Merge pull request #478 from monarch-initiative/bugfix-omimps-ns-and-…

…slurp

Bug fix: OMIMPS namespace && no OMIM parents in migration

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#"
 	}
 }

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/

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_

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
+  OMIMPS: https://omim.org/phenotypicSeries/PS

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		

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)
 
 }