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Lexmatch revamp #397

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Jan 29, 2024
Merged

Lexmatch revamp #397

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282a0a0
Update Sparql queries for preprocessing
matentzn Jan 22, 2024
2fe4c93
Update lexmatch-sssom-compare.py
matentzn Jan 22, 2024
6b04c71
Update various source prefix configs
matentzn Jan 23, 2024
9643d83
Update mondo.sssom.config.yml
matentzn Jan 24, 2024
b20f301
Update mondo-ingest.Makefile
matentzn Jan 24, 2024
0345282
update all
matentzn Jan 25, 2024
f5203b7
Update src/ontology/mondo-ingest.Makefile
matentzn Jan 25, 2024
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27 changes: 13 additions & 14 deletions src/ontology/metadata/doid.metadata.sssom.yml
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Expand Up @@ -6,32 +6,31 @@ license: https://creativecommons.org/licenses/by/4.0/
creator_id: https://orcid.org/0000-0002-2906-7319
curie_map:
ICD10: http://apps.who.int/classifications/icd10/browse/2010/en#/
MedDRA: https://identifiers.org/meddra/
# MedDRA: https://identifiers.org/meddra/
MESH: https://meshb.nlm.nih.gov/record/ui?ui=
OMIM: https://omim.org/entry/
OMIMPS: https://www.omim.org/phenotypicSeries/PS
Orphanet: http://www.orpha.net/ORDO/Orphanet_
# Orphanet: http://www.orpha.net/ORDO/Orphanet_
UMLS: http://linkedlifedata.com/resource/umls/id/
DOID: http://purl.obolibrary.org/obo/DOID_
EFO: http://www.ebi.ac.uk/efo/EFO_
ENVO: http://purl.obolibrary.org/obo/ENVO_
GARD: "https://bioregistry.io/reference/gard:"
GARD: "https://bioregistry.io/gard:"
ICD10CM: https://icd.codes/icd10cm/
ICD9CM: https://icd.codes/icd9cm/
ICD9CM_2005: https://icd.codes/icd9cm/
ICDO: "https://bioregistry.io/reference/gard:"
# ICD9CM_2005: https://icd.codes/icd9cm/
ICDO: "https://bioregistry.io/icdo:"
KEGG: http://www.kegg.jp/entry/
MEDDRA: https://identifiers.org/meddra/
NCI: http://purl.obolibrary.org/obo/NCIT_
OMIT: http://purl.obolibrary.org/obo/ENVO_
OMIT: http://purl.obolibrary.org/obo/OMIT_
ORDO: http://www.orpha.net/ORDO/Orphanet_
SNOMEDCT_US_2020_03_01: http://identifiers.org/snomedct/
SNOMEDCT_US_2020_09_01: http://identifiers.org/snomedct/
SNOMEDCT_US_2021_07_31: http://identifiers.org/snomedct/
SNOMEDCT_US_2021_09_01: http://identifiers.org/snomedct/
SNOMEDCT_US_2022_07_31: http://identifiers.org/snomedct/
SNOMEDCT_US_2022_10_31: http://identifiers.org/snomedct/
SNOMEDCT_US_2023_02_28: http://identifiers.org/snomedct/
# SNOMEDCT_US_2020_09_01: http://identifiers.org/snomedct/
# SNOMEDCT_US_2021_07_31: http://identifiers.org/snomedct/
# SNOMEDCT_US_2021_09_01: http://identifiers.org/snomedct/
# SNOMEDCT_US_2022_07_31: http://identifiers.org/snomedct/
# SNOMEDCT_US_2022_10_31: http://identifiers.org/snomedct/
# SNOMEDCT_US_2023_02_28: http://identifiers.org/snomedct/
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@matentzn why are these commented out vs. removed or what are these comments a reminder of in the future?

SYMP: http://purl.obolibrary.org/obo/SYMP_
UMLS_CUI: http://linkedlifedata.com/resource/umls/id/

# UMLS_CUI: http://linkedlifedata.com/resource/umls/id/
37 changes: 19 additions & 18 deletions src/ontology/metadata/mondo.sssom.config.yml
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Expand Up @@ -5,20 +5,20 @@ curie_map:
DOID: http://purl.obolibrary.org/obo/DOID_
EFO: http://www.ebi.ac.uk/efo/EFO_
HGNC: "http://identifiers.org/hgnc/"
HGNC__2: "https://identifiers.org/hgnc:"
HGNC__3: "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:"
HGNC_symbol: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/
# HGNC__2: "https://identifiers.org/hgnc:"
# HGNC__3: "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:"
# HGNC_symbol: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/
HP: http://purl.obolibrary.org/obo/HP_
SCTID: http://identifiers.org/snomedct/
SCTID__2: http://snomed.info/id/
# SCTID: http://identifiers.org/snomedct/
# SCTID__2: http://snomed.info/id/
OMIM: https://omim.org/entry/
OMIM__2: http://identifiers.org/omim/
OMIM__3: http://purl.obolibrary.org/obo/OMIM_
OMIM__4: http://omim.org/entry/
# OMIM__2: http://identifiers.org/omim/
# OMIM__3: http://purl.obolibrary.org/obo/OMIM_
# OMIM__4: http://omim.org/entry/
MESH: http://identifiers.org/mesh/
Orphanet: http://www.orpha.net/ORDO/Orphanet_
Orphanet__2: https://www.orpha.net/ORDO/Orphanet_
Orphanet__3: http://purl.obolibrary.org/obo/Orphanet_
# Orphanet__2: https://www.orpha.net/ORDO/Orphanet_
# Orphanet__3: http://purl.obolibrary.org/obo/Orphanet_
oboInOwl: http://www.geneontology.org/formats/oboInOwl#
NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
skos: http://www.w3.org/2004/02/skos/core#
Expand All @@ -34,9 +34,9 @@ curie_map:
semapv: https://w3id.org/semapv/vocab/
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
sssom: https://w3id.org/sssom/
oio: http://www.geneontology.org/formats/oboInOwl#
# oio: http://www.geneontology.org/formats/oboInOwl#
GTR: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/GTR/"
NCI: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/NCI/"
# NCI: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/NCI/"
NIFSTD: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/NIFSTD/"
PO_GIT: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/PO_GIT/"
CALOHA: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/CALOHA/"
Expand All @@ -45,7 +45,7 @@ curie_map:
IMDRF: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/IMDRF/"
LOINC: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/LOINC/"
MEDDRA: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/MEDDRA/"
ncithesaurus: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/ncithesaurus/"
# ncithesaurus: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/ncithesaurus/"
COHD: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/COHD/"
ONCOTREE: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/ONCOTREE/"
ICD9: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/ICD9/"
Expand All @@ -63,17 +63,18 @@ curie_map:
Wikipedia: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/Wikipedia/"
Fyler: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/Fyler/"
EPCC: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/EPCC/"
UMLS_CUI: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/UMLS_CUI/"
# UMLS_CUI: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/UMLS_CUI/"
KUPO: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/KUPO/"
OMOP: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/OMOP/"
ICD10: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/ICD10/"
# ICD10: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/ICD10/"
ICD10EXP: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/ICD10EXP/"
DERMO: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/DERMO/"
GARD: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/GARD/"
SNOMEDCT_US: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/SNOMEDCT_US/"
MSH: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/MSH/"
# SNOMEDCT_US: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/SNOMEDCT_US/"
# MSH: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/MSH/"
GC_ID: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/GC_ID/"
SNOMEDCT_2010_1_31: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/SNOMEDCT_2010_1_31/"
# SNOMEDCT_2010_1_31: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/SNOMEDCT_2010_1_31/"
OMIA: "http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/OMIA/"

extended_prefix_map:
- prefix: MONDO
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4 changes: 2 additions & 2 deletions src/ontology/metadata/omim.metadata.sssom.yml
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Expand Up @@ -11,6 +11,6 @@ curie_map:
OMIM: https://omim.org/entry/
Orphanet: http://www.orpha.net/ORDO/Orphanet_
UMLS: http://linkedlifedata.com/resource/umls/id/
HGNC: 'https://identifiers.org/hgnc:'
#HGNC: 'https://identifiers.org/hgnc:'
hgnc.symbol: 'https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/'
ncbigene: https://www.ncbi.nlm.nih.gov/gene/
ncbigene: https://www.ncbi.nlm.nih.gov/gene/
4 changes: 2 additions & 2 deletions src/ontology/metadata/ordo.metadata.sssom.yml
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Expand Up @@ -8,7 +8,7 @@ curie_map:
ICD10: http://apps.who.int/classifications/icd10/browse/2010/en#/
MedDRA: https://identifiers.org/meddra/
MESH: http://identifiers.org/mesh/
MeSH: http://id.nlm.nih.gov/mesh/
#MeSH: http://id.nlm.nih.gov/mesh/
OMIM: https://omim.org/entry/
Orphanet: http://www.orpha.net/ORDO/Orphanet_
UMLS: http://linkedlifedata.com/resource/umls/id/
UMLS: http://linkedlifedata.com/resource/umls/id/