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Merge pull request #90 from INCATools/additional-sources2
additional sources2
2 parents 8b6cb59 + c3d3ad6 commit f488caf

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‎ontologies.Makefile

Lines changed: 79 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -461,7 +461,7 @@ db/enanomapper.owl: download/enanomapper.owl
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463463
download/mlo.owl: STAMP
464-
curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl > $@.tmp
464+
curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl > $@.tmp
465465
sha256sum -b $@.tmp > $@.sha256
466466
mv $@.tmp $@
467467

@@ -482,6 +482,28 @@ db/ito.owl: download/ito.owl
482482
cp $< $@
483483

484484

485+
download/cso.owl: STAMP
486+
curl -L -s https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip > $@.zip.tmp && unzip -p $@.zip.tmp CSO.3.3.owl > $@.tmp && rm $@.zip.tmp
487+
sha256sum -b $@.tmp > $@.sha256
488+
mv $@.tmp $@
489+
490+
.PRECIOUS: download/cso.owl
491+
492+
db/cso.owl: download/cso.owl
493+
cp $< $@
494+
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496+
download/obiws.owl: STAMP
497+
curl -L -s https://data.bioontology.org/ontologies/OBIWS/submissions/2/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
498+
sha256sum -b $@.tmp > $@.sha256
499+
mv $@.tmp $@
500+
501+
.PRECIOUS: download/obiws.owl
502+
503+
db/obiws.owl: download/obiws.owl
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cp $< $@
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485507
download/reactome-hs.owl: STAMP
486508
curl -L -s https://reactome.org/download/current/biopax.zip > $@.zip.tmp && unzip -p $@.zip.tmp Homo_sapiens.owl > $@.tmp && rm $@.zip.tmp
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sha256sum -b $@.tmp > $@.sha256
@@ -548,6 +570,17 @@ db/edam.owl: download/edam.owl
548570
cp $< $@
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download/chr.owl: STAMP
574+
curl -L -s https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr.owl > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
576+
mv $@.tmp $@
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.PRECIOUS: download/chr.owl
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db/chr.owl: download/chr.owl
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cp $< $@
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551584
download/sweetAll.owl: STAMP
552585
curl -L -s http://sweetontology.net/sweetAll > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
@@ -592,6 +625,50 @@ db/prov.owl: download/prov.owl
592625
cp $< $@
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594627

628+
download/dtype.owl: STAMP
629+
curl -L -s http://www.linkedmodel.org/schema/dtype > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
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mv $@.tmp $@
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.PRECIOUS: download/dtype.owl
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db/dtype.owl: download/dtype.owl
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cp $< $@
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download/vaem.owl: STAMP
640+
curl -L -s http://www.linkedmodel.org/schema/vaem > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
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mv $@.tmp $@
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.PRECIOUS: download/vaem.owl
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db/vaem.owl: download/vaem.owl
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cp $< $@
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download/qudtunit.owl: STAMP
651+
curl -L -s http://qudt.org/vocab/unit > $@.tmp
652+
sha256sum -b $@.tmp > $@.sha256
653+
mv $@.tmp $@
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655+
.PRECIOUS: download/qudtunit.owl
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db/qudtunit.owl: download/qudtunit.owl
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robot merge -i $< -o $@
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download/quantitykind.owl: STAMP
662+
curl -L -s http://qudt.org/vocab/quantitykind > $@.tmp
663+
sha256sum -b $@.tmp > $@.sha256
664+
mv $@.tmp $@
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.PRECIOUS: download/quantitykind.owl
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db/quantitykind.owl: download/quantitykind.owl
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robot merge -i $< -o $@
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595672
download/cellosaurus.owl: STAMP
596673
curl -L -s https://raw.githubusercontent.com/calipho-sib/cellosaurus/master/cellosaurus.obo > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
@@ -1009,4 +1086,4 @@ download/%.owl: STAMP
10091086
db/%.owl: download/%.owl
10101087
robot merge -i $< -o $@
10111088

1012-
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
1089+
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

‎src/semsql/builder/cli.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,7 @@ def make(path, docker, **kwargs):
7272
steps = builder.get_postprocessing_steps(ontology, path)
7373
for step in steps:
7474
print(f"RUNNING: {step}")
75-
subprocess.run(step, shell=True)
75+
subprocess.run(step, shell=True) # noqa S602
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@main.command()

‎src/semsql/builder/prefixes/prefixes.csv

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -92,7 +92,20 @@ orcid,https://orcid.org/
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evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
9393
old.fix,http://purl.org/obo/owl/FIX#
9494
mlo,http://www.a2rd.net.br/mlo#
95+
ito,https://identifiers.org/ito:
96+
cso,https://cso.kmi.open.ac.uk/topics/
97+
freebase,http://rdf.freebase.com/ns/
98+
yago,http://yago-knowledge.org/resource/
99+
cyc,http://sw.cyc.com/concept
100+
OBIws,http://purl.obolibrary.org/obo/OBIws_
101+
chr,http://purl.obolibrary.org/obo/CHR_
95102
prov,http://www.w3.org/ns/prov#
103+
voag,http://voag.linkedmodel.org/voag#
104+
dtype,http://www.linkedmodel.org/schema/dtype#
105+
vaem,http://www.linkedmodel.org/schema/vaem#
106+
qudtschema,http://qudt.org/schema/qudt/
107+
qudtunit,http://qudt.org/vocab/unit/
108+
quantitykind,http://qudt.org/vocab/quantitykind/
96109
cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
97110
fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
98111
dbpediaont,http://dbpedia.org/ontology/

‎src/semsql/builder/prefixes/prefixes_local.csv

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,20 @@ orcid,https://orcid.org/
2929
evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
3030
old.fix,http://purl.org/obo/owl/FIX#
3131
mlo,http://www.a2rd.net.br/mlo#
32+
ito,https://identifiers.org/ito:
33+
cso,https://cso.kmi.open.ac.uk/topics/
34+
freebase,http://rdf.freebase.com/ns/
35+
yago,http://yago-knowledge.org/resource/
36+
cyc,http://sw.cyc.com/concept
37+
OBIws,http://purl.obolibrary.org/obo/OBIws_
38+
chr,http://purl.obolibrary.org/obo/CHR_
3239
prov,http://www.w3.org/ns/prov#
40+
dtype,http://www.linkedmodel.org/schema/dtype#
41+
voag,http://voag.linkedmodel.org/voag#
42+
vaem,http://www.linkedmodel.org/schema/vaem#
43+
qudtschema,http://qudt.org/schema/qudt/
44+
qudtunit,http://qudt.org/vocab/unit/
45+
quantitykind,http://qudt.org/vocab/quantitykind/
3346
cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
3447
fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
3548
dbpediaont,http://dbpedia.org/ontology/

‎src/semsql/builder/registry/ontologies.yaml

Lines changed: 45 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -178,13 +178,27 @@ ontologies:
178178
evs.ncit: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
179179
old.fix: http://purl.org/obo/owl/FIX#
180180
mlo:
181-
url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl
181+
url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl
182182
has_imports: true
183183
prefixmap:
184184
mlo: http://www.a2rd.net.br/mlo#
185185
ito:
186186
url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip
187-
zip_extract_file: ITO.owl
187+
zip_extract_file: ITO.owl
188+
prefixmap:
189+
ito: "https://identifiers.org/ito:"
190+
cso:
191+
url: https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip
192+
zip_extract_file: CSO.3.3.owl
193+
prefixmap:
194+
cso: https://cso.kmi.open.ac.uk/topics/
195+
freebase: http://rdf.freebase.com/ns/
196+
yago: http://yago-knowledge.org/resource/
197+
cyc: http://sw.cyc.com/concept
198+
obiws:
199+
url: https://data.bioontology.org/ontologies/OBIWS/submissions/2/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
200+
prefixmap:
201+
OBIws: http://purl.obolibrary.org/obo/OBIws_
188202
reactome-hs:
189203
url: https://reactome.org/download/current/biopax.zip
190204
zip_extract_file: Homo_sapiens.owl
@@ -204,6 +218,10 @@ ontologies:
204218
url: http://purl.obolibrary.org/obo/hp/hp-international.owl
205219
edam:
206220
url: http://edamontology.org/EDAM.owl
221+
chr:
222+
url: https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr.owl
223+
prefixmap:
224+
chr: http://purl.obolibrary.org/obo/CHR_
207225
sweetAll:
208226
url: http://sweetontology.net/sweetAll
209227
has_imports: true
@@ -220,10 +238,32 @@ ontologies:
220238
url: http://www.w3.org/ns/prov.owl
221239
prefixmap:
222240
prov: "http://www.w3.org/ns/prov#"
223-
#qudtunit:
224-
# url: http://qudt.org/2.1/vocab/unit
241+
#voag:
242+
# url: http://voag.linkedmodel.org/voag
243+
# build_command: "robot merge -i $< -o $@"
225244
# prefixmap:
226-
# qudtunit: http://qudt.org/2.1/vocab/unit/
245+
# voag: http://voag.linkedmodel.org/voag#
246+
dtype:
247+
url: http://www.linkedmodel.org/schema/dtype
248+
prefixmap:
249+
dtype: http://www.linkedmodel.org/schema/dtype#
250+
voag: http://voag.linkedmodel.org/voag#
251+
vaem:
252+
url: http://www.linkedmodel.org/schema/vaem
253+
prefixmap:
254+
vaem: http://www.linkedmodel.org/schema/vaem#
255+
qudtunit:
256+
url: http://qudt.org/vocab/unit
257+
build_command: "robot merge -i $< -o $@"
258+
prefixmap:
259+
qudtschema: http://qudt.org/schema/qudt/
260+
qudtunit: http://qudt.org/vocab/unit/
261+
si-quantity: https://si-digital-framework.org/SI/quantities/
262+
quantitykind:
263+
url: http://qudt.org/vocab/quantitykind
264+
build_command: "robot merge -i $< -o $@"
265+
prefixmap:
266+
quantitykind: http://qudt.org/vocab/quantitykind/
227267
cellosaurus:
228268
url: https://raw.githubusercontent.com/calipho-sib/cellosaurus/master/cellosaurus.obo
229269
format: obo

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