From 5d72d57ffc3eb8368c27b135ba22e1153e630f69 Mon Sep 17 00:00:00 2001 From: "J. Allen Baron" Date: Fri, 1 Nov 2024 12:45:46 -0400 Subject: [PATCH] Revert MTPD and revise with subtypes This partially reverts commit e5c943c0, in which MTPD was incorrectly revised to MTPD1. A new disease entity is added for MTPD1 instead. Includes revisions of MTPD & MTPD2. See issue #1394 --- src/ontology/doid-edit.owl | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 71973782..97859f9f 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -2599,6 +2599,7 @@ Declaration(Class(obo:DOID_0070615)) Declaration(Class(obo:DOID_0070616)) Declaration(Class(obo:DOID_0070617)) Declaration(Class(obo:DOID_0070618)) +Declaration(Class(obo:DOID_0070619)) Declaration(Class(obo:DOID_0080000)) Declaration(Class(obo:DOID_0080001)) Declaration(Class(obo:DOID_0080005)) @@ -41783,12 +41784,13 @@ SubClassOf(obo:DOID_0060998 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060999 (mitochondrial trifunctional protein deficiency 2) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/12754706/") obo:IAO_0000115 obo:DOID_0060999 "A lipid metabolism disorder that has_material_basis_in homozygous or compound heterozygous mutation in the HADHB gene the beta subunit of the mitochondrial trifunctional protein, on chromosome 2p23."@en) +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/12754706/") obo:IAO_0000115 obo:DOID_0060999 "A mitochondrial trifunctional protein deficiency that has_material_basis_in homozygous or compound heterozygous mutation in the HADHB gene the beta subunit of the mitochondrial trifunctional protein, on chromosome 2p23.3."@en) AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060999 "MIM:620300") +AnnotationAssertion(Annotation(dc:type obo:OMO_0003012) oboInOwl:hasExactSynonym obo:DOID_0060999 "MTPD2"@en) AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060999 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060999 "DOID:0060999") AnnotationAssertion(rdfs:label obo:DOID_0060999 "mitochondrial trifunctional protein deficiency 2"@en) -SubClassOf(obo:DOID_0060999 obo:DOID_3146) +SubClassOf(obo:DOID_0060999 obo:DOID_0111277) SubClassOf(obo:DOID_0060999 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) # Class: obo:DOID_0061001 (glycine encephalopathy 2) @@ -50174,6 +50176,17 @@ AnnotationAssertion(skos:exactMatch obo:DOID_0070618 "MIM:609322") SubClassOf(obo:DOID_0070618 obo:DOID_0070617) SubClassOf(obo:DOID_0070618 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000147)) +# Class: obo:DOID_0070619 (mitochondrial trifunctional protein deficiency 1) + +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/12754706/") obo:IAO_0000115 obo:DOID_0070619 "A mitochondrial trifunctional protein deficiency that has_material_basis_in homozygous or compound heterozygous mutation in the HADHA gene, the alpha subunit of the mitochondrial trifunctional protein, on chromosome 2p23.3."@en) +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0070619 "MIM:609015") +AnnotationAssertion(Annotation(dc:type obo:OMO_0003012) oboInOwl:hasExactSynonym obo:DOID_0070619 "MTPD1"@en) +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0070619 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0070619 "DOID:0070619") +AnnotationAssertion(rdfs:label obo:DOID_0070619 "mitochondrial trifunctional protein deficiency 1"@en) +AnnotationAssertion(skos:exactMatch obo:DOID_0070619 "MIM:609015") +SubClassOf(obo:DOID_0070619 obo:DOID_0111277) + # Class: obo:DOID_0080000 (muscular disease) AnnotationAssertion(Annotation(dc:type obo:ECO_0007644) Annotation(oboInOwl:hasDbXref "url:http://www.nlm.nih.gov/medlineplus/muscledisorders.html") obo:IAO_0000115 obo:DOID_0080000 "A musculoskeletal system disease that affects the muscles."@en) @@ -86182,12 +86195,12 @@ AnnotationAssertion(rdfs:label obo:DOID_0111276 "sensory ataxic neuropathy, dysa SubClassOf(obo:DOID_0111276 obo:DOID_700) SubClassOf(obo:DOID_0111276 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) -# Class: obo:DOID_0111277 (mitochondrial trifunctional protein deficiency 1) +# Class: obo:DOID_0111277 (mitochondrial trifunctional protein deficiency) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/12754706") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/12838198") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/7738175") obo:IAO_0000115 obo:DOID_0111277 "A lipid metabolism disorder characterized by abnormal fatty acid oxidation resulting a wide range of clinical manifestations from servere neonatal symptoms including cardiomyopathy, hypoglycemia, metabolic acidosis, skeletal myopathy and neuropathy, liver disease and death to a more mild phenotype including peripheral polyneuropathy, episodic rhabdomyolysis and pigmentary retinopathy that has_material_basis_in homozygous or compound heterozygous mutation in either of the subunits of the mitochondrial trifunctional protein; HADHA or HADHB on 2p23.3."@en) +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/12754706") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/12838198") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/7738175") obo:IAO_0000115 obo:DOID_0111277 "A lipid metabolism disorder characterized by abnormal fatty acid oxidation resulting a wide range of clinical manifestations from servere neonatal symptoms including cardiomyopathy, hypoglycemia, metabolic acidosis, skeletal myopathy and neuropathy, liver disease and death to a more mild phenotype including peripheral polyneuropathy, episodic rhabdomyolysis and pigmentary retinopathy."@en) AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0111277 "GARD:3684") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0111277 "MESH:C566945") -AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0111277 "MIM:609015") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0111277 "MIM:PS609015") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0111277 "NCI:C98991") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0111277 "ORDO:746") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0111277 "SNOMEDCT_US_2023_03_01:237999008") @@ -86199,7 +86212,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0111277 "disease_ontology" AnnotationAssertion(oboInOwl:id obo:DOID_0111277 "DOID:0111277") AnnotationAssertion(oboInOwl:inSubset obo:DOID_0111277 doid:DO_rare_slim) AnnotationAssertion(oboInOwl:inSubset obo:DOID_0111277 doid:NCIthesaurus) -AnnotationAssertion(rdfs:label obo:DOID_0111277 "mitochondrial trifunctional protein deficiency 1"@en) +AnnotationAssertion(rdfs:label obo:DOID_0111277 "mitochondrial trifunctional protein deficiency"@en) SubClassOf(obo:DOID_0111277 obo:DOID_3146) SubClassOf(obo:DOID_0111277 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) SubClassOf(obo:DOID_0111277 ObjectSomeValuesFrom(obo:RO_0002200 obo:HP_0000580))