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Adding overrides for SWO prefixes. #91

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Adding overrides for SWO prefixes. #91

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13 changes: 12 additions & 1 deletion ontologies.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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 > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.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 > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -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
14 changes: 13 additions & 1 deletion src/semsql/builder/prefixes/prefixes.csv
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Expand Up @@ -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:
Expand Down Expand Up @@ -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#
Expand Down
12 changes: 12 additions & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
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Original file line number Diff line number Diff line change
@@ -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:
Expand Down Expand Up @@ -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#
Expand Down
16 changes: 16 additions & 0 deletions src/semsql/builder/registry/ontologies.yaml
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Expand Up @@ -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 $@"
Expand Down
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