIRRORDIR)/mfomd.owl
mirror-mfomd: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/mfomd.owl --create-dirs -o $(MIRRORDIR)/mfomd.owl --retry 4 --max-time 400 &&\
$(ROBOT) convert -i $(MIRRORDIR)/mfomd.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/MFOMD --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
MERGE_MIRRORS = true
$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) remove --axioms equivalent --preserve-structure false -o $@; fi
.PRECIOUS: $(MIRRORDIR)/merged.owl
$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
###### END PARTIAL ODK MIGRATION ##############
###### BEGIN CUSTOM IMPORTS ###################
mirror/hgnc_gene.nt: | $(MIRRORDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L https://data.monarchinitiative.org/monarch-kg/latest/rdf/hgnc_gene.nt.gz | gzip -d > [email protected] &&\
perl -npe 's@https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:@http://identifiers.org/hgnc/@g' [email protected] > $@; fi
.PRECIOUS: mirror/hgnc_gene.nt
mirror/ncbi_gene.nt: | $(MIRRORDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene.nt.gz | gzip -d > [email protected] &&\
perl -npe 's@https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:@http://identifiers.org/hgnc/@g' [email protected] > $@; fi
.PRECIOUS: mirror/ncbi_gene.nt
mirror-hgnc: mirror/hgnc_gene.nt | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
query --format ttl --query ../sparql/construct/construct-hgnc.sparql $(TMPDIR)/[email protected]; fi
../sparql/construct/construct-ncbigene.sparql: ../sparql/construct/construct-ncbigene.sparql.template $(IMPORTDIR)/merged_terms_combined.txt
@awk '{print " <" $$0 ">"}' $(IMPORTDIR)/merged_terms_combined.txt | grep ncbigene | paste -sd '\n' > $(TMPDIR)/formatted_values.tmp
@sed "/{{VALUES}}/r $(TMPDIR)/formatted_values.tmp" $< | sed '/{{VALUES}}/d' > $@
@rm "$(TMPDIR)/formatted_values.tmp"
mirror-ncbigene: mirror/ncbi_gene.nt ../sparql/construct/construct-ncbigene.sparql | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then arq --data=mirror/ncbi_gene.nt --query=../sparql/construct/construct-ncbigene.sparql > $(TMPDIR)/[email protected]; fi
$(TMPDIR)/hgnc_import.owl: $(IMPORTDIR)/merged_import.owl
$(ROBOT) filter -i $< --term SO:0000704 --select "annotations self descendants" --signature true \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f owl --output [email protected] && mv [email protected] $@
IMPORTSEED=$(IMPORTDIR)/seed.txt # SHOULD BE TMP
###### END CUSTOM IMPORTS ###################
edit-merged.owl: $(SRC)
$(ROBOT) merge -c true -i $< -o $@
imports/seed.txt: edit-merged.owl imports/manual_seed.txt
$(ROBOT) query -f tsv -i $< -s ../sparql/signature/classes.sparql [email protected]
cat [email protected] imports/manual_seed.txt | perl -npe 's@^\<@@;s@>$$@@' - | sort -u > $@
imports/%_terms.txt: imports/seed.txt
touch $@ && grep -hi $* $< $@ | sort -u > [email protected] && mv [email protected] $@
# ----------------------------------------
# Release
# ----------------------------------------
# copy from staging area (this directory) to top-level
#release: $(ONT).owl $(ONT).obo
# cp $^ $(RELEASEDIR) && cp imports/* $(RELEASEDIR)/imports && cp subsets/* $(RELEASEDIR)/subsets
mondo-lastbuild.owl:
curl -L -s $(OBO)/mondo.owl > [email protected] && mv [email protected] $@
mondo-lastbuild.obo:
curl -L -s $(OBO)/mondo.obo > [email protected] && mv [email protected] $@
#mondo-diff.md: mondo-lastbuild.owl
# owljs-diff -o $@ $< mondo.owl
mondo-diff.txt: mondo-lastbuild.obo
obo-simple-diff.pl $< mondo.obo > [email protected] && mv [email protected] $@
# ----------------------------------------
# Editing
# ----------------------------------------
td:
echo $(ISODATE)
# NOTE: no longer removes redundant
INF: mondo-edit.obo
owltools --use-catalog mondo-edit.obo --assert-inferred-subclass-axioms --always-assert-super-classes --keepRedundant --markIsInferred --merge-axiom-annotations -o -f obo [email protected] && grep -v ^owl-axioms [email protected] | perl -npe 's@is_inferred="true"@source="OWLReasoner:Elk-$(ISODATE)"@' | egrep -v '^relationship:.*is_inferred' | obo-grep.pl --neg -r 'id: (UBERON|CL|ENVO|NCBITaxon|HP|PATO|CHEBI):' - > $@
# normalize obo file
# note we use owltools-compat to ensure standard ordering
NORM: mondo-edit.obo
owltools --use-catalog mondo-edit.obo --merge-axiom-annotations -o -f obo [email protected] && $(ROBOT) convert -i [email protected] -o [email protected] && mv [email protected] $@
# tests roundtripping
roundtrip.obo: mondo-edit.obo
owltools --use-catalog mondo-edit.obo -o -f obo [email protected] && mv [email protected] $@
NEWAXTEST: mondo-edit.owl new.owl
# owltools --use-catalog $^ --merge-support-ontologies --run-reasoner -r elk -u -m z.owl -o $@
owltools --use-catalog $^ --merge-support-ontologies --assert-inferred-subclass-axioms --always-assert-super-classes --markIsInferred --removeRedundant --merge-axiom-annotations -o -f obo [email protected] && grep -v ^owl-axioms [email protected] | egrep -v '^relationship:.*is_inferred' | obo-grep.pl --neg -r 'id: (UBERON|CL|ENVO|NCBITaxon|HP|PATO|CHEBI):' - > $@
# ----------------------------------------
# Sparql queries: Q/C
# ----------------------------------------
SPARQL_MONDO_QC=$(patsubst %.sparql, %, $(notdir $(wildcard $(SPARQLDIR)/qc/mondo/qc-*.sparql)))
SPARQL_GENERAL_QC=$(patsubst %.sparql, %, $(notdir $(wildcard $(SPARQLDIR)/qc/general/qc-*.sparql)))
SPARQL_EDIT_EXCLUDE=
# qc-duplicate-exact-synonym-no-abbrev is excluded from the OBO check because we are running the OBO check on the base file
# There is something super weird about the way the OBO file is generated that causes this to fail
# Because the id of ontology is `ontology: mondo/mondo-base`, all the IRIs to properties related to
# the ontology begin looking like this: http://purl.obolibrary.org/obo/mondo/mondo-base#... This
# will cause the query to fail because it expects the IRI http://purl.obolibrary.org/obo/mondo#ABREVIATION
# for the duplicate-exact-synonym-no-abbrev check.
SPARQL_OBO_EXCLUDE=qc-single-child qc-omimps-should-be-inherited qc-omim-subsumption qc-permitted-properties qc-duplicate-exact-synonym-no-abbrev qc-multiple-gene-associations
SPARQL_OWL_EXCLUDE=qc-permitted-properties
SPARQL_GENERAL_QC_EDIT=$(filter-out $(SPARQL_EDIT_EXCLUDE),$(SPARQL_GENERAL_QC))
SPARQL_GENERAL_QC_OWL=$(filter-out $(SPARQL_OWL_EXCLUDE),$(SPARQL_GENERAL_QC))
SPARQL_GENERAL_QC_OBO=$(filter-out $(SPARQL_OBO_EXCLUDE),$(SPARQL_GENERAL_QC))
SPARQL_MONDO_QC_EDIT=$(filter-out $(SPARQL_EDIT_EXCLUDE),$(SPARQL_MONDO_QC))
SPARQL_MONDO_QC_OWL=$(filter-out $(SPARQL_OWL_EXCLUDE),$(SPARQL_MONDO_QC))
SPARQL_MONDO_QC_OBO=$(filter-out $(SPARQL_OBO_EXCLUDE),$(SPARQL_MONDO_QC))
SPARQL_MONDO_QC_FILES=$(foreach V,$(SPARQL_MONDO_QC),$(SPARQLDIR)/qc/mondo/$V.sparql)
SPARQL_GENERAL_QC_FILES_EDIT=$(foreach V,$(SPARQL_GENERAL_QC_EDIT),$(SPARQLDIR)/qc/general/$V.sparql)
SPARQL_GENERAL_QC_FILES_OBO=$(foreach V,$(SPARQL_GENERAL_QC_OBO),$(SPARQLDIR)/qc/general/$V.sparql)
SPARQL_GENERAL_QC_FILES_OWL=$(foreach V,$(SPARQL_GENERAL_QC_OWL),$(SPARQLDIR)/qc/general/$V.sparql)
SPARQL_MONDO_QC_FILES_EDIT=$(foreach V,$(SPARQL_MONDO_QC_EDIT),$(SPARQLDIR)/qc/mondo/$V.sparql)
SPARQL_MONDO_QC_FILES_OBO=$(foreach V,$(SPARQL_MONDO_QC_OBO),$(SPARQLDIR)/qc/mondo/$V.sparql)
SPARQL_MONDO_QC_FILES_OWL=$(foreach V,$(SPARQL_MONDO_QC_OWL),$(SPARQLDIR)/qc/mondo/$V.sparql)
QSRC = $(SRC)-noimports.owl
$(QSRC): $(SRC)
owltools --use-catalog $< --remove-imports-declarations -o $@
SRC_TAGS_REASONED=mondo-tags-reasoned.owl
tmp/cross-species-mappings.owl: $(SRC)
mkdir -p tmp
$(ROBOT) query -i $< --use-graphs false --query ../sparql/construct/construct-cross-species-analog.sparql $@
$(SRC_TAGS_REASONED): $(SRC) tmp/cross-species-mappings.owl
$(ROBOT) merge -i $< -i components/mondo-tags.owl -i tmp/cross-species-mappings.owl --collapse-import-closure false reason -o $@
# run all violation checks on edit file
sparql_test_edit: $(SRC_TAGS_REASONED)
mkdir -p reports/edit/ &&\
$(ROBOT) verify -i $< --queries $(SPARQL_MONDO_QC_FILES_EDIT) $(SPARQL_GENERAL_QC_FILES_EDIT) -O reports/edit/ && touch $@
sparql_test_main_owl: $(ONT).owl
mkdir -p reports/main_owl/ &&\
$(ROBOT) verify -i $< --queries $(SPARQL_MONDO_QC_FILES_OWL) $(SPARQL_GENERAL_QC_FILES_OWL) -O reports/main_owl/ && touch $@
# See comment about http://purl.obolibrary.org/obo/mondo/mondo-base# above
# if you ever encounter "strange" errors related to Mondo internal property ids.
sparql_test_main_obo: $(ONT)-base.obo
mkdir -p reports/main_obo/ &&\
$(ROBOT) verify -i $< --queries $(SPARQL_MONDO_QC_FILES_OBO) $(SPARQL_GENERAL_QC_FILES_OBO) -O reports/main_obo/ && touch $@
PL2SPARQL = ../plq/pq-mondo
#../sparql/%.sparql:
# $(PL2SPARQL) -v "$*" > [email protected] && mv [email protected] $@
reports/pql-%.tsv: mondo-edit.owl
$(PL2SPARQL) -f tsv -v -i $< -e -l "$*" > [email protected] && mv [email protected] $@
reports/bg-%.tsv:
$(PL2SPARQL) -f tsv -l "$*" > [email protected] && mv [email protected] $@
reports/$(Q)-pqlx-$(Ont).tsv: mondo-edit.owl
$(PL2SPARQL) -f tsv -v -i $< -i mirror/$(Ont).owl -e -l "$(Q)" > [email protected] && mv [email protected] $@
reports/pq-%.tsv: mondo-edit.owl
$(PL2SPARQL) -f tsv -v -i $< -e "$*" > [email protected] && mv [email protected] $@
reports/equiv-obs-%.tsv:
pl2sparql -e -A void.ttl -i mondo_edit -i equivs -i mirror/$*.owl -c ../plq/mondo_queries.pro -l equivalent_to_deprecated > $@
reports/equiv-replaced-by-%.tsv:
pl2sparql -e -A void.ttl -i mondo_edit -i equivs -i mirror/$*.owl -c ../plq/mondo_queries.pro -l equivalent_to_replaced_by > $@
reports/proxy-merge.tsv: mondo.owl
./mq -i all proxy_merge -f tsv -l > [email protected] && sort -u [email protected] > $@
# pl2sparql -f tsv -A void.ttl -e -i all -c ../plq/proxy_merge.pro proxy_merge > [email protected] && mv [email protected] $@
# the main OWL file will have 'pseudo-roots' caused by the fact that external classes
# are referenced; restrict the report to those with labels
%.owl-roots.tsv: %.owl
$(ROBOT) query -f tsv -i $< -s $(SPARQLDIR)/reports/root-labeled-classes.sparql $@
%.obo-roots.tsv: %.obo
$(ROBOT) query -f tsv -i $< -s $(SPARQLDIR)/reports/root-classes.sparql $@
prefixes: mondo-edit.obo
grep ^xref $< | cut -f2 -d : | count-occ.pl
# ----------------------------------------
# Sparql queries: Reports
# ----------------------------------------
all_reports: all_reports_1 fix_reports
all_reports_1: mondo.owl $(ADDITIONAL_REPORT_FILES)
$(ROBOT) query -f tsv -i $< $(REPORT_ARGS) && touch $@
# Will be retired when we have https://github.com/ontodev/robot/issues/176
fix_reports: $(foreach V, $(REPORTS), fix-report-$V)
fix-report-%:
../utils/tidy-sparql-output.pl reports/$*.tmp.tsv > reports/$*.tsv
# TODO: remove hacky script once we improve $(ROBOT) output: https://github.com/ontodev/robot/issues/176
reports/query-%-mondo-edit.obo.tsv: $(SRC) $(SPARQLDIR)/reports/%.sparql
$(ROBOT) query -f tsv -i $< -s $(SPARQLDIR)/reports/$*.sparql [email protected] && ../utils/tidy-sparql-output.pl [email protected] > $@
reports/query-%-mondo.owl.tsv: mondo.owl $(SPARQLDIR)/reports/%.sparql
$(ROBOT) query -f tsv -i $< -s $(SPARQLDIR)/reports/$*.sparql [email protected] && ../utils/tidy-sparql-output.pl [email protected] > $@
# TODO: replace with sparql
#reports/semantic-xref-pairs.tsv: d2p.pro mondo-base.obo
# blip-findall -i mondo-base.obo -i $< -i ../../scratch/mondo-ncit-finding.pro -consult ../utils/xreftbl_maker.pro xrefrow/5 -no_pred > $@
#RR=$(HOME)/repos/rctauber/robot/bin/$(ROBOT) report --fail-on none
RR= $(ROBOT) report --fail-on ERROR --profile profile.txt --print 8
reports/robot-report-%.tsv: %
$(RR) -i $* -o $@
reports/mondo-edit-report.html: $(SRC_TAGS_REASONED)
$(ROBOT) report -i $< --profile profile.txt --fail-on ERROR -o $@
.PRECIOUS: reports/mondo-edit-report.html
mondo_edit_report: reports/mondo-edit-report.html
common_map.tsv:
blip-findall -debug index -goal ix -i imports/equivalencies.obo -i d2p.pro -r mondoe -c ../utils/all_genetic.pro common_to_mondo/2 -label -no_pred -use_tabs | cut -f1,3,4 > $@
# ----------------------------------------
# Sparql constructs
# ----------------------------------------
# generate includes from sparql CONSTRUCT queries;
# these can then be merged in to the main ontology
#include-%.owl: ../sparql/construct/construct-%.sparql $(SRC)
# $(ROBOT) merge -i $(SRC) query -c $< [email protected] -f ttl && $(ROBOT) annotate -i [email protected] -O $(OBO)/mondo/$@ -o $@
imports/external_definitions.owl: ../sparql/construct/construct-embedded-definition.sparql $(SRC)
$(ROBOT) merge -i $(SRC) query -c $< [email protected] -f ttl && $(ROBOT) annotate -i [email protected] -O $(OBO)/mondo/$@ -o $@
FIX_URIS_IN_PLACE = perl -pi -ne $(FIX_URI_EXPR)
all_equivalencies: imports/equivalencies.owl imports/equivalencies.obo imports/equivalencies.json
imports/equivalencies.owl: ../sparql/construct/construct-ecs-from-xrefs.sparql $(SRC)
$(ROBOT) merge -i $(SRC) query -c $< [email protected] -f ttl && $(FIX_URIS_IN_PLACE) [email protected] && $(ROBOT) annotate -i [email protected] -a $(PV_CC0) -O $(OBO)/mondo/$@ -o $@
imports/equivalencies.obo: imports/equivalencies.owl
$(ROBOT) convert -i $< -o $@
clean_imports: $(patsubst %, clean-mirror-%, $(ONTOLOGY_IMPORTS))
clean-mirror-%:
test -f mirror/$*.owl && rm mirror/$*.owl || echo 'no mirror file'
#imports/equivalencies.owl: $(SRC)
# ../utils/xrefs2axioms.pl $< > [email protected] && owltools [email protected] -o $@
# ----------------------------------------
# Merge constructs
# ----------------------------------------
mondo-premerge-%.owl: mondo.owl mirror/%.owl
owltools --use-catalog $^ --merge-support-ontologies -o [email protected] && mv [email protected] $@
mondo-plus-%.owl: mondo-premerge-%.owl
owltools --use-catalog $< --reasoner elk --merge-equivalence-sets -P MONDO -s MONDO 100 --remove-dangling -o [email protected] && mv [email protected] $@
mondo-compat-%: mondo.owl mirror/%.owl
owltools --use-catalog $^ --add-imports-from-supports --run-reasoner -r elk -u -m [email protected] && touch $@
# ----------------------------------------
# External ontologies
# ----------------------------------------
XD = gard ncit-disease obo_orphanet icd10 doid medgen-disease-extract snomed mesh
XD_OWL = $(patsubst %, mirror/%.owl, $(XD))
mirror/xdisease-all.owl: $(patsubst %, mirror/%.owl, $(XD))
owltools $^ --merge-support-ontologies -o $@
mirror/xdisease-labels.owl: mirror/xdisease-all.owl
$(ROBOT) query --format ttl -c ../sparql/construct/construct-labels.sparql $@ -i $<
mirror/labels: $(patsubst %, mirror/%-labels.owl, $(XD))
mirror/%-labels.owl: mirror/%.owl
$(ROBOT) query --format ttl -c ../sparql/construct/construct-labels.sparql $@ -i $<
mirror/%-raw.owl: mirror/%.owl
$(OWLTOOLS) $< --remove-axioms-about -v
mirror/neoplasm-core.owl:
wget --no-check-certificate $(OBO)/ncit/neoplasm-core.owl -O $@ && touch $@
mirror/ncit-disease.uris: mirror/ncit.owl
$(ROBOT) query -i $< -s ../sparql/signature/ncit-subclass-of-disease.sparql $@
mirror/ncit-disease.ids: mirror/ncit-disease.uris
perl -npe 's@http://purl.obolibrary.org/obo/NCIT_@NCIT:@' $< > $@
# Make a disease subset; ensure axioms are relaxed
mirror/ncit-disease.owl: mirror/ncit.owl mirror/ncit-disease.uris
$(ROBOT) extract -i $< -T mirror/ncit-disease.uris --method BOT relax -o $@