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additional sources2 #90

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Aug 14, 2024
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additional sources2 #90

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e8c9b0a
new emtries
cmungall Aug 14, 2024
c3d3ad6
noqa
cmungall Aug 14, 2024
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81 changes: 79 additions & 2 deletions ontologies.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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 > [email protected]
curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

Expand All @@ -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 > [email protected] && unzip -p [email protected] CSO.3.3.owl > [email protected] && rm [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.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 > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.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 > [email protected] && unzip -p [email protected] Homo_sapiens.owl > [email protected] && rm [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -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 > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/chr.owl

db/chr.owl: download/chr.owl
cp $< $@


download/sweetAll.owl: STAMP
curl -L -s http://sweetontology.net/sweetAll > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -592,6 +625,50 @@ db/prov.owl: download/prov.owl
cp $< $@


download/dtype.owl: STAMP
curl -L -s http://www.linkedmodel.org/schema/dtype > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/dtype.owl

db/dtype.owl: download/dtype.owl
cp $< $@


download/vaem.owl: STAMP
curl -L -s http://www.linkedmodel.org/schema/vaem > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.PRECIOUS: download/vaem.owl

db/vaem.owl: download/vaem.owl
cp $< $@


download/qudtunit.owl: STAMP
curl -L -s http://qudt.org/vocab/unit > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.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 > [email protected]
sha256sum -b [email protected] > [email protected]
mv [email protected] $@

.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 > [email protected]
sha256sum -b [email protected] > [email protected]
Expand Down Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/semsql/builder/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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()
Expand Down
13 changes: 13 additions & 0 deletions src/semsql/builder/prefixes/prefixes.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -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/
Expand Down
13 changes: 13 additions & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -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/
Expand Down
50 changes: 45 additions & 5 deletions src/semsql/builder/registry/ontologies.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down
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