From ee8664e700397f485e751b093b67626dcea454dd Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 7 Aug 2023 11:31:16 -0400 Subject: [PATCH 01/33] digenic diseases review --- src/ontology/doid-edit.owl | 111 +++++++++++++++++++++++++++++++++---- 1 file changed, 99 insertions(+), 12 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 8852a6203..c50ed5f6a 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -1888,6 +1888,14 @@ Declaration(Class(obo:DOID_0060902)) Declaration(Class(obo:DOID_0060903)) Declaration(Class(obo:DOID_0060904)) Declaration(Class(obo:DOID_0060911)) +Declaration(Class(obo:DOID_0060912)) +Declaration(Class(obo:DOID_0060913)) +Declaration(Class(obo:DOID_0060914)) +Declaration(Class(obo:DOID_0060915)) +Declaration(Class(obo:DOID_0060916)) +Declaration(Class(obo:DOID_0060917)) +Declaration(Class(obo:DOID_0060918)) +Declaration(Class(obo:DOID_0060919)) Declaration(Class(obo:DOID_0070000)) Declaration(Class(obo:DOID_0070001)) Declaration(Class(obo:DOID_0070002)) @@ -20347,7 +20355,7 @@ SubClassOf(obo:DOID_0050474 ObjectSomeValuesFrom(obo:RO_0002452 obo:SYMP_0000061 # Class: obo:DOID_0050475 (Weill-Marchesani syndrome) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007637) Annotation(dc:type obo:ECO_0007638) Annotation(oboInOwl:hasDbXref "url:http://en.wikipedia.org/wiki/Weill-Marchesani_syndrome") Annotation(oboInOwl:hasDbXref "url:http://ghr.nlm.nih.gov/condition/weill-marchesani-syndrome") obo:IAO_0000115 obo:DOID_0050475 "A syndrome characterized by short stature, bachycephaly and other facial abnormalities, brachydactyly, joint stiffness and distinctive ocular abnormalities.") +AnnotationAssertion(Annotation(dc:type obo:ECO_0007637) Annotation(dc:type obo:ECO_0007638) Annotation(oboInOwl:hasDbXref "url:http://en.wikipedia.org/wiki/Weill-Marchesani_syndrome") Annotation(oboInOwl:hasDbXref "url:http://ghr.nlm.nih.gov/condition/weill-marchesani-syndrome") obo:IAO_0000115 obo:DOID_0050475 "A syndrome characterized by short stature, brachycephaly and other facial abnormalities, brachydactyly, joint stiffness and distinctive ocular abnormalities.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050475 "GARD:4936") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050475 "MESH:D056846") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050475 "NCI:C85226") @@ -23717,10 +23725,12 @@ AnnotationAssertion(oboInOwl:created_by obo:DOID_0050715 "lschriml") AnnotationAssertion(oboInOwl:creation_date obo:DOID_0050715 "2012-05-23T03:26:25Z") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050715 "OMIM:277400") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050715 "Cobalamin C deficiency"@en) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050715 "MAHCC") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050715 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050715 "DOID:0050715") AnnotationAssertion(rdfs:label obo:DOID_0050715 "methylmalonic aciduria and homocystinuria type cblC") -SubClassOf(obo:DOID_0050715 obo:DOID_14749) +SubClassOf(obo:DOID_0050715 obo:DOID_0060915) +SubClassOf(obo:DOID_0050715 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0050716 (methylmalonic aciduria and homocystinuria type cblD) @@ -23729,10 +23739,11 @@ AnnotationAssertion(oboInOwl:created_by obo:DOID_0050716 "lschriml") AnnotationAssertion(oboInOwl:creation_date obo:DOID_0050716 "2012-05-23T03:26:25Z") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050716 "OMIM:277410") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050716 "Cobalamin D deficiency"@en) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050716 "MAHCD") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050716 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050716 "DOID:0050716") AnnotationAssertion(rdfs:label obo:DOID_0050716 "methylmalonic aciduria and homocystinuria type cblD") -SubClassOf(obo:DOID_0050716 obo:DOID_14749) +SubClassOf(obo:DOID_0050716 obo:DOID_0060915) # Class: obo:DOID_0050717 (methylmalonic aciduria and homocystinuria type cblF) @@ -23741,10 +23752,11 @@ AnnotationAssertion(oboInOwl:created_by obo:DOID_0050717 "lschriml") AnnotationAssertion(oboInOwl:creation_date obo:DOID_0050717 "2012-05-23T03:26:25Z") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050717 "OMIM:277380") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050717 "Cobalamin F deficiency"@en) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050717 "MAHCF") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050717 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050717 "DOID:0050717") AnnotationAssertion(rdfs:label obo:DOID_0050717 "methylmalonic aciduria and homocystinuria type cblF") -SubClassOf(obo:DOID_0050717 obo:DOID_14749) +SubClassOf(obo:DOID_0050717 obo:DOID_0060915) # Class: obo:DOID_0050718 (vitamin metabolic disorder) @@ -23934,7 +23946,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:DOID_0050732 "2012-07-17T01:42:35 AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050732 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050732 "DOID:0050732") AnnotationAssertion(rdfs:label obo:DOID_0050732 "methylmalonic aciduria and homocystinuria type cblE") -SubClassOf(obo:DOID_0050732 obo:DOID_14749) +SubClassOf(obo:DOID_0050732 obo:DOID_0060915) # Class: obo:DOID_0050733 (methylmalonic aciduria and homocystinuria type cblG) @@ -23944,7 +23956,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:DOID_0050733 "2012-07-17T01:42:35 AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050733 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050733 "DOID:0050733") AnnotationAssertion(rdfs:label obo:DOID_0050733 "methylmalonic aciduria and homocystinuria type cblG") -SubClassOf(obo:DOID_0050733 obo:DOID_14749) +SubClassOf(obo:DOID_0050733 obo:DOID_0060915) # Class: obo:DOID_0050734 (congenital intrinsic factor deficiency) @@ -36130,7 +36142,7 @@ SubClassOf(obo:DOID_0060585 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060586 (Noonan syndrome 8) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/24939608") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/25124994") obo:IAO_0000115 obo:DOID_0060586 "A Noonan syndrome that has_material_basis_in aused by heterozygous mutation in the RIT1 gene on chromosome 1q22.") +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/24939608") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/25124994") obo:IAO_0000115 obo:DOID_0060586 "A Noonan syndrome that has_material_basis_in caused by heterozygous mutation in the RIT1 gene on chromosome 1q22.") AnnotationAssertion(oboInOwl:hasAlternativeId obo:DOID_0060586 "DOID:0070108") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060586 "ICD10CM:Q87.1") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060586 "OMIM:615355") @@ -40307,6 +40319,81 @@ AnnotationAssertion(rdfs:label obo:DOID_0060911 "karyomegalic interstitial nephr SubClassOf(obo:DOID_0060911 obo:DOID_1063) SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) +# Class: obo:DOID_0060912 (craniosynostosis 7) + +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A synostosis that is characterized by a primary abnormality of skull growth involving premature fusion of the cranial sutures such that the growth velocity of the skull often cannot match that of the developing brain. This produces skull deformity and, in some cases, raises intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability + +Susceptibility to craniosynostosis-7 (CRS7) is conferred by heterozygous mutation in the SMAD6 gene (602931) on chromosome 15q22. Variation in SMAD6 is weakly penetrant except in the presence of a modifier, the risk allele of a common variant near the BMP2 gene (112261) on chromosome 20p12.") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") +AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) +SubClassOf(obo:DOID_0060912 obo:DOID_2340) +SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) + +# Class: obo:DOID_0060913 (Usher syndrome type IIC) + +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "OMIM:605472") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060913 "USH2C") +AnnotationAssertion(rdfs:label obo:DOID_0060913 "Usher syndrome type IIC"@en) +SubClassOf(obo:DOID_0060913 obo:DOID_0050439) +SubClassOf(obo:DOID_0060913 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) + +# Class: obo:DOID_0060914 (Proteasome-associated autoinflammatory syndrome 1) + +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "This autosomal recessive systemic autoinflammatory disorder is characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation. More variable features include recurrent fever, severe joint contractures, muscle weakness and atrophy, hepatosplenomegaly, basal ganglia calcifications, and microcytic anemia") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") +AnnotationAssertion(rdfs:label obo:DOID_0060914 "Proteasome-associated autoinflammatory syndrome 1"@en) +SubClassOf(obo:DOID_0060914 obo:DOID_0050737) +SubClassOf(obo:DOID_0060914 obo:DOID_0060919) +SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) + +# Class: obo:DOID_0060915 (methylmalonic aciduria and homocystinuria) + +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060915 "A rare inborn error of vitamin B12 (cobalamin) metabolism characterized by megaloblastic anemia, lethargy, failure to thrive, developmental delay, intellectual deficit and seizures. There are four complementation classes of cobalamin defects (cblC, cblD, cblF and cblJ) that are responsible for methylmalonic acidemia - homocystinuria (methylmalonic acidemia - homocystinuria cblC, cblD cblF and cblJ). + +https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=26") +AnnotationAssertion(rdfs:label obo:DOID_0060915 "methylmalonic aciduria and homocystinuria"@en) +SubClassOf(obo:DOID_0060915 obo:DOID_14749) + +# Class: obo:DOID_0060916 (Proteasome-associated autoinflammatory syndrome 3) + +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome-3 is an autosomal recessive syndrome with onset in early infancy. Affected individuals present with nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy, and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression patterns. Additional features are highly variable, but may include joint contractures, hepatosplenomegaly, anemia, thrombocytopenia, recurrent infections, autoantibodies, and hypergammaglobulinemia. Some patients may have intracranial calcifications + +https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=26524591") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060916 "OMIM:617591") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") +AnnotationAssertion(rdfs:label obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome 3"@en) +SubClassOf(obo:DOID_0060916 obo:DOID_0050737) +SubClassOf(obo:DOID_0060916 obo:DOID_0060919) +SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) + +# Class: obo:DOID_0060917 (facioscapulohumeral muscular dystrophy 3) + +AnnotationAssertion(dc:description obo:DOID_0060917 "Facioscapulohumeral muscular dystrophy-3 (FSHD3) is a digenic muscle disorder characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs. Muscle involvement is usually asymmetric, and other muscle groups may become involved with progression of the disease") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "facioscapulohumeral muscular dystrophy type 3") +AnnotationAssertion(rdfs:label obo:DOID_0060917 "facioscapulohumeral muscular dystrophy 3"@en) +SubClassOf(obo:DOID_0060917 obo:DOID_11727) +SubClassOf(obo:DOID_0060917 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) + +# Class: obo:DOID_0060918 (facioscapulohumeral muscular dystrophy 4) + +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "Facioscapulohumeral muscular dystrophy (FSHD) is a skeletal muscle disorder characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles. With disease progression, other muscles also may become affected. There is significant clinical variability and incomplete penetrance + +https://pubmed.ncbi.nlm.nih.gov/27153398/") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "OMIM:619478") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "FSHD4") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "facioscapulohumeral muscular dystrophy type 4") +AnnotationAssertion(rdfs:label obo:DOID_0060918 "facioscapulohumeral muscular dystrophy 4"@en) +SubClassOf(obo:DOID_0060918 obo:DOID_11727) + +# Class: obo:DOID_0060919 (autoinflammatory disease) + +AnnotationAssertion(rdfs:label obo:DOID_0060919 "autoinflammatory disease"@en) +SubClassOf(obo:DOID_0060919 obo:DOID_0090061) + # Class: obo:DOID_0070000 (3-methylglutaconic aciduria type 8) AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/27208207") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/27696117") obo:IAO_0000115 obo:DOID_0070000 "A 3-methylglutaconic aciduria that has_material_basis_in homozygous mutation in the HTRA2 gene on chromosome 2p13.") @@ -53427,7 +53514,7 @@ SubClassOf(obo:DOID_0080626 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0080627 (alopecia-mental retardation syndrome) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/17451405") obo:IAO_0000115 obo:DOID_0080627 "A syndrome that is characterized by loss of hair on the scalp, absence of eyebrows, eyelashes, and axillary and pubic hair, and mild to severe mental retardation.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/17451405") obo:IAO_0000115 obo:DOID_0080627 "A syndrome that is characterized by loss of hair on the scalp, absence of hair in eyebrows, eyelashes, axillas and mild to severe mental retardation.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080627 "GARD:612") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080627 "OMIM:PS203650") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080627 "ORDO:2850") @@ -56594,8 +56681,8 @@ SubClassOf(obo:DOID_0080924 obo:DOID_0080918) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/books/NBK1419/") obo:IAO_0000115 obo:DOID_0080925 "A steroid inherited metabolic disorder that is characterized by combined deficiency of P450C17 and P450C21 and accumulation of steroid metabolites and that has_material_basis_in homozygous or compound heterozygous mutations in the POR gene, which encodes cytochrome p450 oxidoreductase, on chromosome 7q11.2.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "GARD:12664") -AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "NCI:131302") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "OMIM:613571") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "NCI:C131302") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0080925 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0080925 "DOID:0080925") AnnotationAssertion(oboInOwl:inSubset obo:DOID_0080925 doid:DO_rare_slim) @@ -89020,7 +89107,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0111814 "disease_ontology" AnnotationAssertion(oboInOwl:id obo:DOID_0111814 "DOID:0111814") AnnotationAssertion(oboInOwl:inSubset obo:DOID_0111814 doid:DO_rare_slim) AnnotationAssertion(rdfs:label obo:DOID_0111814 "methylmalonic acidemia and homocysteinemia cblX type") -SubClassOf(obo:DOID_0111814 obo:DOID_14749) +SubClassOf(obo:DOID_0111814 obo:DOID_0060915) SubClassOf(obo:DOID_0111814 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000149)) # Class: obo:DOID_0111815 (low molecular weight proteinuria with hypercalciuric nephrocalcinosis) @@ -132799,7 +132886,7 @@ SubClassOf(obo:DOID_1686 obo:DOID_5614) # Class: obo:DOID_1687 (neovascular glaucoma) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://journalretinavitreous.biomedcentral.com/articles/10.1186/s40942-016-0051-x") obo:IAO_0000115 obo:DOID_1687 "A glaucoma characterized by narrowing of the anterior chamber angle secondary to neovascularization along the iris and iridocorneal angle such that the aqueous fluid outflow is blocked and intraocular pressure becomes inappropriately elevated leading to optic nerve damage and visual field loss. Neovascular glaucoma has_symptom progressive peripheral vision loss, decreased vision, and pain, redness, and headache in acute cases. Neovascular glaucoma can be related to abnormal angiogenesis with ischemic retinal diseases, inflammation, diabetes mellitus, intraocular malignancy, and autoinmmune diseases.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://journalretinavitreous.biomedcentral.com/articles/10.1186/s40942-016-0051-x") obo:IAO_0000115 obo:DOID_1687 "A glaucoma characterized by narrowing of the anterior chamber angle secondary to neovascularization along the iris and iridocorneal angle such that the aqueous fluid outflow is blocked and intraocular pressure becomes inappropriately elevated leading to optic nerve damage and visual field loss. Neovascular glaucoma has_symptom progressive peripheral vision loss, decreased vision, and pain, redness, and headache in acute cases. Neovascular glaucoma can be related to abnormal angiogenesis with ischemic retinal diseases, inflammation, diabetes mellitus, intraocular malignancy, and autoimmune diseases.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_1687 "MESH:D015355") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_1687 "SNOMEDCT_US_2022_09_01:193564003") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_1687 "UMLS_CUI:C0017609") @@ -189120,7 +189207,7 @@ SubClassOf(obo:DOID_8178 obo:DOID_4995) # Class: obo:DOID_8179 (cervical atypical polypoid adenomyoma) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/23805464") obo:IAO_0000115 obo:DOID_8179 "A cervical adenomyoma that is aumor of endometrium, lower uterine segment and endocervix and is characterized by atypical complex glands with squamous metaplasia mixed with myofibromatous stroma.") +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/23805464") obo:IAO_0000115 obo:DOID_8179 "A cervical adenomyoma that is tumor of endometrium, lower uterine segment and endocervix and is characterized by atypical complex glands with squamous metaplasia mixed with myofibromatous stroma.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_8179 "NCI:C40234") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_8179 "UMLS_CUI:C1516409") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_8179 "disease_ontology") From c2fd8ee6f147d88b395dd0d0aa31c57f7633bd7c Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 7 Aug 2023 15:07:34 -0400 Subject: [PATCH 02/33] Update doid-edit.owl --- src/ontology/doid-edit.owl | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index c50ed5f6a..cfa8d23a5 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40326,6 +40326,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A synostosis that is chara Susceptibility to craniosynostosis-7 (CRS7) is conferred by heterozygous mutation in the SMAD6 gene (602931) on chromosome 15q22. Variation in SMAD6 is weakly penetrant except in the presence of a modifier, the risk allele of a common variant near the BMP2 gene (112261) on chromosome 20p12.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "DOID:0060912") AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) SubClassOf(obo:DOID_0060912 obo:DOID_2340) SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) @@ -40334,6 +40335,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "OMIM:605472") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060913 "USH2C") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060913 "DOID:0060913") AnnotationAssertion(rdfs:label obo:DOID_0060913 "Usher syndrome type IIC"@en) SubClassOf(obo:DOID_0060913 obo:DOID_0050439) SubClassOf(obo:DOID_0060913 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) @@ -40343,6 +40345,7 @@ SubClassOf(obo:DOID_0060913 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "This autosomal recessive systemic autoinflammatory disorder is characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation. More variable features include recurrent fever, severe joint contractures, muscle weakness and atrophy, hepatosplenomegaly, basal ganglia calcifications, and microcytic anemia") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "DOID:0060914") AnnotationAssertion(rdfs:label obo:DOID_0060914 "Proteasome-associated autoinflammatory syndrome 1"@en) SubClassOf(obo:DOID_0060914 obo:DOID_0050737) SubClassOf(obo:DOID_0060914 obo:DOID_0060919) @@ -40353,6 +40356,7 @@ SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060915 "A rare inborn error of vitamin B12 (cobalamin) metabolism characterized by megaloblastic anemia, lethargy, failure to thrive, developmental delay, intellectual deficit and seizures. There are four complementation classes of cobalamin defects (cblC, cblD, cblF and cblJ) that are responsible for methylmalonic acidemia - homocystinuria (methylmalonic acidemia - homocystinuria cblC, cblD cblF and cblJ). https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=26") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060915 "DOID:0060915") AnnotationAssertion(rdfs:label obo:DOID_0060915 "methylmalonic aciduria and homocystinuria"@en) SubClassOf(obo:DOID_0060915 obo:DOID_14749) @@ -40363,6 +40367,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "Proteasome-associated auto https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=26524591") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060916 "OMIM:617591") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "DOID:0060916") AnnotationAssertion(rdfs:label obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome 3"@en) SubClassOf(obo:DOID_0060916 obo:DOID_0050737) SubClassOf(obo:DOID_0060916 obo:DOID_0060919) @@ -40374,6 +40379,7 @@ AnnotationAssertion(dc:description obo:DOID_0060917 "Facioscapulohumeral muscula AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "facioscapulohumeral muscular dystrophy type 3") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060917 "DOID:0060917") AnnotationAssertion(rdfs:label obo:DOID_0060917 "facioscapulohumeral muscular dystrophy 3"@en) SubClassOf(obo:DOID_0060917 obo:DOID_11727) SubClassOf(obo:DOID_0060917 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) @@ -40386,11 +40392,13 @@ https://pubmed.ncbi.nlm.nih.gov/27153398/") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "OMIM:619478") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "FSHD4") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "facioscapulohumeral muscular dystrophy type 4") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060918 "DOID:0060918") AnnotationAssertion(rdfs:label obo:DOID_0060918 "facioscapulohumeral muscular dystrophy 4"@en) SubClassOf(obo:DOID_0060918 obo:DOID_11727) # Class: obo:DOID_0060919 (autoinflammatory disease) +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060919 "DOID:0060919") AnnotationAssertion(rdfs:label obo:DOID_0060919 "autoinflammatory disease"@en) SubClassOf(obo:DOID_0060919 obo:DOID_0090061) From 271c6d2a294b080074699dc1d336ef349e9c9e81 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 7 Aug 2023 15:30:24 -0400 Subject: [PATCH 03/33] missing_obo_namespace correction --- src/ontology/doid-edit.owl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index cfa8d23a5..2603da638 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40326,7 +40326,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A synostosis that is chara Susceptibility to craniosynostosis-7 (CRS7) is conferred by heterozygous mutation in the SMAD6 gene (602931) on chromosome 15q22. Variation in SMAD6 is weakly penetrant except in the presence of a modifier, the risk allele of a common variant near the BMP2 gene (112261) on chromosome 20p12.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "DOID:0060912") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060912 "DOID:0060912") AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) SubClassOf(obo:DOID_0060912 obo:DOID_2340) SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) From 15cfae0274965deb35eb5a137054cbc1a1270b23 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 7 Aug 2023 16:19:36 -0400 Subject: [PATCH 04/33] Make test digenic disease corrections --- src/ontology/doid-edit.owl | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 2603da638..67fb3315d 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40334,19 +40334,22 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060913 (Usher syndrome type IIC) +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060913 "A Usher syndrome characterized by by a homozygous or compound heterozygous mutation in the ADGRV1 gene (602851) on chromosome 5q14. It is also caused by biallelic digenic mutation in the ADGRV1 and PDZD7 (612971) genes.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "OMIM:605472") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060913 "USH2C") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060913 "DOID:0060913") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060913 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060913 "DOID:0060913") AnnotationAssertion(rdfs:label obo:DOID_0060913 "Usher syndrome type IIC"@en) SubClassOf(obo:DOID_0060913 obo:DOID_0050439) SubClassOf(obo:DOID_0060913 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0060914 (Proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "This autosomal recessive systemic autoinflammatory disorder is characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation. More variable features include recurrent fever, severe joint contractures, muscle weakness and atrophy, hepatosplenomegaly, basal ganglia calcifications, and microcytic anemia") +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "This autosomal recessive systemic autoinflammatory disorder is characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation. More variable features include recurrent fever, severe joint contractures, muscle weakness and atrophy, hepatosplenomegaly, basal ganglia calcifications, and microcytic anemia.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "DOID:0060914") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060914 "DOID:0060914") AnnotationAssertion(rdfs:label obo:DOID_0060914 "Proteasome-associated autoinflammatory syndrome 1"@en) SubClassOf(obo:DOID_0060914 obo:DOID_0050737) SubClassOf(obo:DOID_0060914 obo:DOID_0060919) @@ -40363,12 +40366,13 @@ SubClassOf(obo:DOID_0060915 obo:DOID_14749) # Class: obo:DOID_0060916 (Proteasome-associated autoinflammatory syndrome 3) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome-3 is an autosomal recessive syndrome with onset in early infancy. Affected individuals present with nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy, and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression patterns. Additional features are highly variable, but may include joint contractures, hepatosplenomegaly, anemia, thrombocytopenia, recurrent infections, autoantibodies, and hypergammaglobulinemia. Some patients may have intracranial calcifications +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome-3 is an autosomal recessive syndrome with onset in early infancy. Affected individuals present with nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy, and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression patterns. Additional features are highly variable, but may include joint contractures, hepatosplenomegaly, anemia, thrombocytopenia, recurrent infections, autoantibodies, and hypergammaglobulinemia. Some patients may have intracranial calcifications. https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=26524591") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060916 "OMIM:617591") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "DOID:0060916") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060916 "DOID:0060916") AnnotationAssertion(rdfs:label obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome 3"@en) SubClassOf(obo:DOID_0060916 obo:DOID_0050737) SubClassOf(obo:DOID_0060916 obo:DOID_0060919) @@ -40380,26 +40384,29 @@ AnnotationAssertion(dc:description obo:DOID_0060917 "Facioscapulohumeral muscula AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "facioscapulohumeral muscular dystrophy type 3") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060917 "DOID:0060917") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060917 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060917 "DOID:0060917") AnnotationAssertion(rdfs:label obo:DOID_0060917 "facioscapulohumeral muscular dystrophy 3"@en) SubClassOf(obo:DOID_0060917 obo:DOID_11727) SubClassOf(obo:DOID_0060917 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0060918 (facioscapulohumeral muscular dystrophy 4) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "Facioscapulohumeral muscular dystrophy (FSHD) is a skeletal muscle disorder characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles. With disease progression, other muscles also may become affected. There is significant clinical variability and incomplete penetrance +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "Facioscapulohumeral muscular dystrophy (FSHD) is a skeletal muscle disorder characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles. With disease progression, other muscles also may become affected. There is significant clinical variability and incomplete penetrance. https://pubmed.ncbi.nlm.nih.gov/27153398/") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "OMIM:619478") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "FSHD4") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "facioscapulohumeral muscular dystrophy type 4") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060918 "DOID:0060918") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060918 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060918 "DOID:0060918") AnnotationAssertion(rdfs:label obo:DOID_0060918 "facioscapulohumeral muscular dystrophy 4"@en) SubClassOf(obo:DOID_0060918 obo:DOID_11727) # Class: obo:DOID_0060919 (autoinflammatory disease) -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060919 "DOID:0060919") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060919 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060919 "DOID:0060919") AnnotationAssertion(rdfs:label obo:DOID_0060919 "autoinflammatory disease"@en) SubClassOf(obo:DOID_0060919 obo:DOID_0090061) From b7e24871c10a04104053fc24e9ddac97c400bac6 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Tue, 8 Aug 2023 15:08:57 -0400 Subject: [PATCH 05/33] Update of definition to DOID:0080627 --- src/ontology/doid-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 67fb3315d..5698db8a9 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -53530,7 +53530,7 @@ SubClassOf(obo:DOID_0080626 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0080627 (alopecia-mental retardation syndrome) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/17451405") obo:IAO_0000115 obo:DOID_0080627 "A syndrome that is characterized by loss of hair on the scalp, absence of hair in eyebrows, eyelashes, axillas and mild to severe mental retardation.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/17451405") obo:IAO_0000115 obo:DOID_0080627 "A syndrome that is characterized by loss of hair on the scalp, eyebrows, eyelashes, axillas and pubic hair, in addition to mild to severe intellectual disability.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080627 "GARD:612") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080627 "OMIM:PS203650") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080627 "ORDO:2850") From 2d6c44fea069193bce15fe77e6d5102e46ab5cf4 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Tue, 8 Aug 2023 15:19:20 -0400 Subject: [PATCH 06/33] Removed unnecessary parent term of MAHC --- src/ontology/doid-edit.owl | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 5698db8a9..6b1248704 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -1891,7 +1891,6 @@ Declaration(Class(obo:DOID_0060911)) Declaration(Class(obo:DOID_0060912)) Declaration(Class(obo:DOID_0060913)) Declaration(Class(obo:DOID_0060914)) -Declaration(Class(obo:DOID_0060915)) Declaration(Class(obo:DOID_0060916)) Declaration(Class(obo:DOID_0060917)) Declaration(Class(obo:DOID_0060918)) @@ -23729,7 +23728,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050715 "MAHCC") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050715 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050715 "DOID:0050715") AnnotationAssertion(rdfs:label obo:DOID_0050715 "methylmalonic aciduria and homocystinuria type cblC") -SubClassOf(obo:DOID_0050715 obo:DOID_0060915) +SubClassOf(obo:DOID_0050715 obo:DOID_14749) SubClassOf(obo:DOID_0050715 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0050716 (methylmalonic aciduria and homocystinuria type cblD) @@ -23743,7 +23742,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050716 "MAHCD") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050716 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050716 "DOID:0050716") AnnotationAssertion(rdfs:label obo:DOID_0050716 "methylmalonic aciduria and homocystinuria type cblD") -SubClassOf(obo:DOID_0050716 obo:DOID_0060915) +SubClassOf(obo:DOID_0050716 obo:DOID_14749) # Class: obo:DOID_0050717 (methylmalonic aciduria and homocystinuria type cblF) @@ -23756,7 +23755,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050717 "MAHCF") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050717 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050717 "DOID:0050717") AnnotationAssertion(rdfs:label obo:DOID_0050717 "methylmalonic aciduria and homocystinuria type cblF") -SubClassOf(obo:DOID_0050717 obo:DOID_0060915) +SubClassOf(obo:DOID_0050717 obo:DOID_14749) # Class: obo:DOID_0050718 (vitamin metabolic disorder) @@ -23946,7 +23945,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:DOID_0050732 "2012-07-17T01:42:35 AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050732 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050732 "DOID:0050732") AnnotationAssertion(rdfs:label obo:DOID_0050732 "methylmalonic aciduria and homocystinuria type cblE") -SubClassOf(obo:DOID_0050732 obo:DOID_0060915) +SubClassOf(obo:DOID_0050732 obo:DOID_14749) # Class: obo:DOID_0050733 (methylmalonic aciduria and homocystinuria type cblG) @@ -23956,7 +23955,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:DOID_0050733 "2012-07-17T01:42:35 AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050733 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050733 "DOID:0050733") AnnotationAssertion(rdfs:label obo:DOID_0050733 "methylmalonic aciduria and homocystinuria type cblG") -SubClassOf(obo:DOID_0050733 obo:DOID_0060915) +SubClassOf(obo:DOID_0050733 obo:DOID_14749) # Class: obo:DOID_0050734 (congenital intrinsic factor deficiency) @@ -40355,15 +40354,6 @@ SubClassOf(obo:DOID_0060914 obo:DOID_0050737) SubClassOf(obo:DOID_0060914 obo:DOID_0060919) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) -# Class: obo:DOID_0060915 (methylmalonic aciduria and homocystinuria) - -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060915 "A rare inborn error of vitamin B12 (cobalamin) metabolism characterized by megaloblastic anemia, lethargy, failure to thrive, developmental delay, intellectual deficit and seizures. There are four complementation classes of cobalamin defects (cblC, cblD, cblF and cblJ) that are responsible for methylmalonic acidemia - homocystinuria (methylmalonic acidemia - homocystinuria cblC, cblD cblF and cblJ). - -https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=26") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060915 "DOID:0060915") -AnnotationAssertion(rdfs:label obo:DOID_0060915 "methylmalonic aciduria and homocystinuria"@en) -SubClassOf(obo:DOID_0060915 obo:DOID_14749) - # Class: obo:DOID_0060916 (Proteasome-associated autoinflammatory syndrome 3) AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome-3 is an autosomal recessive syndrome with onset in early infancy. Affected individuals present with nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy, and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression patterns. Additional features are highly variable, but may include joint contractures, hepatosplenomegaly, anemia, thrombocytopenia, recurrent infections, autoantibodies, and hypergammaglobulinemia. Some patients may have intracranial calcifications. @@ -89123,7 +89113,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0111814 "disease_ontology" AnnotationAssertion(oboInOwl:id obo:DOID_0111814 "DOID:0111814") AnnotationAssertion(oboInOwl:inSubset obo:DOID_0111814 doid:DO_rare_slim) AnnotationAssertion(rdfs:label obo:DOID_0111814 "methylmalonic acidemia and homocysteinemia cblX type") -SubClassOf(obo:DOID_0111814 obo:DOID_0060915) +SubClassOf(obo:DOID_0111814 obo:DOID_14749) SubClassOf(obo:DOID_0111814 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000149)) # Class: obo:DOID_0111815 (low molecular weight proteinuria with hypercalciuric nephrocalcinosis) From 43173f92b55a26195ef59affa4fc3453bab20ccc Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 14 Aug 2023 17:12:45 -0400 Subject: [PATCH 07/33] Refinement of craniosynostosis 7 definition Refer to #1232 for more details --- src/ontology/doid-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 6b1248704..6568c2092 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40320,9 +40320,9 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A synostosis that is characterized by a primary abnormality of skull growth involving premature fusion of the cranial sutures such that the growth velocity of the skull often cannot match that of the developing brain. This produces skull deformity and, in some cases, raises intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis condition characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. -Susceptibility to craniosynostosis-7 (CRS7) is conferred by heterozygous mutation in the SMAD6 gene (602931) on chromosome 15q22. Variation in SMAD6 is weakly penetrant except in the presence of a modifier, the risk allele of a common variant near the BMP2 gene (112261) on chromosome 20p12.") +The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") From fbd2d30a8e4d8a15b91f1b68146be4c3edf40c4b Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Tue, 15 Aug 2023 16:33:36 -0400 Subject: [PATCH 08/33] Update Usher syndrome type 2C --- src/ontology/doid-edit.owl | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 6568c2092..d6268796d 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40331,17 +40331,6 @@ AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) SubClassOf(obo:DOID_0060912 obo:DOID_2340) SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) -# Class: obo:DOID_0060913 (Usher syndrome type IIC) - -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060913 "A Usher syndrome characterized by by a homozygous or compound heterozygous mutation in the ADGRV1 gene (602851) on chromosome 5q14. It is also caused by biallelic digenic mutation in the ADGRV1 and PDZD7 (612971) genes.") -AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "OMIM:605472") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060913 "USH2C") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060913 "disease_ontology") -AnnotationAssertion(oboInOwl:id obo:DOID_0060913 "DOID:0060913") -AnnotationAssertion(rdfs:label obo:DOID_0060913 "Usher syndrome type IIC"@en) -SubClassOf(obo:DOID_0060913 obo:DOID_0050439) -SubClassOf(obo:DOID_0060913 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) - # Class: obo:DOID_0060914 (Proteasome-associated autoinflammatory syndrome 1) AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "This autosomal recessive systemic autoinflammatory disorder is characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation. More variable features include recurrent fever, severe joint contractures, muscle weakness and atrophy, hepatosplenomegaly, basal ganglia calcifications, and microcytic anemia.") From 82c51dfb38539b34ebf0cb40def8f602a79039d3 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Tue, 15 Aug 2023 16:35:11 -0400 Subject: [PATCH 09/33] Update doid-edit.owl --- src/ontology/doid-edit.owl | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index d6268796d..ef0f6e379 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -1889,7 +1889,6 @@ Declaration(Class(obo:DOID_0060903)) Declaration(Class(obo:DOID_0060904)) Declaration(Class(obo:DOID_0060911)) Declaration(Class(obo:DOID_0060912)) -Declaration(Class(obo:DOID_0060913)) Declaration(Class(obo:DOID_0060914)) Declaration(Class(obo:DOID_0060916)) Declaration(Class(obo:DOID_0060917)) @@ -13942,7 +13941,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://purl.obolibrary.or AnnotationAssertion(rdfs:isDefinedBy obo:IAO_0000119 obo:iao.owl) AnnotationAssertion(rdfs:label obo:IAO_0000119 "definition source") -# Annotation Property: obo:IAO_0000700 (has ontology root term) +# Annotation Property: obo:IAO_0000700 (has_ontology_root_term) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://purl.obolibrary.org/obo/IAO_0000700") obo:IAO_0000115 obo:IAO_0000700 "Has ontology root term.") AnnotationAssertion(rdfs:label obo:IAO_0000700 "has_ontology_root_term") @@ -14128,7 +14127,7 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://www.geneontology.org/formats/oboInOwl#hasDbXref") obo:IAO_0000115 oboInOwl:hasDbXref "Reference database or publication source.") AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://www.geneontology.org/formats/oboInOwl#hasExactSynonym") obo:IAO_0000115 oboInOwl:hasExactSynonym "Exact synonym.") AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") @@ -40387,7 +40386,7 @@ SubClassOf(obo:DOID_0060918 obo:DOID_11727) AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060919 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060919 "DOID:0060919") AnnotationAssertion(rdfs:label obo:DOID_0060919 "autoinflammatory disease"@en) -SubClassOf(obo:DOID_0060919 obo:DOID_0090061) +SubClassOf(obo:DOID_0060919 obo:DOID_2914) # Class: obo:DOID_0070000 (3-methylglutaconic aciduria type 8) @@ -56676,8 +56675,8 @@ SubClassOf(obo:DOID_0080924 obo:DOID_0080918) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/books/NBK1419/") obo:IAO_0000115 obo:DOID_0080925 "A steroid inherited metabolic disorder that is characterized by combined deficiency of P450C17 and P450C21 and accumulation of steroid metabolites and that has_material_basis_in homozygous or compound heterozygous mutations in the POR gene, which encodes cytochrome p450 oxidoreductase, on chromosome 7q11.2.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "GARD:12664") -AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "OMIM:613571") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "NCI:C131302") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0080925 "OMIM:613571") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0080925 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0080925 "DOID:0080925") AnnotationAssertion(oboInOwl:inSubset obo:DOID_0080925 doid:DO_rare_slim) @@ -74813,11 +74812,13 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0110839 "ICD10CM:H35.5") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0110839 "OMIM:605472") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0110839 "USH2C"@en) AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0110839 "Usher syndrome type IIC"@en) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0110839 "Usher syndrome IIC") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0110839 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0110839 "DOID:0110839") AnnotationAssertion(rdfs:label obo:DOID_0110839 "Usher syndrome type 2C") SubClassOf(obo:DOID_0110839 obo:DOID_0110827) SubClassOf(obo:DOID_0110839 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) +SubClassOf(obo:DOID_0110839 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0110840 (Usher syndrome type 2D) From 32dfcd56571c387b6b70717d8914d747063b04ea Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Tue, 15 Aug 2023 16:36:43 -0400 Subject: [PATCH 10/33] Adjustment of craniosynostosis 7 --- src/ontology/doid-edit.owl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index ef0f6e379..3983a6e58 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40319,9 +40319,7 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis condition characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. - -The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis condition characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") From c50333104ae9845515a080d1b1610884e0371548 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 18 Aug 2023 10:56:52 -0400 Subject: [PATCH 11/33] Incorporation of lowercase in proteasome-associated autoinflammatory syndrome 1 --- src/ontology/doid-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 3983a6e58..be632b205 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40328,14 +40328,14 @@ AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) SubClassOf(obo:DOID_0060912 obo:DOID_2340) SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) -# Class: obo:DOID_0060914 (Proteasome-associated autoinflammatory syndrome 1) +# Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "This autosomal recessive systemic autoinflammatory disorder is characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation. More variable features include recurrent fever, severe joint contractures, muscle weakness and atrophy, hepatosplenomegaly, basal ganglia calcifications, and microcytic anemia.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060914 "DOID:0060914") -AnnotationAssertion(rdfs:label obo:DOID_0060914 "Proteasome-associated autoinflammatory syndrome 1"@en) +AnnotationAssertion(rdfs:label obo:DOID_0060914 "proteasome-associated autoinflammatory syndrome 1"@en) SubClassOf(obo:DOID_0060914 obo:DOID_0050737) SubClassOf(obo:DOID_0060914 obo:DOID_0060919) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) From aeb9c4c4f08e1ee6cafaac3f43e99242a8364982 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 18 Aug 2023 11:06:29 -0400 Subject: [PATCH 12/33] Adjustment of proteasome-associated autoinflammatory syndrome 1's definition --- src/ontology/doid-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index be632b205..a6fad9dba 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40330,7 +40330,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "This autosomal recessive systemic autoinflammatory disorder is characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation. More variable features include recurrent fever, severe joint contractures, muscle weakness and atrophy, hepatosplenomegaly, basal ganglia calcifications, and microcytic anemia.") +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in digenic inheritance") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") From 794ea607a6d64b37dfc078276c85cc6b94abd0f5 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 18 Aug 2023 11:12:22 -0400 Subject: [PATCH 13/33] Definition and capitalization adjustment of proteasome-associated autoinflammatory syndrome 3 --- src/ontology/doid-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index a6fad9dba..6edf4457b 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40340,16 +40340,16 @@ SubClassOf(obo:DOID_0060914 obo:DOID_0050737) SubClassOf(obo:DOID_0060914 obo:DOID_0060919) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) -# Class: obo:DOID_0060916 (Proteasome-associated autoinflammatory syndrome 3) +# Class: obo:DOID_0060916 (proteasome-associated autoinflammatory syndrome 3) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome-3 is an autosomal recessive syndrome with onset in early infancy. Affected individuals present with nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy, and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression patterns. Additional features are highly variable, but may include joint contractures, hepatosplenomegaly, anemia, thrombocytopenia, recurrent infections, autoantibodies, and hypergammaglobulinemia. Some patients may have intracranial calcifications. +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "An autosomal recessive disorder characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in genetic inheritance. https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=26524591") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060916 "OMIM:617591") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060916 "DOID:0060916") -AnnotationAssertion(rdfs:label obo:DOID_0060916 "Proteasome-associated autoinflammatory syndrome 3"@en) +AnnotationAssertion(rdfs:label obo:DOID_0060916 "proteasome-associated autoinflammatory syndrome 3"@en) SubClassOf(obo:DOID_0060916 obo:DOID_0050737) SubClassOf(obo:DOID_0060916 obo:DOID_0060919) SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) From ce3c89425a3e3fb34811918c937a8bb5fb9a9131 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 18 Aug 2023 11:20:21 -0400 Subject: [PATCH 14/33] Adjustment of definition of facioscapulohumeral muscular dystrophy 3 --- src/ontology/doid-edit.owl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 6edf4457b..6f2b1aeee 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40356,7 +40356,9 @@ SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060917 (facioscapulohumeral muscular dystrophy 3) -AnnotationAssertion(dc:description obo:DOID_0060917 "Facioscapulohumeral muscular dystrophy-3 (FSHD3) is a digenic muscle disorder characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs. Muscle involvement is usually asymmetric, and other muscle groups may become involved with progression of the disease") +AnnotationAssertion(dc:description obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression. + +https://pubmed.ncbi.nlm.nih.gov/32467133/") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "facioscapulohumeral muscular dystrophy type 3") From 65ec088d0289d1a9f76d15495951a3354e12bd01 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 18 Aug 2023 11:25:10 -0400 Subject: [PATCH 15/33] Adjustment of definition of facioscapulohumeral muscular dystrophy 4 --- src/ontology/doid-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 6f2b1aeee..d332eacd1 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40370,7 +40370,7 @@ SubClassOf(obo:DOID_0060917 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060918 (facioscapulohumeral muscular dystrophy 4) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "Facioscapulohumeral muscular dystrophy (FSHD) is a skeletal muscle disorder characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles. With disease progression, other muscles also may become affected. There is significant clinical variability and incomplete penetrance. +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "A facioscapulohumeral muscular dystrophy characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles with disease progression that has_material_basis_in the combination of a heterozygous mutation in the DNMT3B gene on chromosome 20q11 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression. https://pubmed.ncbi.nlm.nih.gov/27153398/") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "OMIM:619478") From 7ee043c12f9cab96d6507a635b50365a177ad95e Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 18 Aug 2023 11:33:54 -0400 Subject: [PATCH 16/33] Adjustment of crossreference's position --- src/ontology/doid-edit.owl | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index d332eacd1..da2d5fa6c 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40356,10 +40356,9 @@ SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060917 (facioscapulohumeral muscular dystrophy 3) -AnnotationAssertion(dc:description obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression. - -https://pubmed.ncbi.nlm.nih.gov/32467133/") +AnnotationAssertion(dc:description obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "https://pubmed.ncbi.nlm.nih.gov/32467133/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "facioscapulohumeral muscular dystrophy type 3") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060917 "disease_ontology") @@ -40370,10 +40369,9 @@ SubClassOf(obo:DOID_0060917 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060918 (facioscapulohumeral muscular dystrophy 4) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "A facioscapulohumeral muscular dystrophy characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles with disease progression that has_material_basis_in the combination of a heterozygous mutation in the DNMT3B gene on chromosome 20q11 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression. - -https://pubmed.ncbi.nlm.nih.gov/27153398/") +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "A facioscapulohumeral muscular dystrophy characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles with disease progression that has_material_basis_in the combination of a heterozygous mutation in the DNMT3B gene on chromosome 20q11 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "OMIM:619478") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "https://pubmed.ncbi.nlm.nih.gov/27153398/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "FSHD4") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "facioscapulohumeral muscular dystrophy type 4") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060918 "disease_ontology") From 7fab34e26083ff3fa4f147d0ffeb809ff5855dad Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 18 Aug 2023 12:03:53 -0400 Subject: [PATCH 17/33] Definition category change of facioscapulohumeral muscular dystrophy 3 --- src/ontology/doid-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index da2d5fa6c..7af38a2ed 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40356,7 +40356,7 @@ SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060917 (facioscapulohumeral muscular dystrophy 3) -AnnotationAssertion(dc:description obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "https://pubmed.ncbi.nlm.nih.gov/32467133/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") From 98c0302100bacfda6e232982fe3af42d72eec0bb Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Thu, 24 Aug 2023 12:20:33 -0400 Subject: [PATCH 18/33] Adjustments of digenic disease definitions --- src/ontology/doid-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 7af38a2ed..e1044f9e7 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40319,7 +40319,7 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis condition characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/23438589/") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") @@ -40330,7 +40330,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in digenic inheritance") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in a heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 (176843) gene on chromosome 14q23 or in the PSMB4 (602177) on chromosome 1q21.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") @@ -74809,8 +74809,8 @@ AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasD AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0110839 "ICD10CM:H35.5") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0110839 "OMIM:605472") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0110839 "USH2C"@en) -AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0110839 "Usher syndrome type IIC"@en) AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0110839 "Usher syndrome IIC") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0110839 "Usher syndrome type IIC"@en) AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0110839 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0110839 "DOID:0110839") AnnotationAssertion(rdfs:label obo:DOID_0110839 "Usher syndrome type 2C") From 67480920647b2b7e75e8a0662679b519ca9ca4df Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Thu, 24 Aug 2023 15:42:51 -0400 Subject: [PATCH 19/33] update of digenic disease crossreferences --- src/ontology/doid-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index e1044f9e7..ac7c85f0f 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40319,7 +40319,7 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/23438589/") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/23438589/") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") @@ -40330,7 +40330,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in a heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 (176843) gene on chromosome 14q23 or in the PSMB4 (602177) on chromosome 1q21.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in a heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 (176843) gene on chromosome 14q23 or in the PSMB4 (602177) on chromosome 1q21.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") From b2594b01a2ff0a693bb55c8a81b46ac53b199866 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 25 Sep 2023 13:17:32 -0400 Subject: [PATCH 20/33] stashed digenic edits --- src/ontology/doid-edit.owl | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index ac7c85f0f..c8bed4e41 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40319,7 +40319,11 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) +<<<<<<< Updated upstream AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/23438589/") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") +======= +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by skull deformity and the inability of the skull's growth to keep up with the developing brain that has_material_basis_in a weakly penetrant heterozygous mutation in the SMAD6 gene on chromosome 15q22, typically with the risk allele of a common variant near the BMP2 gene on chromosome 20p12, resulting in potential intracranial pressure elevation.") +>>>>>>> Stashed changes AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") @@ -40330,21 +40334,23 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) +<<<<<<< Updated upstream AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in a heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 (176843) gene on chromosome 14q23 or in the PSMB4 (602177) on chromosome 1q21.") +======= +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 on chromosome 1q21.") +>>>>>>> Stashed changes AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060914 "DOID:0060914") AnnotationAssertion(rdfs:label obo:DOID_0060914 "proteasome-associated autoinflammatory syndrome 1"@en) -SubClassOf(obo:DOID_0060914 obo:DOID_0050737) SubClassOf(obo:DOID_0060914 obo:DOID_0060919) +SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0060916 (proteasome-associated autoinflammatory syndrome 3) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060916 "An autosomal recessive disorder characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in genetic inheritance. - -https://pubmed.ncbi.nlm.nih.gov/?cmd=link&linkname=pubmed_pubmed&from_uid=26524591") +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/26524591/") obo:IAO_0000115 obo:DOID_0060916 "An autosomal recessive disorder characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in genetic inheritance.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060916 "OMIM:617591") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "disease_ontology") @@ -170282,7 +170288,7 @@ SubClassOf(obo:DOID_5520 ObjectSomeValuesFrom(obo:RO_0001000 obo:CL_0000076)) # Class: obo:DOID_5521 (keratinizing squamous cell carcinoma) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007646) Annotation(oboInOwl:hasDbXref "url:http://books.google.com/books?id=TQju7e__pRIC&pg=PA1132&lpg=PA1132&dq#v=onepage&q&f=false") obo:IAO_0000115 obo:DOID_5521 "A squamous cell carcinoma that presents as single, isolated cells with bizzare cytoplasmic shapes, intense cytoplasmic eosinophilia, and intensely hyperchromatic, angular nuclei in a background of necrotic and keratinous debris.") +AnnotationAssertion(Annotation(dc:type obo:ECO_0007646) Annotation(oboInOwl:hasDbXref "url:http://books.google.com/books?id=TQju7e__pRIC&pg=PA1132&lpg=PA1132&dq#v=onepage&q&f=false") obo:IAO_0000115 obo:DOID_5521 "A squamous cell carcinoma that presents as single, isolated cells with bizarre cytoplasmic shapes, intense cytoplasmic eosinophilia, and intensely hyperchromatic, angular nuclei in a background of necrotic and keratinous debris.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_5521 "NCI:C4105") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_5521 "SNOMEDCT_US_2022_09_01:18048008") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_5521 "UMLS_CUI:C0334247") From c9902e6b8212d2f98e6bedb421e38bb7eea886c4 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 25 Sep 2023 13:25:12 -0400 Subject: [PATCH 21/33] stashed digenic edits --- src/ontology/doid-edit.owl | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index c8bed4e41..c0f83a1be 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40319,11 +40319,7 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) -<<<<<<< Updated upstream -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/23438589/") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by the premature fusion of cranial sutures leading to potential intracranial pressure elevation, skull deformity and inability of the skull's growth to keep up with the developing brain, potentially causing neurodevelopmental issues. The susceptibility has_material_basis_in a heterozygous mutation in the SMAD6 gene on chromosome 15q22. This genetic variation is typically weakly penetrant, unless a modifier is present – the risk allele of a common variant near the BMP2 gene on chromosome 20p12.") -======= AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by skull deformity and the inability of the skull's growth to keep up with the developing brain that has_material_basis_in a weakly penetrant heterozygous mutation in the SMAD6 gene on chromosome 15q22, typically with the risk allele of a common variant near the BMP2 gene on chromosome 20p12, resulting in potential intracranial pressure elevation.") ->>>>>>> Stashed changes AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") @@ -40334,11 +40330,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) -<<<<<<< Updated upstream -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in a heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 (176843) gene on chromosome 14q23 or in the PSMB4 (602177) on chromosome 1q21.") -======= AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 on chromosome 1q21.") ->>>>>>> Stashed changes AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") From f064006a8d0adf91e42054061ab69820f35fedb6 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Wed, 27 Sep 2023 14:21:58 -0400 Subject: [PATCH 22/33] Digenic definition fix In response to #1232 --- src/ontology/doid-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index c0f83a1be..7e4498f4a 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40330,7 +40330,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 on chromosome 1q21.") +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") From 80cd2dde64876d865ffeb9117b0d43cd2263fa28 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 29 Sep 2023 10:57:04 -0400 Subject: [PATCH 23/33] digenic disease definition update --- src/ontology/doid-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 7e4498f4a..005cced7e 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40330,7 +40330,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or has_material_basis_in heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") From b6d1311bd99812b2589cb65ead95e979b9ca6db9 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Tue, 17 Oct 2023 13:10:45 -0400 Subject: [PATCH 24/33] digenic definition adjustments --- src/ontology/doid-edit.owl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 005cced7e..0ad20c084 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40319,7 +40319,7 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by skull deformity and the inability of the skull's growth to keep up with the developing brain that has_material_basis_in a weakly penetrant heterozygous mutation in the SMAD6 gene on chromosome 15q22, typically with the risk allele of a common variant near the BMP2 gene on chromosome 20p12, resulting in potential intracranial pressure elevation.") +AnnotationAssertion(Annotation(obo:IAO_0000119 "url:https://www.nature.com/articles/ng.2557") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by skull deformity and the inability of the skull's growth to keep up with the developing brain that has_material_basis_in a weakly penetrant heterozygous mutation in the SMAD6 gene on chromosome 15q22, typically with the risk allele of a common variant near the BMP2 gene on chromosome 20p12, resulting in potential intracranial pressure elevation.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") @@ -40342,7 +40342,7 @@ SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060916 (proteasome-associated autoinflammatory syndrome 3) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/26524591/") obo:IAO_0000115 obo:DOID_0060916 "An autosomal recessive disorder characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in genetic inheritance.") +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/26524591/") obo:IAO_0000115 obo:DOID_0060916 "An autosomal recessive disorder characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in a homozygous mutation in the PSMB4 gene on chromosome 1q21 or a heterozygous mutation in the PSMB4 gene and a heterozygous mutation in the PSMB9 gene on chromosome 6p21.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060916 "OMIM:617591") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "disease_ontology") @@ -40354,7 +40354,7 @@ SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060917 (facioscapulohumeral muscular dystrophy 3) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") +AnnotationAssertion(Annotation(obo:IAO_0000119 "url:https://pubmed.ncbi.nlm.nih.gov/32467133/") obo:IAO_0000115 obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "https://pubmed.ncbi.nlm.nih.gov/32467133/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") @@ -40367,7 +40367,7 @@ SubClassOf(obo:DOID_0060917 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060918 (facioscapulohumeral muscular dystrophy 4) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060918 "A facioscapulohumeral muscular dystrophy characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles with disease progression that has_material_basis_in the combination of a heterozygous mutation in the DNMT3B gene on chromosome 20q11 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") +AnnotationAssertion(Annotation(obo:IAO_0000119 "url:https://pubmed.ncbi.nlm.nih.gov/27153398/") obo:IAO_0000115 obo:DOID_0060918 "A facioscapulohumeral muscular dystrophy characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles with disease progression that has_material_basis_in the combination of a heterozygous mutation in the DNMT3B gene on chromosome 20q11 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "OMIM:619478") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "https://pubmed.ncbi.nlm.nih.gov/27153398/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "FSHD4") From 37d80f2c25d5aa66be36e7efdf16a1351f26fb1e Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Tue, 17 Oct 2023 15:36:59 -0400 Subject: [PATCH 25/33] definition crossreference updates --- src/ontology/doid-edit.owl | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 0ad20c084..f8122d414 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40319,7 +40319,7 @@ SubClassOf(obo:DOID_0060911 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000014 # Class: obo:DOID_0060912 (craniosynostosis 7) -AnnotationAssertion(Annotation(obo:IAO_0000119 "url:https://www.nature.com/articles/ng.2557") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by skull deformity and the inability of the skull's growth to keep up with the developing brain that has_material_basis_in a weakly penetrant heterozygous mutation in the SMAD6 gene on chromosome 15q22, typically with the risk allele of a common variant near the BMP2 gene on chromosome 20p12, resulting in potential intracranial pressure elevation.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/23438589/") obo:IAO_0000115 obo:DOID_0060912 "A craniosynostosis characterized by skull deformity and the inability of the skull's growth to keep up with the developing brain that has_material_basis_in a weakly penetrant heterozygous mutation in the SMAD6 gene on chromosome 15q22, typically with the risk allele of a common variant near the BMP2 gene on chromosome 20p12, resulting in potential intracranial pressure elevation.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060912 "OMIM:617439") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060912 "CRS7") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060912 "disease_ontology") @@ -40330,7 +40330,7 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") @@ -40354,7 +40354,7 @@ SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060917 (facioscapulohumeral muscular dystrophy 3) -AnnotationAssertion(Annotation(obo:IAO_0000119 "url:https://pubmed.ncbi.nlm.nih.gov/32467133/") obo:IAO_0000115 obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/32467133/") obo:IAO_0000115 obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "https://pubmed.ncbi.nlm.nih.gov/32467133/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") @@ -40367,9 +40367,8 @@ SubClassOf(obo:DOID_0060917 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 # Class: obo:DOID_0060918 (facioscapulohumeral muscular dystrophy 4) -AnnotationAssertion(Annotation(obo:IAO_0000119 "url:https://pubmed.ncbi.nlm.nih.gov/27153398/") obo:IAO_0000115 obo:DOID_0060918 "A facioscapulohumeral muscular dystrophy characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles with disease progression that has_material_basis_in the combination of a heterozygous mutation in the DNMT3B gene on chromosome 20q11 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/27153398/") obo:IAO_0000115 obo:DOID_0060918 "A facioscapulohumeral muscular dystrophy characterized by adult onset of progressive muscle weakness of the face and upper extremity muscles with disease progression that has_material_basis_in the combination of a heterozygous mutation in the DNMT3B gene on chromosome 20q11 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "OMIM:619478") -AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060918 "https://pubmed.ncbi.nlm.nih.gov/27153398/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "FSHD4") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060918 "facioscapulohumeral muscular dystrophy type 4") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060918 "disease_ontology") From d9736fc4fbbea34413624a8b34123a0dbc658561 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Wed, 18 Oct 2023 12:34:01 -0400 Subject: [PATCH 26/33] url and definition adjustments --- src/ontology/doid-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index f8122d414..07d414b3f 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40356,7 +40356,6 @@ SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/32467133/") obo:IAO_0000115 obo:DOID_0060917 "A facioscapulohumeral muscular dystrophy characterized by adult onset of proximal muscle weakness affecting the face, neck, scapular muscles, and upper and lower limbs that has_material_basis_in the combination of a homozygous mutation in the LRIF1 gene on chromosome 1p13 and presence of a haplotype on chromosome 4 that is permissive for DUX4 expression.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "OMIM:619477") -AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060917 "https://pubmed.ncbi.nlm.nih.gov/32467133/") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "FSHD3") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060917 "facioscapulohumeral muscular dystrophy type 3") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060917 "disease_ontology") From 7437955f60df35d28a3f8ed9ad2745e0755444b0 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Thu, 19 Oct 2023 12:04:02 -0400 Subject: [PATCH 27/33] digenic inheritance axiom added --- src/ontology/doid-edit.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 07d414b3f..96e88fe65 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40374,6 +40374,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060918 "disease_ontology" AnnotationAssertion(oboInOwl:id obo:DOID_0060918 "DOID:0060918") AnnotationAssertion(rdfs:label obo:DOID_0060918 "facioscapulohumeral muscular dystrophy 4"@en) SubClassOf(obo:DOID_0060918 obo:DOID_11727) +SubClassOf(obo:DOID_0060918 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0060919 (autoinflammatory disease) From 97409712c99fedbc83dab168e43576b4cba957e8 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 20 Oct 2023 13:57:41 -0400 Subject: [PATCH 28/33] Addition of parent term to proteasome-associated autoinflammatory syndrome 1 --- src/ontology/doid-edit.owl | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 96e88fe65..3a188f8a5 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -13873,6 +13873,23 @@ Declaration(Class(obo:DOID_999)) Declaration(Class(obo:DOID_9993)) Declaration(Class(obo:DOID_9995)) Declaration(Class(obo:DOID_9997)) +Declaration(Class(obo:NCBITaxon_11103)) +Declaration(Class(obo:NCBITaxon_11269)) +Declaration(Class(obo:NCBITaxon_11620)) +Declaration(Class(obo:NCBITaxon_11623)) +Declaration(Class(obo:NCBITaxon_11628)) +Declaration(Class(obo:NCBITaxon_1980459)) +Declaration(Class(obo:NCBITaxon_1980467)) +Declaration(Class(obo:NCBITaxon_1980471)) +Declaration(Class(obo:NCBITaxon_1980476)) +Declaration(Class(obo:NCBITaxon_1980486)) +Declaration(Class(obo:NCBITaxon_1980490)) +Declaration(Class(obo:NCBITaxon_1980491)) +Declaration(Class(obo:NCBITaxon_1980519)) +Declaration(Class(obo:NCBITaxon_2169992)) +Declaration(Class(obo:NCBITaxon_45219)) +Declaration(Class(obo:NCBITaxon_46919)) +Declaration(Class(obo:NCBITaxon_499556)) Declaration(ObjectProperty(obo:IDO_0000664)) Declaration(ObjectProperty()) Declaration(AnnotationProperty(obo:IAO_0000115)) @@ -13941,7 +13958,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://purl.obolibrary.or AnnotationAssertion(rdfs:isDefinedBy obo:IAO_0000119 obo:iao.owl) AnnotationAssertion(rdfs:label obo:IAO_0000119 "definition source") -# Annotation Property: obo:IAO_0000700 (has_ontology_root_term) +# Annotation Property: obo:IAO_0000700 (has ontology root term) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://purl.obolibrary.org/obo/IAO_0000700") obo:IAO_0000115 obo:IAO_0000700 "Has ontology root term.") AnnotationAssertion(rdfs:label obo:IAO_0000700 "has_ontology_root_term") @@ -40336,7 +40353,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060914 "DOID:0060914") AnnotationAssertion(rdfs:label obo:DOID_0060914 "proteasome-associated autoinflammatory syndrome 1"@en) -SubClassOf(obo:DOID_0060914 obo:DOID_0060919) +SubClassOf(obo:DOID_0060914 obo:DOID_225) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) From 47f3151686974a31a6826595251045a0b34e6341 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 20 Oct 2023 15:04:30 -0400 Subject: [PATCH 29/33] Revert "Addition of parent term to proteasome-associated autoinflammatory syndrome 1" This reverts commit 97409712c99fedbc83dab168e43576b4cba957e8. --- src/ontology/doid-edit.owl | 21 ++------------------- 1 file changed, 2 insertions(+), 19 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 3a188f8a5..96e88fe65 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -13873,23 +13873,6 @@ Declaration(Class(obo:DOID_999)) Declaration(Class(obo:DOID_9993)) Declaration(Class(obo:DOID_9995)) Declaration(Class(obo:DOID_9997)) -Declaration(Class(obo:NCBITaxon_11103)) -Declaration(Class(obo:NCBITaxon_11269)) -Declaration(Class(obo:NCBITaxon_11620)) -Declaration(Class(obo:NCBITaxon_11623)) -Declaration(Class(obo:NCBITaxon_11628)) -Declaration(Class(obo:NCBITaxon_1980459)) -Declaration(Class(obo:NCBITaxon_1980467)) -Declaration(Class(obo:NCBITaxon_1980471)) -Declaration(Class(obo:NCBITaxon_1980476)) -Declaration(Class(obo:NCBITaxon_1980486)) -Declaration(Class(obo:NCBITaxon_1980490)) -Declaration(Class(obo:NCBITaxon_1980491)) -Declaration(Class(obo:NCBITaxon_1980519)) -Declaration(Class(obo:NCBITaxon_2169992)) -Declaration(Class(obo:NCBITaxon_45219)) -Declaration(Class(obo:NCBITaxon_46919)) -Declaration(Class(obo:NCBITaxon_499556)) Declaration(ObjectProperty(obo:IDO_0000664)) Declaration(ObjectProperty()) Declaration(AnnotationProperty(obo:IAO_0000115)) @@ -13958,7 +13941,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://purl.obolibrary.or AnnotationAssertion(rdfs:isDefinedBy obo:IAO_0000119 obo:iao.owl) AnnotationAssertion(rdfs:label obo:IAO_0000119 "definition source") -# Annotation Property: obo:IAO_0000700 (has ontology root term) +# Annotation Property: obo:IAO_0000700 (has_ontology_root_term) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:http://purl.obolibrary.org/obo/IAO_0000700") obo:IAO_0000115 obo:IAO_0000700 "Has ontology root term.") AnnotationAssertion(rdfs:label obo:IAO_0000700 "has_ontology_root_term") @@ -40353,7 +40336,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060914 "DOID:0060914") AnnotationAssertion(rdfs:label obo:DOID_0060914 "proteasome-associated autoinflammatory syndrome 1"@en) -SubClassOf(obo:DOID_0060914 obo:DOID_225) +SubClassOf(obo:DOID_0060914 obo:DOID_0060919) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) From ae13b69daec35326f48a06b82817431931bce192 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 20 Oct 2023 15:56:30 -0400 Subject: [PATCH 30/33] Edits to proteasome-associated autoinflammatory syndrome 1 --- src/ontology/doid-edit.owl | 39 +++++++++++++------------------------- 1 file changed, 13 insertions(+), 26 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 96e88fe65..8aabc6c66 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -1889,11 +1889,9 @@ Declaration(Class(obo:DOID_0060903)) Declaration(Class(obo:DOID_0060904)) Declaration(Class(obo:DOID_0060911)) Declaration(Class(obo:DOID_0060912)) -Declaration(Class(obo:DOID_0060914)) Declaration(Class(obo:DOID_0060916)) Declaration(Class(obo:DOID_0060917)) Declaration(Class(obo:DOID_0060918)) -Declaration(Class(obo:DOID_0060919)) Declaration(Class(obo:DOID_0070000)) Declaration(Class(obo:DOID_0070001)) Declaration(Class(obo:DOID_0070002)) @@ -21428,19 +21426,27 @@ AnnotationAssertion(rdfs:comment obo:DOID_0050551 "OMIM mapping confirmed by DO. AnnotationAssertion(rdfs:label obo:DOID_0050551 "obsolete Verma-Naumoff syndrome") AnnotationAssertion(owl:deprecated obo:DOID_0050551 "true"^^xsd:boolean) -# Class: obo:DOID_0050553 (JMP syndrome) +# Class: obo:DOID_0050553 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:http://www.eurekalert.org/pub_releases/2010-12/usmc-rig120110.php") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/21129723") obo:IAO_0000115 obo:DOID_0050553 "A syndrome that is characterized by childhood onset of joint stiffness and severe contractures of the hands and feet, erythematous skin lesions with subsequent development of severe lipodystrophy that has_material_basis_in homozygous or compound heterozygous mutation in the PSMB8 gene on chromosome 6p21.32.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0050553 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") +AnnotationAssertion(oboInOwl:hasAlternativeId obo:DOID_0050553 "DOID:0060914") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "GARD:10988") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "OMIM:256040") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "ORDO:324999") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "JMP syndrome"@en) AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "JOINT CONTRACTURES, MUSCULAR ATROPHY, MICROCYTIC ANEMIA, AND PANNICULITIS-INDUCED LIPODYSTROPHY"@en) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "PRAAS1") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "CANDLE") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "NKJO") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "Nakajo-Nishimura syndrome") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature syndrome") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050553 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050553 "DOID:0050553") AnnotationAssertion(oboInOwl:inSubset obo:DOID_0050553 doid:DO_rare_slim) -AnnotationAssertion(rdfs:label obo:DOID_0050553 "JMP syndrome") +AnnotationAssertion(rdfs:label obo:DOID_0050553 "proteasome-associated autoinflammatory syndrome 1") SubClassOf(obo:DOID_0050553 obo:DOID_225) SubClassOf(obo:DOID_0050553 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) +SubClassOf(obo:DOID_0050553 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0050554 (X-linked sideroblastic anemia with ataxia) @@ -40328,18 +40334,6 @@ AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) SubClassOf(obo:DOID_0060912 obo:DOID_2340) SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) -# Class: obo:DOID_0060914 (proteasome-associated autoinflammatory syndrome 1) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0060914 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") -AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060914 "OMIM:256040") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060914 "PRAAS1") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060914 "disease_ontology") -AnnotationAssertion(oboInOwl:id obo:DOID_0060914 "DOID:0060914") -AnnotationAssertion(rdfs:label obo:DOID_0060914 "proteasome-associated autoinflammatory syndrome 1"@en) -SubClassOf(obo:DOID_0060914 obo:DOID_0060919) -SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) -SubClassOf(obo:DOID_0060914 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) - # Class: obo:DOID_0060916 (proteasome-associated autoinflammatory syndrome 3) AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/26524591/") obo:IAO_0000115 obo:DOID_0060916 "An autosomal recessive disorder characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in a homozygous mutation in the PSMB4 gene on chromosome 1q21 or a heterozygous mutation in the PSMB4 gene and a heterozygous mutation in the PSMB9 gene on chromosome 6p21.") @@ -40348,8 +40342,8 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060916 "DOID:0060916") AnnotationAssertion(rdfs:label obo:DOID_0060916 "proteasome-associated autoinflammatory syndrome 3"@en) -SubClassOf(obo:DOID_0060916 obo:DOID_0050737) -SubClassOf(obo:DOID_0060916 obo:DOID_0060919) +SubClassOf(obo:DOID_0060916 obo:DOID_225) +SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) # Class: obo:DOID_0060917 (facioscapulohumeral muscular dystrophy 3) @@ -40376,13 +40370,6 @@ AnnotationAssertion(rdfs:label obo:DOID_0060918 "facioscapulohumeral muscular dy SubClassOf(obo:DOID_0060918 obo:DOID_11727) SubClassOf(obo:DOID_0060918 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) -# Class: obo:DOID_0060919 (autoinflammatory disease) - -AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060919 "disease_ontology") -AnnotationAssertion(oboInOwl:id obo:DOID_0060919 "DOID:0060919") -AnnotationAssertion(rdfs:label obo:DOID_0060919 "autoinflammatory disease"@en) -SubClassOf(obo:DOID_0060919 obo:DOID_2914) - # Class: obo:DOID_0070000 (3-methylglutaconic aciduria type 8) AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/27208207") Annotation(oboInOwl:hasDbXref "url:https://www.ncbi.nlm.nih.gov/pubmed/27696117") obo:IAO_0000115 obo:DOID_0070000 "A 3-methylglutaconic aciduria that has_material_basis_in homozygous mutation in the HTRA2 gene on chromosome 2p13.") From b06ef33bf35107d1e1d98301a8a40a10e3714ea0 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Mon, 23 Oct 2023 17:01:17 -0400 Subject: [PATCH 31/33] Proteasome-associated autoinflammatory syndrome PS --- src/ontology/doid-edit.owl | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 8aabc6c66..9de426afd 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -1889,6 +1889,7 @@ Declaration(Class(obo:DOID_0060903)) Declaration(Class(obo:DOID_0060904)) Declaration(Class(obo:DOID_0060911)) Declaration(Class(obo:DOID_0060912)) +Declaration(Class(obo:DOID_0060913)) Declaration(Class(obo:DOID_0060916)) Declaration(Class(obo:DOID_0060917)) Declaration(Class(obo:DOID_0060918)) @@ -21428,23 +21429,23 @@ AnnotationAssertion(owl:deprecated obo:DOID_0050551 "true"^^xsd:boolean) # Class: obo:DOID_0050553 (proteasome-associated autoinflammatory syndrome 1) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0050553 "An autosomal recessive disease characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0050553 "A proteasome-associated autoinflammatory syndrome characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") AnnotationAssertion(oboInOwl:hasAlternativeId obo:DOID_0050553 "DOID:0060914") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "GARD:10988") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "OMIM:256040") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "ORDO:324999") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "CANDLE") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "JMP syndrome"@en) AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "JOINT CONTRACTURES, MUSCULAR ATROPHY, MICROCYTIC ANEMIA, AND PANNICULITIS-INDUCED LIPODYSTROPHY"@en) -AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "PRAAS1") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "CANDLE") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "NKJO") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "Nakajo-Nishimura syndrome") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "PRAAS1") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature syndrome") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0050553 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0050553 "DOID:0050553") AnnotationAssertion(oboInOwl:inSubset obo:DOID_0050553 doid:DO_rare_slim) AnnotationAssertion(rdfs:label obo:DOID_0050553 "proteasome-associated autoinflammatory syndrome 1") -SubClassOf(obo:DOID_0050553 obo:DOID_225) +SubClassOf(obo:DOID_0050553 obo:DOID_0060913) SubClassOf(obo:DOID_0050553 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) SubClassOf(obo:DOID_0050553 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) @@ -40334,15 +40335,22 @@ AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) SubClassOf(obo:DOID_0060912 obo:DOID_2340) SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) +# Class: obo:DOID_0060913 (Proteosome-associated autoinflammatory syndrome) + +AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060913 "A syndrome that is characterized by early onset, dermatitis, lipodystrophy, dysregulation of the immune response, recurrent fever, joint contractures, hepatosplenomegaly, anemia and calcifications.") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "OMIM:PS256040") +AnnotationAssertion(rdfs:label obo:DOID_0060913 "Proteosome-associated autoinflammatory syndrome"@en) +SubClassOf(obo:DOID_0060913 obo:DOID_225) + # Class: obo:DOID_0060916 (proteasome-associated autoinflammatory syndrome 3) -AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/26524591/") obo:IAO_0000115 obo:DOID_0060916 "An autosomal recessive disorder characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in a homozygous mutation in the PSMB4 gene on chromosome 1q21 or a heterozygous mutation in the PSMB4 gene and a heterozygous mutation in the PSMB9 gene on chromosome 6p21.") +AnnotationAssertion(Annotation(dc:type obo:ECO_0007645) Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/26524591/") obo:IAO_0000115 obo:DOID_0060916 "A proteasome-associated autoinflammatory syndrome characterized by nodular dermatitis, recurrent fever, myositis, panniculitis-induced lipodystrophy, lymphadenopathy and dysregulation of the immune response, particularly associated with abnormal type I interferon-induced gene expression pattern with onset in early infancy that has_material_basis_in a homozygous mutation in the PSMB4 gene on chromosome 1q21 or a heterozygous mutation in the PSMB4 gene and a heterozygous mutation in the PSMB9 gene on chromosome 6p21.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060916 "OMIM:617591") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0060916 "PRAAS3") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060916 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060916 "DOID:0060916") AnnotationAssertion(rdfs:label obo:DOID_0060916 "proteasome-associated autoinflammatory syndrome 3"@en) -SubClassOf(obo:DOID_0060916 obo:DOID_225) +SubClassOf(obo:DOID_0060916 obo:DOID_0060913) SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000148)) SubClassOf(obo:DOID_0060916 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) From b6e25f2c256297ba1be808c5d550fe999c1bcab5 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Wed, 25 Oct 2023 12:00:35 -0400 Subject: [PATCH 32/33] New Proteosome-associated autoinflammatory syndrome term --- src/ontology/doid-edit.owl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index 9de426afd..ae6af50c2 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -40339,6 +40339,8 @@ SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_000093 AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060913 "A syndrome that is characterized by early onset, dermatitis, lipodystrophy, dysregulation of the immune response, recurrent fever, joint contractures, hepatosplenomegaly, anemia and calcifications.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "OMIM:PS256040") +AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060913 "disease_ontology") +AnnotationAssertion(oboInOwl:id obo:DOID_0060913 "DOID:0060913") AnnotationAssertion(rdfs:label obo:DOID_0060913 "Proteosome-associated autoinflammatory syndrome"@en) SubClassOf(obo:DOID_0060913 obo:DOID_225) From 6d7aead66925a40e0dbdae39ced6b48066aab907 Mon Sep 17 00:00:00 2001 From: csbjohnson Date: Fri, 27 Oct 2023 10:28:52 -0400 Subject: [PATCH 33/33] Annotations proteosome-associated autoinflammatory syndrome --- src/ontology/doid-edit.owl | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/ontology/doid-edit.owl b/src/ontology/doid-edit.owl index ae6af50c2..2f0661b2a 100644 --- a/src/ontology/doid-edit.owl +++ b/src/ontology/doid-edit.owl @@ -21432,6 +21432,8 @@ AnnotationAssertion(owl:deprecated obo:DOID_0050551 "true"^^xsd:boolean) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21129723/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21852578/") Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/21881205/") obo:IAO_0000115 obo:DOID_0050553 "A proteasome-associated autoinflammatory syndrome characterized by early childhood onset of annular erythematous plaques on the face and extremities with subsequent development of partial lipodystrophy and laboratory evidence of immune dysregulation that has_material_basis_in homozygous mutation in the PSMB8 gene on chromosome 6p21 or heterozygous mutation in the PSMB8 gene and heterozygous mutation in either the PSMA3 gene on chromosome 14q23 or in the PSMB4 gene on chromosome 1q21.") AnnotationAssertion(oboInOwl:hasAlternativeId obo:DOID_0050553 "DOID:0060914") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "GARD:10988") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "GARD:3916") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "GARD:3917") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "OMIM:256040") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0050553 "ORDO:324999") AnnotationAssertion(oboInOwl:hasExactSynonym obo:DOID_0050553 "CANDLE") @@ -40335,13 +40337,14 @@ AnnotationAssertion(rdfs:label obo:DOID_0060912 "craniosynostosis 7"@en) SubClassOf(obo:DOID_0060912 obo:DOID_2340) SubClassOf(obo:DOID_0060912 ObjectSomeValuesFrom(obo:IDO_0000664 obo:GENO_0000930)) -# Class: obo:DOID_0060913 (Proteosome-associated autoinflammatory syndrome) +# Class: obo:DOID_0060913 (proteosome-associated autoinflammatory syndrome) -AnnotationAssertion(obo:IAO_0000115 obo:DOID_0060913 "A syndrome that is characterized by early onset, dermatitis, lipodystrophy, dysregulation of the immune response, recurrent fever, joint contractures, hepatosplenomegaly, anemia and calcifications.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "url:https://pubmed.ncbi.nlm.nih.gov/25521013/") obo:IAO_0000115 obo:DOID_0060913 "A syndrome that is characterized by early onset, dermatitis, dysregulation of the immune response and variable features of recurrent fever, joint contractures, lipodystrophy, hepatosplenomegaly, anemia and calcifications.") AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "OMIM:PS256040") +AnnotationAssertion(oboInOwl:hasDbXref obo:DOID_0060913 "ORDO:324977") AnnotationAssertion(oboInOwl:hasOBONamespace obo:DOID_0060913 "disease_ontology") AnnotationAssertion(oboInOwl:id obo:DOID_0060913 "DOID:0060913") -AnnotationAssertion(rdfs:label obo:DOID_0060913 "Proteosome-associated autoinflammatory syndrome"@en) +AnnotationAssertion(rdfs:label obo:DOID_0060913 "proteosome-associated autoinflammatory syndrome"@en) SubClassOf(obo:DOID_0060913 obo:DOID_225) # Class: obo:DOID_0060916 (proteasome-associated autoinflammatory syndrome 3)