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Adding matportal ontologies #100

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98 changes: 66 additions & 32 deletions src/semsql/builder/registry/ontologies.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,6 @@ ontologies:
ENSEMBL: http://identifiers.org/ensembl/
chemessence:
url: https://github.com/cmungall/chemessence/releases/latest/download/chemessence.owl
prefixmap:
chemrof: https://w3id.org/chemrof/
ogco:
url: https://raw.githubusercontent.com/cmungall/chemessence/refs/heads/main/src/ontology/components/ogco.owl
prefixmap:
Expand All @@ -62,11 +60,39 @@ ontologies:
prefixmap:
MSIO: http://purl.obolibrary.org/obo/MSIO_
nmrCV: "http://nmrML.org/nmrCV#NMR:"
chemrof:
url: https://w3id.org/chemrof/chemrof.owl.ttl
prefixmap:
chemrof: https://w3id.org/chemrof/
deb:
url: "http://rest.matportal.org/ontologies/DEB/submissions/1/download?apikey=66c82e77-ce0d-4385-8056-a95898e47ebb"
prefixmap:
DEB: "http://www.semanticweb.org/osnathakimi/ontologies/deb#"
pride:
url: https://raw.githubusercontent.com/PRIDE-Archive/pride-ontology/master/pride_cv.obo
build_command: "robot relax -i $< merge -o $@"
prefixmap:
PRIDE: http://purl.obolibrary.org/obo/PRIDE_
sosa:
url: http://www.w3.org/ns/sosa/
build_command: "robot merge -i $< -o $@"
prefixmap:
sosa: http://www.w3.org/ns/sosa/
vann: http://purl.org/vocab/vann/
schema: http://schema.org/
emi:
url: https://purl.org/emi
build_command: "robot merge -i $< -o $@"
prefixmap:
emi: "https://purl.org/emi#"
genex: http://purl.org/genex#
bibo: http://purl.org/ontology/bibo/
wgs84_pos: http://www.w3.org/2003/01/geo/wgs84_pos#
npc:
url: https://purl.org/npc
build_command: "robot convert -i $< -o $@"
prefixmap:
npc: "https://purl.org/npc#"
modl:
url: https://raw.githubusercontent.com/Data-Semantics-Laboratory/modular-ontology-design-library/master/MODL.owl
prefixmap:
Expand All @@ -84,18 +110,6 @@ ontologies:
- RO:0002202
prefixmap:
biolink: https://w3id.org/biolink/vocab/
phenio_test:
description: Monarch Phenomics Integrated Ontology (Test)
url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-test.owl
relation_graph_settings:
properties:
- BFO:0000050
- BFO:0000051
- UPHENO:0000001
- UPHENO:0000003
- RO:0002202
prefixmap:
biolink: https://w3id.org/biolink/vocab/
comploinc:
url: https://github.com/loinc/comp-loinc/releases/download/v2022-11-05/merged_reasoned_loinc.owl
build_command: "robot relax -i $< merge -o $@"
Expand Down Expand Up @@ -146,22 +160,27 @@ ontologies:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10who.owl
prefixmap:
icd10who: https://icd.who.int/browse10/2019/en#/
#icd11f:
# url: https://github.com/monarch-initiative/icd11/releases/latest/download/icd11foundation.owl
# prefixmap:
# icd11f: http://id.who.int/icd/entity/
icd11f:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd11foundation.owl
prefixmap:
icd11f: http://id.who.int/icd/entity/
ordo:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/ordo.owl
gard:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/gard.owl
prefixmap:
GARD: http://purl.obolibrary.org/obo/GARD_
mondo-ingest:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/mondo-ingest.owl
icd10cm:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10cm.owl
prefixmap:
ICD10CM: http://purl.bioontology.org/ontology/ICD10CM/
omim:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl
prefixmap:
OMIM: https://omim.org/entry/
OMIMPS: https://www.omim.org/phenotypicSeries/PS
CHR: http://purl.obolibrary.org/obo/CHR_
OMIMPS: https://omim.org/phenotypicSeries/PS
mondo-ingest:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/mondo-ingest.owl
oeo:
url: https://openenergyplatform.org/ontology/oeo/releases/oeo-full.owl
prefixmap:
Expand Down Expand Up @@ -197,6 +216,11 @@ ontologies:
build_command: "robot reason -i $< -o $@"
prefixmap:
KIN: "http://purl.org/ga4gh/kin.owl#KIN_"
metpo:
url: https://raw.githubusercontent.com/berkeleybop/metpo/refs/heads/main/metpo.owl
build_command: "robot reason -i $< -o $@"
prefixmap:
METPO: "http://purl.obolibrary.org/obo/METPO_"
biovoices:
url: https://zenodo.org/record/5589773/files/ontology.owl?download=1
build_command: "robot relax -i $< merge -o $@"
Expand Down Expand Up @@ -236,6 +260,19 @@ ontologies:
url: http://purl.obolibrary.org/obo/go/extensions/go-amigo.owl
neo:
url: http://purl.obolibrary.org/obo/go/noctua/neo.owl
prefixmap:
NCBIGene: http://identifiers.org/ncbigene/
UniProtKB.neo: http://identifiers.org/uniprot/
XenBase: http://identifiers.org/xenbase/
RGD: http://identifiers.org/rgd/
ZFIN: http://identifiers.org/zfin/
SGD.neo: http://identifiers.org/sgd/
FB: http://identifiers.org/flybase/
PomBase: http://identifiers.org/pombase/
DictyBase: http://identifiers.org/dictybase.gene/
MGI: "http://identifiers.org/mgi/MGI:"
TAIR.LOCUS: http://arabidopsis.org/servlets/TairObject?type=locus&name=
EcoCyc: "https://ecocyc.org/gene?id="
bao:
url: http://www.bioassayontology.org/bao/bao_complete.owl
has_imports: true
Expand Down Expand Up @@ -394,15 +431,6 @@ ontologies:
dbpedia: http://dbpedia.org/
uberoncm:
url: https://github.com/obophenotype/uberon/releases/latest/download/composite-metazoan.owl
icd10cm:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10cm.owl
prefixmap:
ICD10CM: http://purl.bioontology.org/ontology/ICD10CM/
omim:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl
prefixmap:
OMIM: https://omim.org/entry/
OMIMPS: https://www.omim.org/phenotypicSeries/PS
#sdtm:
# url: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM%20Terminology.OWL.zip
#empathi:
Expand Down Expand Up @@ -462,7 +490,13 @@ ontologies:
compression: gzip
prefixmap:
EC: "https://bioregistry.io/eccode:"
UniProtKB: "https://bioregistry.io/uniprot:"
UniProtKB.br: "https://bioregistry.io/uniprot:"
#eccode:
# url: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz
# compression: gzip
# prefixmap:
# EC.legacy: "https://bioregistry.io/eccode:"
# UniProtKB: "https://bioregistry.io/uniprot:"
uniprot:
url: https://w3id.org/biopragmatics/resources/uniprot/uniprot.owl.gz
compression: gzip
Expand Down