From e8c9b0ae91449a8c97a34da6fabc0815f9385fa5 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 13 Aug 2024 18:10:17 -0700 Subject: [PATCH 1/2] new emtries --- ontologies.Makefile | 81 ++++++++++++++++++- src/semsql/builder/prefixes/prefixes.csv | 13 +++ .../builder/prefixes/prefixes_local.csv | 13 +++ src/semsql/builder/registry/ontologies.yaml | 50 ++++++++++-- 4 files changed, 150 insertions(+), 7 deletions(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index d187d88..4ff13ee 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -461,7 +461,7 @@ db/enanomapper.owl: download/enanomapper.owl download/mlo.owl: STAMP - curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl > $@.tmp + curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ @@ -482,6 +482,28 @@ db/ito.owl: download/ito.owl cp $< $@ +download/cso.owl: STAMP + curl -L -s https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip > $@.zip.tmp && unzip -p $@.zip.tmp CSO.3.3.owl > $@.tmp && rm $@.zip.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/cso.owl + +db/cso.owl: download/cso.owl + cp $< $@ + + +download/obiws.owl: STAMP + curl -L -s https://data.bioontology.org/ontologies/OBIWS/submissions/2/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/obiws.owl + +db/obiws.owl: download/obiws.owl + cp $< $@ + + download/reactome-hs.owl: STAMP curl -L -s https://reactome.org/download/current/biopax.zip > $@.zip.tmp && unzip -p $@.zip.tmp Homo_sapiens.owl > $@.tmp && rm $@.zip.tmp sha256sum -b $@.tmp > $@.sha256 @@ -548,6 +570,17 @@ db/edam.owl: download/edam.owl cp $< $@ +download/chr.owl: STAMP + curl -L -s https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/chr.owl + +db/chr.owl: download/chr.owl + cp $< $@ + + download/sweetAll.owl: STAMP curl -L -s http://sweetontology.net/sweetAll > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -592,6 +625,50 @@ db/prov.owl: download/prov.owl cp $< $@ +download/dtype.owl: STAMP + curl -L -s http://www.linkedmodel.org/schema/dtype > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/dtype.owl + +db/dtype.owl: download/dtype.owl + cp $< $@ + + +download/vaem.owl: STAMP + curl -L -s http://www.linkedmodel.org/schema/vaem > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/vaem.owl + +db/vaem.owl: download/vaem.owl + cp $< $@ + + +download/qudtunit.owl: STAMP + curl -L -s http://qudt.org/vocab/unit > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/qudtunit.owl + +db/qudtunit.owl: download/qudtunit.owl + robot merge -i $< -o $@ + + +download/quantitykind.owl: STAMP + curl -L -s http://qudt.org/vocab/quantitykind > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/quantitykind.owl + +db/quantitykind.owl: download/quantitykind.owl + robot merge -i $< -o $@ + + download/cellosaurus.owl: STAMP curl -L -s https://raw.githubusercontent.com/calipho-sib/cellosaurus/master/cellosaurus.obo > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1009,4 +1086,4 @@ download/%.owl: STAMP db/%.owl: download/%.owl robot merge -i $< -o $@ -EXTRA_ONTOLOGIES = upheno chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito reactome-hs reactome-mm efo hcao hpinternational edam sweetAll lov schema-dot-org prov cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time +EXTRA_ONTOLOGIES = upheno chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito cso obiws reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 691a2a5..95054a6 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -92,7 +92,20 @@ orcid,https://orcid.org/ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# old.fix,http://purl.org/obo/owl/FIX# mlo,http://www.a2rd.net.br/mlo# +ito,https://identifiers.org/ito: +cso,https://cso.kmi.open.ac.uk/topics/ +freebase,http://rdf.freebase.com/ns/ +yago,http://yago-knowledge.org/resource/ +cyc,http://sw.cyc.com/concept +OBIws,http://purl.obolibrary.org/obo/OBIws_ +chr,http://purl.obolibrary.org/obo/CHR_ prov,http://www.w3.org/ns/prov# +voag,http://voag.linkedmodel.org/voag# +dtype,http://www.linkedmodel.org/schema/dtype# +vaem,http://www.linkedmodel.org/schema/vaem# +qudtschema,http://qudt.org/schema/qudt/ +qudtunit,http://qudt.org/vocab/unit/ +quantitykind,http://qudt.org/vocab/quantitykind/ cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# dbpediaont,http://dbpedia.org/ontology/ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index 00f0e6a..ca8188c 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -29,7 +29,20 @@ orcid,https://orcid.org/ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# old.fix,http://purl.org/obo/owl/FIX# mlo,http://www.a2rd.net.br/mlo# +ito,https://identifiers.org/ito: +cso,https://cso.kmi.open.ac.uk/topics/ +freebase,http://rdf.freebase.com/ns/ +yago,http://yago-knowledge.org/resource/ +cyc,http://sw.cyc.com/concept +OBIws,http://purl.obolibrary.org/obo/OBIws_ +chr,http://purl.obolibrary.org/obo/CHR_ prov,http://www.w3.org/ns/prov# +dtype,http://www.linkedmodel.org/schema/dtype# +voag,http://voag.linkedmodel.org/voag# +vaem,http://www.linkedmodel.org/schema/vaem# +qudtschema,http://qudt.org/schema/qudt/ +qudtunit,http://qudt.org/vocab/unit/ +quantitykind,http://qudt.org/vocab/quantitykind/ cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# dbpediaont,http://dbpedia.org/ontology/ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index fe16e92..a9a1e67 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -178,13 +178,27 @@ ontologies: evs.ncit: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# old.fix: http://purl.org/obo/owl/FIX# mlo: - url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl + url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl has_imports: true prefixmap: mlo: http://www.a2rd.net.br/mlo# ito: url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip - zip_extract_file: ITO.owl + zip_extract_file: ITO.owl + prefixmap: + ito: "https://identifiers.org/ito:" + cso: + url: https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip + zip_extract_file: CSO.3.3.owl + prefixmap: + cso: https://cso.kmi.open.ac.uk/topics/ + freebase: http://rdf.freebase.com/ns/ + yago: http://yago-knowledge.org/resource/ + cyc: http://sw.cyc.com/concept + obiws: + url: https://data.bioontology.org/ontologies/OBIWS/submissions/2/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb + prefixmap: + OBIws: http://purl.obolibrary.org/obo/OBIws_ reactome-hs: url: https://reactome.org/download/current/biopax.zip zip_extract_file: Homo_sapiens.owl @@ -204,6 +218,10 @@ ontologies: url: http://purl.obolibrary.org/obo/hp/hp-international.owl edam: url: http://edamontology.org/EDAM.owl + chr: + url: https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr.owl + prefixmap: + chr: http://purl.obolibrary.org/obo/CHR_ sweetAll: url: http://sweetontology.net/sweetAll has_imports: true @@ -220,10 +238,32 @@ ontologies: url: http://www.w3.org/ns/prov.owl prefixmap: prov: "http://www.w3.org/ns/prov#" - #qudtunit: - # url: http://qudt.org/2.1/vocab/unit + #voag: + # url: http://voag.linkedmodel.org/voag + # build_command: "robot merge -i $< -o $@" # prefixmap: - # qudtunit: http://qudt.org/2.1/vocab/unit/ + # voag: http://voag.linkedmodel.org/voag# + dtype: + url: http://www.linkedmodel.org/schema/dtype + prefixmap: + dtype: http://www.linkedmodel.org/schema/dtype# + voag: http://voag.linkedmodel.org/voag# + vaem: + url: http://www.linkedmodel.org/schema/vaem + prefixmap: + vaem: http://www.linkedmodel.org/schema/vaem# + qudtunit: + url: http://qudt.org/vocab/unit + build_command: "robot merge -i $< -o $@" + prefixmap: + qudtschema: http://qudt.org/schema/qudt/ + qudtunit: http://qudt.org/vocab/unit/ + si-quantity: https://si-digital-framework.org/SI/quantities/ + quantitykind: + url: http://qudt.org/vocab/quantitykind + build_command: "robot merge -i $< -o $@" + prefixmap: + quantitykind: http://qudt.org/vocab/quantitykind/ cellosaurus: url: https://raw.githubusercontent.com/calipho-sib/cellosaurus/master/cellosaurus.obo format: obo From c3d3ad6fcb19b478c4770e654c1f2359502e9230 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 13 Aug 2024 18:23:11 -0700 Subject: [PATCH 2/2] noqa --- src/semsql/builder/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/semsql/builder/cli.py b/src/semsql/builder/cli.py index 7838d7b..6aa8fd5 100644 --- a/src/semsql/builder/cli.py +++ b/src/semsql/builder/cli.py @@ -72,7 +72,7 @@ def make(path, docker, **kwargs): steps = builder.get_postprocessing_steps(ontology, path) for step in steps: print(f"RUNNING: {step}") - subprocess.run(step, shell=True) + subprocess.run(step, shell=True) # noqa S602 @main.command()