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Adding gistBFO #103

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Merged
cmungall merged 1 commit into from
Oct 31, 2025
Merged

Adding gistBFO #103

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15 changes: 13 additions & 2 deletions ontologies.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -1040,7 +1040,18 @@ download/gist.owl: STAMP
.PRECIOUS: download/gist.owl

db/gist.owl: download/gist.owl
cp $< $@
robot merge -i $< -o $@


download/gistBFO.owl: STAMP
curl -L -s https://w3id.org/semanticarts/ontology/gistBFO > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/gistBFO.owl

db/gistBFO.owl: download/gistBFO.owl
robot merge -i $< -o $@


download/fhkb.owl: STAMP
Expand Down Expand Up @@ -1548,4 +1559,4 @@ download/%.owl: STAMP
db/%.owl: download/%.owl
robot merge -i $< -o $@

EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio chemrof deb matpo panet phenx pride sosa emi npc modl phenio comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who icd11f ordo gard icd10cm omim mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin metpo d3o biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid ror cpont biolink biopax enanomapper mlo ito chemont molgenie cso obiws biopragmatics-reactome reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll oboe-core oboe-standards lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo gist fhkb dbpendiaont uberoncm co_324 ppeo interpro pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context cbo ontie pain como ecosim bervo valuesets nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio chemrof deb matpo panet phenx pride sosa emi npc modl phenio comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who icd11f ordo gard icd10cm omim mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin metpo d3o biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid ror cpont biolink biopax enanomapper mlo ito chemont molgenie cso obiws biopragmatics-reactome reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll oboe-core oboe-standards lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo gist gistBFO fhkb dbpendiaont uberoncm co_324 ppeo interpro pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context cbo ontie pain como ecosim bervo valuesets nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
1 change: 1 addition & 0 deletions src/semsql/builder/prefixes/prefixes.csv
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Expand Up @@ -173,6 +173,7 @@ quantitykind,http://qudt.org/vocab/quantitykind/
cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
gist,https://w3id.org/semanticarts/ns/ontology/gist/
gistd,https://w3id.org/semanticarts/ns/data/gist/
gist,https://w3id.org/semanticarts/ns/ontology/gist/
fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
dbpediaont,http://dbpedia.org/ontology/
dbpedia,http://dbpedia.org/
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1 change: 1 addition & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
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Expand Up @@ -110,6 +110,7 @@ quantitykind,http://qudt.org/vocab/quantitykind/
cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
gist,https://w3id.org/semanticarts/ns/ontology/gist/
gistd,https://w3id.org/semanticarts/ns/data/gist/
gist,https://w3id.org/semanticarts/ns/ontology/gist/
fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
dbpediaont,http://dbpedia.org/ontology/
dbpedia,http://dbpedia.org/
Expand Down
8 changes: 8 additions & 0 deletions src/semsql/builder/registry/ontologies.yaml
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Expand Up @@ -442,9 +442,17 @@ ontologies:
has_imports: true
gist:
url: https://w3id.org/semanticarts/ontology/gistCore
# gist.owl contains DTD elements, rdftab doesn't like this
build_command: "robot merge -i $< -o $@"
prefixmap:
gist: https://w3id.org/semanticarts/ns/ontology/gist/
gistd: https://w3id.org/semanticarts/ns/data/gist/
gistBFO:
url: https://w3id.org/semanticarts/ontology/gistBFO
# merge import closure
build_command: "robot merge -i $< -o $@"
prefixmap:
gist: https://w3id.org/semanticarts/ns/ontology/gist/
fhkb:
prefixmap:
fhkb: http://owl.cs.manchester.ac.uk/tutorials/fhkb#
Expand Down
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