Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Adding overrides for SWO prefixes. #91

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Adding overrides for SWO prefixes. #91

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 12 additions & 1 deletion ontologies.Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,17 @@ db/upheno.owl: download/upheno.owl
robot merge -i $< -o $@


download/swo.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/swo.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/swo.owl

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


download/chiro.owl: STAMP
curl -L -s http://purl.obolibrary.org/obo/chiro.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -1086,4 +1097,4 @@ 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 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
EXTRA_ONTOLOGIES = upheno swo 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
14 changes: 13 additions & 1 deletion src/semsql/builder/prefixes/prefixes.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,17 @@ semapv,https://w3id.org/semapv/vocab/
sssom,https://w3id.org/sssom/
CLINGEN,https://www.clinicalgenome.org/affiliation/
prefix,base
SWO,http://www.ebi.ac.uk/swo/SWO_
SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_
SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_
SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_
SWO.license,http://www.ebi.ac.uk/swo/license/SWO_
SWO.version,http://www.ebi.ac.uk/swo/version/SWO_
SWO.data,http://www.ebi.ac.uk/swo/data/SWO_
SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_
SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_
OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_
OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD
FMA,http://purl.org/sig/ont/fma/fma
MSIO,http://purl.obolibrary.org/obo/MSIO_
nmrCV,http://nmrML.org/nmrCV#NMR:
Expand Down Expand Up @@ -100,11 +111,12 @@ 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#
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/
si-quantity,https://si-digital-framework.org/SI/quantities/
quantitykind,http://qudt.org/vocab/quantitykind/
cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
Expand Down
12 changes: 12 additions & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,15 @@
prefix,base
SWO,http://www.ebi.ac.uk/swo/SWO_
SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_
SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_
SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_
SWO.license,http://www.ebi.ac.uk/swo/license/SWO_
SWO.version,http://www.ebi.ac.uk/swo/version/SWO_
SWO.data,http://www.ebi.ac.uk/swo/data/SWO_
SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_
SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_
OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_
OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD
FMA,http://purl.org/sig/ont/fma/fma
MSIO,http://purl.obolibrary.org/obo/MSIO_
nmrCV,http://nmrML.org/nmrCV#NMR:
Expand Down Expand Up @@ -42,6 +53,7 @@ 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/
si-quantity,https://si-digital-framework.org/SI/quantities/
quantitykind,http://qudt.org/vocab/quantitykind/
cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
Expand Down
16 changes: 16 additions & 0 deletions src/semsql/builder/registry/ontologies.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,22 @@ ontologies:
upheno:
url: http://purl.obolibrary.org/obo/upheno.owl
build_command: "robot merge -i $< -o $@"
swo:
url: http://purl.obolibrary.org/obo/swo.owl
build_command: "robot merge -i $< -o $@"
# runoak -i sqlite:obo:swo
prefixmap:
SWO: http://www.ebi.ac.uk/swo/SWO_
SWO.organization: http://www.ebi.ac.uk/swo/organization/SWO_
SWO.maturity: http://www.ebi.ac.uk/swo/maturity/SWO_
SWO.objective: http://www.ebi.ac.uk/swo/objective/SWO_
SWO.license: http://www.ebi.ac.uk/swo/license/SWO_
SWO.version: http://www.ebi.ac.uk/swo/version/SWO_
SWO.data: http://www.ebi.ac.uk/swo/data/SWO_
SWO.interface: http://www.ebi.ac.uk/swo/interface/SWO_
SWO.algorithm: http://www.ebi.ac.uk/swo/algorithm/SWO_
OntoDM: http://www.ontodm.com/OntoDM-core/OntoDM_
OntoDM.kdd: "http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD"
chiro:
url: http://purl.obolibrary.org/obo/chiro.owl
build_command: "robot relax -i $< merge -o $@"
Expand Down
Loading