From ac9c70ddba67f85f6029f11c1929f54ce7602e19 Mon Sep 17 00:00:00 2001 From: Joe Flack Date: Thu, 21 Mar 2024 19:25:08 -0400 Subject: [PATCH 1/2] Bugfix: OMIMPS namespace Updated OMIMPS namespace to remove www, following change from source. --- src/ontology/config/context.json | 2 +- src/ontology/config/prefixes.csv | 2 +- src/ontology/metadata/doid.metadata.sssom.yml | 2 +- src/ontology/metadata/omim.yml | 4 ++-- src/sparql/fix_make_omim_exact.ru | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/ontology/config/context.json b/src/ontology/config/context.json index 85abe98b..89834463 100644 --- a/src/ontology/config/context.json +++ b/src/ontology/config/context.json @@ -31,7 +31,7 @@ "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", "ICD10CM": "http://purl.bioontology.org/ontology/ICD10CM/", "ICD10WHO": "http://apps.who.int/classifications/icd10/browse/2010/en#/", - "OMIMPS": "https://www.omim.org/phenotypicSeries/PS", + "OMIMPS": "https://omim.org/phenotypicSeries/PS", "MONDOREL": "http://purl.obolibrary.org/obo/mondo#" } } \ No newline at end of file diff --git a/src/ontology/config/prefixes.csv b/src/ontology/config/prefixes.csv index 2d6bbc19..75fb892f 100644 --- a/src/ontology/config/prefixes.csv +++ b/src/ontology/config/prefixes.csv @@ -250,7 +250,7 @@ semapv,https://w3id.org/semapv/vocab/ HGNC_SYMBOL,https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/ HGNC,https://identifiers.org/hgnc/ ncbi.gene,https://www.ncbi.nlm.nih.gov/gene/ -OMIMPS,https://www.omim.org/phenotypicSeries/PS +OMIMPS,https://omim.org/phenotypicSeries/PS STY,http://purl.bioontology.org/ontology/STY/ sssom,https://w3id.org/sssom/ biolink,https://w3id.org/biolink/vocab/ diff --git a/src/ontology/metadata/doid.metadata.sssom.yml b/src/ontology/metadata/doid.metadata.sssom.yml index 4397d026..46c1af35 100644 --- a/src/ontology/metadata/doid.metadata.sssom.yml +++ b/src/ontology/metadata/doid.metadata.sssom.yml @@ -9,7 +9,7 @@ curie_map: # 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 + OMIMPS: https://omim.org/phenotypicSeries/PS # Orphanet: http://www.orpha.net/ORDO/Orphanet_ UMLS: http://linkedlifedata.com/resource/umls/id/ DOID: http://purl.obolibrary.org/obo/DOID_ diff --git a/src/ontology/metadata/omim.yml b/src/ontology/metadata/omim.yml index f87273d2..2b7dba88 100644 --- a/src/ontology/metadata/omim.yml +++ b/src/ontology/metadata/omim.yml @@ -2,7 +2,7 @@ id: OMIM label: Online Mendelian Inheritance in Man prefix_map: OMIM: https://omim.org/entry/ - OMIMPS: https://www.omim.org/phenotypicSeries/PS + OMIMPS: https://omim.org/phenotypicSeries/PS CHR: http://purl.obolibrary.org/obo/CHR_ CL: http://purl.obolibrary.org/obo/CL_ HGNC: "https://identifiers.org/hgnc:" @@ -28,4 +28,4 @@ description: > homepage: https://www.omim.org/ base_prefix_map: OMIM: https://omim.org/entry/ - OMIMPS: https://www.omim.org/phenotypicSeries/PS \ No newline at end of file + OMIMPS: https://omim.org/phenotypicSeries/PS \ No newline at end of file diff --git a/src/sparql/fix_make_omim_exact.ru b/src/sparql/fix_make_omim_exact.ru index d6d09ae8..47b0ba1d 100644 --- a/src/sparql/fix_make_omim_exact.ru +++ b/src/sparql/fix_make_omim_exact.ru @@ -29,6 +29,6 @@ WHERE FILTER( STRSTARTS(str(?value), "OMIM")) FILTER( !isBlank(?cls) && STRSTARTS(str(?cls), "http://purl.obolibrary.org/obo/DOID_")) - BIND(IRI(REPLACE(REPLACE(STR(?value), "OMIMPS:", "https://www.omim.org/phenotypicSeries/PS"), "OMIM:", "https://omim.org/entry/")) as ?iri) + BIND(IRI(REPLACE(REPLACE(STR(?value), "OMIMPS:", "https://omim.org/phenotypicSeries/PS"), "OMIM:", "https://omim.org/entry/")) as ?iri) } From 86b4abff6687c96765762d7644531a6df17263cc Mon Sep 17 00:00:00 2001 From: Joe Flack Date: Thu, 21 Mar 2024 19:26:10 -0400 Subject: [PATCH 2/2] Update slurp/omim.tsv Updated file directly without running any prerequisites. Proof of bugfix on slurp following previous commit. --- src/ontology/slurp/omim.tsv | 28 ++++++++-------------------- 1 file changed, 8 insertions(+), 20 deletions(-) diff --git a/src/ontology/slurp/omim.tsv b/src/ontology/slurp/omim.tsv index ef77d1aa..999a975f 100644 --- a/src/ontology/slurp/omim.tsv +++ b/src/ontology/slurp/omim.tsv @@ -2,25 +2,13 @@ mondo_id mondo_label xref xref_source original_label definition parents ID LABEL A oboInOwl:hasDbXref >A oboInOwl:source SPLIT=| A IAO:0000115 SC % MONDO:0958222 maple syrup urine disease, iia 1b OMIM:620698 MONDO:equivalentTo maple syrup urine disease, iia 1b MONDO:0958223 maple syrup urine disease, iia 2 OMIM:620699 MONDO:equivalentTo maple syrup urine disease, iia 2 -MONDO:0958224 encephalopathy, porphyria-related OMIM:620704 MONDO:equivalentTo encephalopathy, porphyria-related -MONDO:0958225 epidermolytic hyperkeratosis 2b, autosomal recessive OMIM:620707 MONDO:equivalentTo epidermolytic hyperkeratosis 2b, autosomal recessive -MONDO:0958226 leukoencephalopathy, porphyria-related OMIM:620711 MONDO:equivalentTo leukoencephalopathy, porphyria-related +MONDO:0958225 epidermolytic hyperkeratosis 2b, autosomal recessive OMIM:620707 MONDO:equivalentTo epidermolytic hyperkeratosis 2b, autosomal recessive MONDO:0957316 MONDO:0958227 polydactyly-macrocephaly syndrome OMIM:620712 MONDO:equivalentTo polydactyly-macrocephaly syndrome -MONDO:0958228 deafness, autosomal recessive 122 OMIM:620714 MONDO:equivalentTo deafness, autosomal recessive 122 +MONDO:0958228 deafness, autosomal recessive 122 OMIM:620714 MONDO:equivalentTo deafness, autosomal recessive 122 MONDO:0019588 MONDO:0958229 bleeding disorder, vascular-type OMIM:620715 MONDO:equivalentTo bleeding disorder, vascular-type -MONDO:0958230 orofaciodigital syndrome 20 OMIM:620718 MONDO:equivalentTo orofaciodigital syndrome 20 -MONDO:0958231 neurodevelopmental disorder with motor abnormalities, seizures, and facial dysmorphism OMIM:620719 MONDO:equivalentTo neurodevelopmental disorder with motor abnormalities, seizures, and facial dysmorphism -MONDO:0958232 deafness, autosomal dominant 90 OMIM:620722 MONDO:equivalentTo deafness, autosomal dominant 90 -MONDO:0958233 bethlem myopathy 1b OMIM:620725 MONDO:equivalentTo bethlem myopathy 1b -MONDO:0958234 bethlem myopathy 1c OMIM:620726 MONDO:equivalentTo bethlem myopathy 1c -MONDO:0958235 ullrich congenital muscular dystrophy 1b OMIM:620727 MONDO:equivalentTo ullrich congenital muscular dystrophy 1b -MONDO:0958236 ullrich congenital muscular dystrophy 1c OMIM:620728 MONDO:equivalentTo ullrich congenital muscular dystrophy 1c -MONDO:0958237 hyperferritinemia OMIM:620729 MONDO:equivalentTo hyperferritinemia -MONDO:0958238 hyperemesis gravidarum, susceptibility to OMIM:620730 MONDO:equivalentTo hyperemesis gravidarum, susceptibility to -MONDO:0958239 microphthalmia/coloboma 11 OMIM:620731 MONDO:equivalentTo microphthalmia/coloboma 11 -MONDO:0958240 neurodevelopmental disorder with hyperkinetic movements, seizures, and structural brain abnormalities OMIM:620732 MONDO:equivalentTo neurodevelopmental disorder with hyperkinetic movements, seizures, and structural brain abnormalities -MONDO:0958241 cardiomyopathy, familial hypertrophic, 30, atrial OMIM:620734 MONDO:equivalentTo cardiomyopathy, familial hypertrophic, 30, atrial -MONDO:0958242 spermatogenic failure 90 OMIM:620744 MONDO:equivalentTo spermatogenic failure 90 -MONDO:0958277 deafness, autosomal recessive 123 OMIM:620745 MONDO:equivalentTo deafness, autosomal recessive 123 -MONDO:0958278 neurodevelopmental disorder with hypotonia and characteristic brain abnormalities OMIM:620746 MONDO:equivalentTo neurodevelopmental disorder with hypotonia and characteristic brain abnormalities -MONDO:0958279 megalencephaly-polydactyly syndrome OMIM:620748 MONDO:equivalentTo megalencephaly-polydactyly syndrome +MONDO:0958230 orofaciodigital syndrome 20 OMIM:620718 MONDO:equivalentTo orofaciodigital syndrome 20 MONDO:0015375 +MONDO:0958232 deafness, autosomal dominant 90 OMIM:620722 MONDO:equivalentTo deafness, autosomal dominant 90 MONDO:0019587 +MONDO:0958281 branchiootorenal syndrome OMIMPS:113650 MONDO:equivalentTo Branchiootorenal syndrome +MONDO:0958282 palmoplantar keratoderma, epidermolytic OMIMPS:144200 MONDO:equivalentTo Palmoplantar keratoderma, epidermolytic +MONDO:0958283 li-fraumeni syndrome OMIMPS:151623 MONDO:equivalentTo Li-Fraumeni syndrome +MONDO:0958284 branchiootic syndrome OMIMPS:602588 MONDO:equivalentTo Branchiootic syndrome