Skip to content

Commit 763819d

Browse files
cmungallcmungall
committed
Adding phenio-test
1 parent b87e623 commit 763819d

File tree

4 files changed

+159
-1
lines changed

4 files changed

+159
-1
lines changed

‎ontologies.Makefile‎

Lines changed: 100 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -97,6 +97,17 @@ db/phenio.owl: download/phenio.owl
9797
cp $< $@
9898

9999

100+
download/phenio_test.owl: STAMP
101+
curl -L -s https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-test.owl > $@.tmp
102+
sha256sum -b $@.tmp > $@.sha256
103+
mv $@.tmp $@
104+
105+
.PRECIOUS: download/phenio_test.owl
106+
107+
db/phenio_test.owl: download/phenio_test.owl
108+
cp $< $@
109+
110+
100111
download/comploinc.owl: STAMP
101112
curl -L -s https://github.com/loinc/comp-loinc/releases/download/v2022-11-05/merged_reasoned_loinc.owl > $@.tmp
102113
sha256sum -b $@.tmp > $@.sha256
@@ -251,6 +262,17 @@ db/iof.owl: download/iof.owl
251262
robot relax -i $< merge -o $@
252263

253264

265+
download/upa.owl: STAMP
266+
curl -L -s http://purl.obolibrary.org/obo/upa.owl > $@.tmp
267+
sha256sum -b $@.tmp > $@.sha256
268+
mv $@.tmp $@
269+
270+
.PRECIOUS: download/upa.owl
271+
272+
db/upa.owl: download/upa.owl
273+
cp $< $@
274+
275+
254276
download/go.owl: STAMP
255277
curl -L -s http://purl.obolibrary.org/obo/go/extensions/go-plus.owl > $@.tmp
256278
sha256sum -b $@.tmp > $@.sha256
@@ -273,6 +295,17 @@ db/go-lego.owl: download/go-lego.owl
273295
cp $< $@
274296

275297

298+
download/neo.owl: STAMP
299+
curl -L -s http://purl.obolibrary.org/obo/go/noctua/neo.owl > $@.tmp
300+
sha256sum -b $@.tmp > $@.sha256
301+
mv $@.tmp $@
302+
303+
.PRECIOUS: download/neo.owl
304+
305+
db/neo.owl: download/neo.owl
306+
cp $< $@
307+
308+
276309
download/bao.owl: STAMP
277310
curl -L -s http://www.bioassayontology.org/bao/bao_complete.owl > $@.tmp
278311
sha256sum -b $@.tmp > $@.sha256
@@ -669,6 +702,17 @@ db/complexportal.owl: download/complexportal.owl
669702
cp $< $@
670703

671704

705+
download/wikipathways.owl: STAMP
706+
curl -L -s https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.owl > $@.tmp
707+
sha256sum -b $@.tmp > $@.sha256
708+
mv $@.tmp $@
709+
710+
.PRECIOUS: download/wikipathways.owl
711+
712+
db/wikipathways.owl: download/wikipathways.owl
713+
cp $< $@
714+
715+
672716
download/drugmechdb.owl: STAMP
673717
curl -L -s None > $@.tmp
674718
sha256sum -b $@.tmp > $@.sha256
@@ -746,6 +790,61 @@ db/mixs.owl: download/mixs.owl
746790
robot merge -i $< reason -o $@.tmp.owl && perl -npe 's@_6_2_rc@@g;s@-6-2-rc@@g' $@.tmp.owl > $@
747791

748792

793+
download/fibo.owl: STAMP
794+
curl -L -s https://spec.edmcouncil.org/fibo/ontology/AboutFIBOProd/ > $@.tmp
795+
sha256sum -b $@.tmp > $@.sha256
796+
mv $@.tmp $@
797+
798+
.PRECIOUS: download/fibo.owl
799+
800+
db/fibo.owl: download/fibo.owl
801+
robot merge -i $< -o $@
802+
803+
804+
download/bfo2020.owl: STAMP
805+
curl -L -s http://purl.obolibrary.org/obo/bfo/2020/bfo.owl > $@.tmp
806+
sha256sum -b $@.tmp > $@.sha256
807+
mv $@.tmp $@
808+
809+
.PRECIOUS: download/bfo2020.owl
810+
811+
db/bfo2020.owl: download/bfo2020.owl
812+
cp $< $@
813+
814+
815+
download/bfo2020_core.owl: STAMP
816+
curl -L -s http://purl.obolibrary.org/obo/bfo/2020/bfo-core.owl > $@.tmp
817+
sha256sum -b $@.tmp > $@.sha256
818+
mv $@.tmp $@
819+
820+
.PRECIOUS: download/bfo2020_core.owl
821+
822+
db/bfo2020_core.owl: download/bfo2020_core.owl
823+
cp $< $@
824+
825+
826+
download/bfo2020_notime.owl: STAMP
827+
curl -L -s http://purl.obolibrary.org/obo/bfo/2020/notime/bfo.owl > $@.tmp
828+
sha256sum -b $@.tmp > $@.sha256
829+
mv $@.tmp $@
830+
831+
.PRECIOUS: download/bfo2020_notime.owl
832+
833+
db/bfo2020_notime.owl: download/bfo2020_notime.owl
834+
cp $< $@
835+
836+
837+
download/bfo2020_time.owl: STAMP
838+
curl -L -s https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/profiles/temporal%20extensions/temporalized%20relations/owl/bfo-temporalized-relations.owl > $@.tmp
839+
sha256sum -b $@.tmp > $@.sha256
840+
mv $@.tmp $@
841+
842+
.PRECIOUS: download/bfo2020_time.owl
843+
844+
db/bfo2020_time.owl: download/bfo2020_time.owl
845+
cp $< $@
846+
847+
749848
download/%.owl: STAMP
750849
curl -L -s http://purl.obolibrary.org/obo/$*.owl > $@.tmp
751850
sha256sum -b $@.tmp > $@.sha256
@@ -756,4 +855,4 @@ download/%.owl: STAMP
756855
db/%.owl: download/%.owl
757856
robot merge -i $< -o $@
758857

759-
EXTRA_ONTOLOGIES = chiro ncit fma maxo foodon chebiplus msio modl phenio comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo biovoices omop occo iof go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao hpinternational edam sweetAll lov schema-dot-org prov cellosaurus cosmo fhkb dbpendiaont uberoncm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal drugmechdb rxnorm vccf ontobiotope ecosim nmdc_schema mixs
858+
EXTRA_ONTOLOGIES = chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo biovoices omop occo iof upa go go-lego neo bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao hpinternational edam sweetAll lov schema-dot-org prov cellosaurus cosmo fhkb dbpendiaont uberoncm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time

‎src/semsql/builder/prefixes/prefixes.csv‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -49,6 +49,18 @@ wikidata,http://www.wikidata.org/entity/
4949
schema,https://schema.org/
5050
ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/
5151
snomedct,http://snomed.info/id/
52+
cc,http://creativecommons.org/licenses/
53+
HGNC,http://identifiers.org/hgnc/
54+
MEDDRA,http://identifiers.org/meddra/
55+
MESH,http://identifiers.org/mesh/
56+
MEDGEN,http://identifiers.org/medgen/
57+
SCTID,http://identifiers.org/snomedct/
58+
UMLS,http://linkedlifedata.com/resource/umls/id/
59+
orcid,https://orcid.org/
60+
swrl,http://www.w3.org/2003/11/swrl#
61+
semapv,https://w3id.org/semapv/vocab/
62+
sssom,https://w3id.org/sssom/
63+
CLINGEN,https://www.clinicalgenome.org/affiliation/
5264
prefix,base
5365
FMA,http://purl.org/sig/ont/fma/fma
5466
MSIO,http://purl.obolibrary.org/obo/MSIO_
@@ -68,6 +80,7 @@ ontorion,http://ontorion.com/namespace#
6880
omop,https://athena.ohdsi.org/search-terms/terms/
6981
OccO,http://purl.obolibrary.org/obo/OccO_
7082
IOFcore,https://spec.industrialontologies.org/ontology/
83+
UPa,http://purl.obolibrary.org/obo/UPa_
7184
orcid,https://orcid.org/
7285
evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
7386
old.fix,http://purl.org/obo/owl/FIX#
@@ -93,6 +106,7 @@ swisslipid,http://purl.obolibrary.org/obo/swisslipid_
93106
drugbank,http://purl.obolibrary.org/obo/drugbank_
94107
drugbank,http://purl.obolibrary.org/obo/drugcentral_
95108
complexportal,http://purl.obolibrary.org/obo/complexportal_
109+
complexportal,http://purl.obolibrary.org/obo/wikipathways_
96110
MESH,http://id.nlm.nih.gov/mesh/
97111
RXNORM,http://purl.bioontology.org/ontology/RXNORM/
98112
OBT,http://purl.obolibrary.org/obo/OBT_
@@ -102,6 +116,8 @@ nmdc,https://w3id.org/nmdc/
102116
linkml,https://w3id.org/linkml/
103117
mixs,https://w3id.org/mixs/
104118
mixs,https://w3id.org/mixs/
119+
fibo,https://spec.edmcouncil.org/fibo/ontology/
120+
cmnsav,https://www.omg.org/spec/Commons/AnnotationVocabulary/
105121
RBO,http://purl.obolibrary.org/obo/RBO_
106122
RBO,http://purl.obolibrary.org/obo/RBO_
107123
CLYH,http://purl.obolibrary.org/obo/CLYH_

‎src/semsql/builder/prefixes/prefixes_local.csv‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@ MSIO,http://purl.obolibrary.org/obo/MSIO_
44
nmrCV,http://nmrML.org/nmrCV#NMR:
55
modl,https://archive.org/services/purl/purl/modular_ontology_design_library#
66
biolink,https://w3id.org/biolink/vocab/
7+
biolink,https://w3id.org/biolink/vocab/
78
loinc,https://loinc.org/
89
BCIO,http://humanbehaviourchange.org/ontology/BCIO_
910
BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_
@@ -17,6 +18,7 @@ ontorion,http://ontorion.com/namespace#
1718
omop,https://athena.ohdsi.org/search-terms/terms/
1819
OccO,http://purl.obolibrary.org/obo/OccO_
1920
IOFcore,https://spec.industrialontologies.org/ontology/
21+
UPa,http://purl.obolibrary.org/obo/UPa_
2022
orcid,https://orcid.org/
2123
evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
2224
old.fix,http://purl.org/obo/owl/FIX#
@@ -42,6 +44,7 @@ swisslipid,http://purl.obolibrary.org/obo/swisslipid_
4244
drugbank,http://purl.obolibrary.org/obo/drugbank_
4345
drugbank,http://purl.obolibrary.org/obo/drugcentral_
4446
complexportal,http://purl.obolibrary.org/obo/complexportal_
47+
complexportal,http://purl.obolibrary.org/obo/wikipathways_
4548
MESH,http://id.nlm.nih.gov/mesh/
4649
RXNORM,http://purl.bioontology.org/ontology/RXNORM/
4750
OBT,http://purl.obolibrary.org/obo/OBT_
@@ -51,3 +54,5 @@ nmdc,https://w3id.org/nmdc/
5154
linkml,https://w3id.org/linkml/
5255
mixs,https://w3id.org/mixs/
5356
mixs,https://w3id.org/mixs/
57+
fibo,https://spec.edmcouncil.org/fibo/ontology/
58+
cmnsav,https://www.omg.org/spec/Commons/AnnotationVocabulary/

‎src/semsql/builder/registry/ontologies.yaml‎

Lines changed: 38 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -43,6 +43,18 @@ ontologies:
4343
- RO:0002202
4444
prefixmap:
4545
biolink: https://w3id.org/biolink/vocab/
46+
phenio_test:
47+
description: Monarch Phenomics Integrated Ontology (Test)
48+
url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-test.owl
49+
relation_graph_settings:
50+
properties:
51+
- BFO:0000050
52+
- BFO:0000051
53+
- UPHENO:0000001
54+
- UPHENO:0000003
55+
- RO:0002202
56+
prefixmap:
57+
biolink: https://w3id.org/biolink/vocab/
4658
comploinc:
4759
url: https://github.com/loinc/comp-loinc/releases/download/v2022-11-05/merged_reasoned_loinc.owl
4860
build_command: "robot relax -i $< merge -o $@"
@@ -96,10 +108,16 @@ ontologies:
96108
build_command: "robot relax -i $< merge -o $@"
97109
prefixmap:
98110
IOFcore: https://spec.industrialontologies.org/ontology/
111+
upa:
112+
url: http://purl.obolibrary.org/obo/upa.owl
113+
prefixmap:
114+
UPa: http://purl.obolibrary.org/obo/UPa_
99115
go:
100116
url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
101117
go-lego:
102118
url: http://purl.obolibrary.org/obo/go/extensions/go-lego.owl
119+
neo:
120+
url: http://purl.obolibrary.org/obo/go/noctua/neo.owl
103121
bao:
104122
url: http://www.bioassayontology.org/bao/bao_complete.owl
105123
has_imports: true
@@ -268,6 +286,10 @@ ontologies:
268286
compression: gzip
269287
prefixmap:
270288
complexportal: http://purl.obolibrary.org/obo/complexportal_
289+
wikipathways:
290+
url: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.owl
291+
prefixmap:
292+
complexportal: http://purl.obolibrary.org/obo/wikipathways_
271293
drugmechdb:
272294
prefixmap:
273295
MESH: http://id.nlm.nih.gov/mesh/
@@ -301,3 +323,19 @@ ontologies:
301323
build_command: "robot merge -i $< reason -o [email protected] && perl -npe 's@_6_2_rc@@g;s@-6-2-rc@@g' [email protected] > $@"
302324
prefixmap:
303325
mixs: https://w3id.org/mixs/
326+
fibo:
327+
url: https://spec.edmcouncil.org/fibo/ontology/AboutFIBOProd/
328+
build_command: "robot merge -i $< -o $@"
329+
prefixmap:
330+
fibo: https://spec.edmcouncil.org/fibo/ontology/
331+
cmnsav: https://www.omg.org/spec/Commons/AnnotationVocabulary/
332+
333+
# BFO variant products
334+
bfo2020:
335+
url: http://purl.obolibrary.org/obo/bfo/2020/bfo.owl
336+
bfo2020_core:
337+
url: http://purl.obolibrary.org/obo/bfo/2020/bfo-core.owl
338+
bfo2020_notime:
339+
url: http://purl.obolibrary.org/obo/bfo/2020/notime/bfo.owl
340+
bfo2020_time:
341+
url: https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/profiles/temporal%20extensions/temporalized%20relations/owl/bfo-temporalized-relations.owl

0 commit comments

Comments
 (0)