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Merged
cmungall merged 2 commits into from
Oct 31, 2025
Merged

Adding matportal ontologies #100

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aa7fc3e
Adding matportal ontologies
cmungall Apr 25, 2025
903a26d
additional sources
cmungall Oct 31, 2025
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244 changes: 210 additions & 34 deletions ontologies.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,61 @@ db/msio.owl: download/msio.owl
cp $< $@


download/chemrof.owl: STAMP
curl -L -s https://w3id.org/chemrof/chemrof.owl.ttl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/chemrof.owl

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


download/deb.owl: STAMP
curl -L -s http://rest.matportal.org/ontologies/DEB/submissions/1/download?apikey=66c82e77-ce0d-4385-8056-a95898e47ebb > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/deb.owl

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


download/matpo.owl: STAMP
curl -L -s http://bimerr.iot.linkeddata.es/def/material-properties# > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/matpo.owl

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


download/panet.owl: STAMP
curl -L -s http://purl.org/pan-science/PaNET/PaNET.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/panet.owl

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


download/phenx.owl: STAMP
curl -L -s https://data.bioontology.org/ontologies/PHENX/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/phenx.owl

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


download/pride.owl: STAMP
curl -L -s https://raw.githubusercontent.com/PRIDE-Archive/pride-ontology/master/pride_cv.obo > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand All @@ -130,6 +185,39 @@ db/pride.owl: download/pride.owl
robot relax -i $< merge -o $@


download/sosa.owl: STAMP
curl -L -s http://www.w3.org/ns/sosa/ > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/sosa.owl

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


download/emi.owl: STAMP
curl -L -s https://purl.org/emi > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/emi.owl

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


download/npc.owl: STAMP
curl -L -s https://purl.org/npc > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/npc.owl

db/npc.owl: download/npc.owl
robot convert -i $< -o $@


download/modl.owl: STAMP
curl -L -s https://raw.githubusercontent.com/Data-Semantics-Laboratory/modular-ontology-design-library/master/MODL.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand All @@ -152,17 +240,6 @@ db/phenio.owl: download/phenio.owl
cp $< $@


download/phenio_test.owl: STAMP
curl -L -s https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-test.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/phenio_test.owl

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


download/comploinc.owl: STAMP
curl -L -s https://github.com/loinc/comp-loinc/releases/download/v2022-11-05/merged_reasoned_loinc.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -306,6 +383,17 @@ db/icd10who.owl: download/icd10who.owl
cp $< $@


download/icd11f.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd11foundation.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/icd11f.owl

db/icd11f.owl: download/icd11f.owl
cp $< $@


download/ordo.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/ordo.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand All @@ -328,6 +416,28 @@ db/gard.owl: download/gard.owl
cp $< $@


download/icd10cm.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10cm.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/icd10cm.owl

db/icd10cm.owl: download/icd10cm.owl
cp $< $@


download/omim.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/omim.owl

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


download/mondo-ingest.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/mondo-ingest.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -416,6 +526,28 @@ db/kin.owl: download/kin.owl
robot reason -i $< -o $@


download/metpo.owl: STAMP
curl -L -s https://raw.githubusercontent.com/berkeleybop/metpo/refs/heads/main/metpo.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/metpo.owl

db/metpo.owl: download/metpo.owl
robot reason -i $< -o $@


download/d3o.owl: STAMP
curl -L -s https://data.bioontology.org/ontologies/D3O/submissions/3/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/d3o.owl

db/d3o.owl: download/d3o.owl
robot convert -i $< -o $@


download/biovoices.owl: STAMP
curl -L -s https://zenodo.org/record/5589773/files/ontology.owl?download=1 > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -900,6 +1032,17 @@ db/cosmo.owl: download/cosmo.owl
robot merge -i $< -o $@


download/gist.owl: STAMP
curl -L -s https://w3id.org/semanticarts/ontology/gistCore > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/gist.owl

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


download/fhkb.owl: STAMP
curl -L -s None > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -933,28 +1076,6 @@ db/uberoncm.owl: download/uberoncm.owl
cp $< $@


download/icd10cm.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10cm.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/icd10cm.owl

db/icd10cm.owl: download/icd10cm.owl
cp $< $@


download/omim.owl: STAMP
curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/omim.owl

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


download/co_324.owl: STAMP
curl -L -s https://cropontology.org/ontology/CO_324/rdf > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -1252,6 +1373,17 @@ db/enigma_context.owl: download/enigma_context.owl
robot merge -i $< -o $@


download/cbo.owl: STAMP
curl -L -s https://data.bioontology.org/ontologies/CBO/submissions/25/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/cbo.owl

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


download/ontie.owl: STAMP
curl -L -s https://ontology.iedb.org/file/ontie.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand All @@ -1263,6 +1395,28 @@ db/ontie.owl: download/ontie.owl
cp $< $@


download/pain.owl: STAMP
curl -L -s https://raw.githubusercontent.com/uflcod/pain-ontology/refs/heads/main/pain.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/pain.owl

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


download/como.owl: STAMP
curl -L -s https://data.bioontology.org/ontologies/COMO/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/como.owl

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


download/ecosim.owl: STAMP
curl -L -s https://data.bioontology.org/ontologies/ECOSIM/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand All @@ -1274,6 +1428,28 @@ db/ecosim.owl: download/ecosim.owl
cp $< $@


download/bervo.owl: STAMP
curl -L -s https://data.bioontology.org/ontologies/BERVO/submissions/1/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/bervo.owl

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


download/valuesets.owl: STAMP
curl -L -s https://w3id.org/valuesets/valuesets.owl.ttl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/valuesets.owl

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


download/nmdc_schema.owl: STAMP
curl -L -s https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/project/owl/nmdc.owl.ttl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -1372,4 +1548,4 @@ download/%.owl: STAMP
db/%.owl: download/%.owl
robot merge -i $< -o $@

EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio pride modl phenio phenio_test comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who ordo gard mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin 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 fhkb dbpendiaont uberoncm icd10cm omim 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 ontie ecosim 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 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
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