From 61b51661a8c90fdb540f0d55a575db884a263182 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 13 Aug 2024 18:25:03 -0700 Subject: [PATCH] Adding overrides for SWO prefixes. See https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2307#issuecomment-2287584654 --- ontologies.Makefile | 13 ++++++++++++- src/semsql/builder/prefixes/prefixes.csv | 14 +++++++++++++- src/semsql/builder/prefixes/prefixes_local.csv | 12 ++++++++++++ src/semsql/builder/registry/ontologies.yaml | 16 ++++++++++++++++ 4 files changed, 53 insertions(+), 2 deletions(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index 4ff13ee..ef0c223 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -9,6 +9,17 @@ db/upheno.owl: download/upheno.owl robot merge -i $< -o $@ +download/swo.owl: STAMP + curl -L -s http://purl.obolibrary.org/obo/swo.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/swo.owl + +db/swo.owl: download/swo.owl + robot merge -i $< -o $@ + + download/chiro.owl: STAMP curl -L -s http://purl.obolibrary.org/obo/chiro.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1086,4 +1097,4 @@ 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 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 +EXTRA_ONTOLOGIES = upheno swo 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 95054a6..6707b19 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -62,6 +62,17 @@ semapv,https://w3id.org/semapv/vocab/ sssom,https://w3id.org/sssom/ CLINGEN,https://www.clinicalgenome.org/affiliation/ prefix,base +SWO,http://www.ebi.ac.uk/swo/SWO_ +SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_ +SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_ +SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_ +SWO.license,http://www.ebi.ac.uk/swo/license/SWO_ +SWO.version,http://www.ebi.ac.uk/swo/version/SWO_ +SWO.data,http://www.ebi.ac.uk/swo/data/SWO_ +SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_ +SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_ +OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_ +OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD FMA,http://purl.org/sig/ont/fma/fma MSIO,http://purl.obolibrary.org/obo/MSIO_ nmrCV,http://nmrML.org/nmrCV#NMR: @@ -100,11 +111,12 @@ 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# +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/ +si-quantity,https://si-digital-framework.org/SI/quantities/ quantitykind,http://qudt.org/vocab/quantitykind/ cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index ca8188c..05f2935 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -1,4 +1,15 @@ prefix,base +SWO,http://www.ebi.ac.uk/swo/SWO_ +SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_ +SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_ +SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_ +SWO.license,http://www.ebi.ac.uk/swo/license/SWO_ +SWO.version,http://www.ebi.ac.uk/swo/version/SWO_ +SWO.data,http://www.ebi.ac.uk/swo/data/SWO_ +SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_ +SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_ +OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_ +OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD FMA,http://purl.org/sig/ont/fma/fma MSIO,http://purl.obolibrary.org/obo/MSIO_ nmrCV,http://nmrML.org/nmrCV#NMR: @@ -42,6 +53,7 @@ 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/ +si-quantity,https://si-digital-framework.org/SI/quantities/ quantitykind,http://qudt.org/vocab/quantitykind/ cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_ fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb# diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index a9a1e67..22d08de 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -5,6 +5,22 @@ ontologies: upheno: url: http://purl.obolibrary.org/obo/upheno.owl build_command: "robot merge -i $< -o $@" + swo: + url: http://purl.obolibrary.org/obo/swo.owl + build_command: "robot merge -i $< -o $@" + # runoak -i sqlite:obo:swo + prefixmap: + SWO: http://www.ebi.ac.uk/swo/SWO_ + SWO.organization: http://www.ebi.ac.uk/swo/organization/SWO_ + SWO.maturity: http://www.ebi.ac.uk/swo/maturity/SWO_ + SWO.objective: http://www.ebi.ac.uk/swo/objective/SWO_ + SWO.license: http://www.ebi.ac.uk/swo/license/SWO_ + SWO.version: http://www.ebi.ac.uk/swo/version/SWO_ + SWO.data: http://www.ebi.ac.uk/swo/data/SWO_ + SWO.interface: http://www.ebi.ac.uk/swo/interface/SWO_ + SWO.algorithm: http://www.ebi.ac.uk/swo/algorithm/SWO_ + OntoDM: http://www.ontodm.com/OntoDM-core/OntoDM_ + OntoDM.kdd: "http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD" chiro: url: http://purl.obolibrary.org/obo/chiro.owl build_command: "robot relax -i $< merge -o $@"