From af7ec1d331f837063e467796065335e0f6f54ed3 Mon Sep 17 00:00:00 2001 From: cmungall Date: Wed, 4 Dec 2019 22:12:19 -0800 Subject: [PATCH 1/2] BBS text def, see https://github.com/monarch-initiative/hpo-annotation-data/issues/402 --- src/ontology/mondo-edit.obo | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 3c99f3f7cd..cd7bbedcd2 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -128613,7 +128613,7 @@ id: MONDO:0007229 name: Brachymetatarsus 4 synonym: "BRACHYMETATARSUS IV" RELATED [OMIM:113475] synonym: "Brachymetatarsus type 4" EXACT [MONDORULE:1, OMIM:113475] -synonym: "metatarsus Iv, short" RELATED [OMIM:113475] +synonym: "metatarsus IV, short" RELATED [OMIM:113475] synonym: "toe, fourth, short" RELATED [OMIM:113475] xref: OMIM:113475 {source="MONDO:equivalentTo"} xref: UMLS:C1862083 {source="NCBI:mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="OMIM:113475"} @@ -182237,7 +182237,7 @@ synonym: "methemoglobinemia caused by mutation in CYB5A" EXACT [MONDO:design_pat synonym: "methemoglobinemia due to deficiency of cytochrome B5" RELATED [OMIM:250790] synonym: "methemoglobinemia due to deficiency of cytochrome B5, formerly" RELATED [OMIM:250790] synonym: "methemoglobinemia type IV" RELATED [OMIM:250790] -synonym: "methemoglobinemia type Iv, formerly" RELATED [OMIM:250790] +synonym: "methemoglobinemia type IV, formerly" RELATED [OMIM:250790] xref: MESH:C567102 {source="MONDO:equivalentTo", source="MONDO:ontobio"} xref: OMIM:250790 {source="MONDO:equivalentTo"} xref: Orphanet:621 {source="MONDO:subClassOf", source="OMIM:250790"} @@ -208889,9 +208889,9 @@ synonym: "panhypopituitarism X-linked" RELATED [GARD:0006737] synonym: "panhypopituitarism, X-linked" EXACT [MONDO:Lexical, OMIM:312000] synonym: "panhypopituitarism, X-linked; PHPX" RELATED [OMIM:312000] synonym: "PHPX" RELATED [MONDO:Lexical, OMIM:312000] -synonym: "pituitary dwarfism Iv" RELATED [OMIM:312000] +synonym: "pituitary dwarfism IV" RELATED [OMIM:312000] synonym: "pituitary dwarfism IV (formerly)" RELATED [GARD:0006737] -synonym: "pituitary dwarfism Iv, formerly" RELATED [OMIM:312000] +synonym: "pituitary dwarfism IV, formerly" RELATED [OMIM:312000] xref: GARD:0006737 {source="MONDO:equivalentTo"} xref: MESH:C538613 {source="MONDO:equivalentTo"} xref: OMIM:312000 {source="MONDO:equivalentTo"} @@ -279792,13 +279792,13 @@ subset: clingen subset: ordo_disease {source="Orphanet:404454"} synonym: "alacrimia - choreoathetosis - liver dysfunction syndrome" RELATED [Orphanet:404454] synonym: "CDDG" RELATED [MONDO:Lexical, OMIM:615273] -synonym: "CDG Iv" RELATED [OMIM:615273] -synonym: "CDG Iv, formerly" RELATED [OMIM:615273] +synonym: "CDG IV" RELATED [OMIM:615273] +synonym: "CDG IV, formerly" RELATED [OMIM:615273] synonym: "congenital disorder of deglycosylation" EXACT [DOID:0060728, MONDO:Lexical, OMIM:615273] synonym: "congenital disorder of deglycosylation; CDDG" RELATED [OMIM:615273] synonym: "congenital disorder of deglycosylation;CDDG" RELATED [GARD:0012315] synonym: "congenital disorder of glycosylation type IV" EXACT [DOID:0060728] -synonym: "congenital disorder of glycosylation type Iv; CDG1V" RELATED [GARD:0012315] +synonym: "congenital disorder of glycosylation type IV; CDG1V" RELATED [GARD:0012315] synonym: "congenital disorder of glycosylation, type IV" RELATED [OMIM:615273] synonym: "congenital disorder of glycosylation, type IV, formerly" RELATED [OMIM:615273] synonym: "deficiency of N-glycanase 1" EXACT [DOID:0060728] @@ -279815,6 +279815,7 @@ xref: UMLS:C3808991 {source="NCBI:mim2gene_medline", source="MONDO:equivalentTo" is_a: MONDO:0000508 {source="Orphanet:404454"} ! syndromic intellectual disability is_a: MONDO:0019214 {source="DOID:0060728"} ! inborn carbohydrate metabolic disorder is_a: MONDO:0019602 {source="Orphanet:404454"} ! other inborn metabolic disease +relationship: disease_has_basis_in_disruption_of GO:0000224 ! peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity relationship: disease_has_basis_in_disruption_of GO:0006517 ! protein deglycosylation relationship: disease_has_basis_in_dysfunction_of http://identifiers.org/hgnc/17646 {source="mim2gene_medgen"} ! NGLY1 relationship: has_modifier MONDO:0021136 {source="MONDO:0015983"} ! rare @@ -300826,13 +300827,13 @@ is_a: MONDO:0017002 {source="Orphanet:11"} ! polysomy of X chromosome [Term] id: MONDO:0015229 name: Bardet-Biedl syndrome -def: "Bardet-Biedl syndrome (BBS) is a ciliopathy with multisystem involvement." [Orphanet:110] +def: "Bardet-Biedl syndrome (BBS) is a ciliopathy with multisystem involvement. It is invariantly characterized by rod-cone dystrophy, and at least three additional non-ocular features such as intellectual disability, obesity, polydactyly, hypogonadism, or renal anomalies as primary manifestations. In the absence of one of these four primary clinical features, the diagnosis of BBS is made when at least two secondary features are observed, including hepatic fibrosis, diabetes mellitus, reproductive and developmental abnormalities, growth retardation, speech delays, or cardiovascular problems" [Orphanet:110, PMID:10874630] subset: clingen subset: ordo_disease {source="Orphanet:110"} synonym: "BBS" EXACT [Orphanet:110] -synonym: "Laurence-Moon syndrome" EXACT [NCIT:C118632] -synonym: "Laurence-Moon-Bardet-Biedl syndrome" EXACT [NCIT:C118632] -synonym: "Laurence-Moon-Biedl syndrome" EXACT [NCIT:C118632] +synonym: "Laurence-Moon syndrome" EXACT EXCLUDE [NCIT:C118632] +synonym: "Laurence-Moon-Bardet-Biedl syndrome" EXACT EXCLUDE [NCIT:C118632] +synonym: "Laurence-Moon-Biedl syndrome" EXACT EXCLUDE [NCIT:C118632] xref: DOID:1935 {source="MONDO:equivalentTo"} xref: GARD:0006866 {source="MONDO:equivalentTo"} xref: ICD10:Q87.8 {source="ORDO:110/inclusion", source="ORDO:110/ntbt", source="Orphanet:110"} From 3e24b897cdb0ba98bfb1252aed190d667c8d0f7c Mon Sep 17 00:00:00 2001 From: cmungall Date: Wed, 18 Dec 2019 09:34:57 -0800 Subject: [PATCH 2/2] PXE minor changes (see also #1046 for other PXE changes) --- src/ontology/mondo-edit.obo | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index cd7bbedcd2..ca68dda8da 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -190435,7 +190435,7 @@ is_a: MONDO:0024299 {source="MONDO:cjm", source="MONDOLEX:0009924", source="link [Term] id: MONDO:0009925 name: inherited pseudoxanthoma elasticum -def: "Pseudoxanthoma elasticum , PXE, is an inherited disorder that causes calcium and other minerals to accumulate in the elasticfibers of the skin, eyes, and blood vessels, and less frequently in other areas such as the digestive tract. PXE may cause the following symptoms: growth of yellowish bumps on the skin of the neck, under the arms, or in the groin area; reduced vision; periodic weakness in the legs ( claudication ); or bleeding in the gastrointestinal tract , particularly the stomach. A clinical diagnosis of PXEcan be madewhenan individual is found to have both the characteristic eye findings and yellow bumps on the skin. ABCC6 is the only gene known to be associated with this condition. Currently, there is no treatment for this condition, but affected individuals may benefit from routine visits to an eye doctor who specializes in retinal disorders , and by having regular physical examinationswith their primary physician." [https://rarediseases.info.nih.gov/diseases/9643/pseudoxanthoma-elasticum] +def: "Pseudoxanthoma elasticum , PXE, is an inherited disorder that causes calcium and other minerals to accumulate in the elasticfibers of the skin, eyes, and blood vessels, and less frequently in other areas such as the digestive tract. PXE may cause the following symptoms: growth of yellowish bumps on the skin of the neck, under the arms, or in the groin area; reduced vision; periodic weakness in the legs (claudication); or bleeding in the gastrointestinal tract, particularly the stomach. A clinical diagnosis of PXE can be made when an individual is found to have both the characteristic eye findings and yellow bumps on the skin. ABCC6 is the only gene known to be associated with this condition. Currently, there is no treatment for this condition, but affected individuals may benefit from routine visits to an eye doctor who specializes in retinal disorders, and by having regular physical examinationswith their primary physician." [https://rarediseases.info.nih.gov/diseases/9643/pseudoxanthoma-elasticum] comment: Pathophysiology: In PXE, there is mineralization (accumulation of calcium and other minerals) and fragmentation of the elastin-containing fibers in connective tissue, but primarily in the midlaminar layer of the dermis, Bruch's membrane and the midsized arteries.[12] Recent studies hypothesize that PXE is a metabolic disease, and that its features arise because metabolites of vitamin K cannot reach peripheral tissues subset: gard_rare {source="GARD:0009643"} subset: ordo_disease {source="Orphanet:758"} @@ -248169,6 +248169,7 @@ xref: UMLS:C4049241 {source="MONDO:equivalentTo", source="MEDGEN:kboom-pr95-c96" is_a: MONDO:0019292 {source="Orphanet:91135", source="Orphanet:91135/inferred"} ! dermis elastic tissue disorder relationship: disease_arises_from_feature HP:0001928 ! Abnormality of coagulation relationship: disease_has_basis_in_dysfunction_of http://identifiers.org/hgnc/4247 {source="mim2gene_medgen"} ! GGCX +relationship: disease_shares_features_of MONDO:0024308 ! pseudoxanthoma elasticum (inherited or acquired) property_value: confidence "3.533333333333334" xsd:double [Term] @@ -319991,9 +319992,11 @@ name: pseudoxanthoma elasticum-like papillary dermal elastolysis def: "Pseudoxanthoma elasticum-like papillary dermal elastolysis (PXE-PDE) is a rare, acquired, idiopathic dermal tissue disorder characterized by numerous, asymptomatic, 2-3 mm, yellowish, non-follicular papules that tend to converge into cobblestone-like plaques which are distributed symmetrically over the posterior neck, supraclavicular region, axillae, and sometimes abdomen. Unlike PXE, these skin lesions show select elimination (absence or marked loss) of elastic fibers in the papillary dermis and there is no systemic involvement." [Orphanet:228293] subset: ordo_disease {source="Orphanet:228293"} synonym: "PXE-like papillary dermal elastolysis" EXACT [Orphanet:228293] +synonym: "PXE-PDE" EXACT [] xref: Orphanet:228293 {source="MONDO:equivalentTo"} xref: SCTID:764105002 {source="MONDO:equivalentTo"} is_a: MONDO:0016435 {source="Orphanet:228293"} ! acquired dermis elastic tissue disorder with decreased elastic tissue +relationship: disease_shares_features_of MONDO:0024308 ! pseudoxanthoma elasticum (inherited or acquired) [Term] id: MONDO:0016449 @@ -352572,6 +352575,7 @@ xref: Orphanet:436274 {source="MONDO:equivalentTo"} xref: UMLS:CN237597 {source="MEDGEN:kboom-pr98-c99", source="MONDO:equivalentTo"} is_a: MONDO:0019292 {source="Orphanet:436274", source="Orphanet:436274/inferred"} ! dermis elastic tissue disorder is_a: MONDO:0020240 {source="Orphanet:436274"} ! syndromic retinitis pigmentosa +relationship: disease_shares_features_of MONDO:0024308 ! pseudoxanthoma elasticum (inherited or acquired) [Term] id: MONDO:0018578 @@ -407485,11 +407489,11 @@ is_a: MONDO:0011786 {source="MONDOLEX:0024332", source="NCIT:C92189", source="li [Term] id: MONDO:0024333 name: sciatica -def: "A condition characterized by pain radiating from the back into the buttock and posterior/lateral aspects of the leg. Sciatica may be a manifestation of SCIATIC NEUROPATHY; RADICULOPATHY (involving the SPINAL NERVE ROOTS; L4, L5, S1, or S2, often associated with INTERVERTEBRAL DISK DISPLACEMENT); or lesions of the CAUDA EQUINA." [MESH:D012585] +def: "A condition characterized by pain radiating from the back into the buttock and posterior/lateral aspects of the leg. Sciatica may be a manifestation of sciatic neuropathy; radiculopathy (involving the spinal nerve roots; L4, L5, S1, or S2, often associated with intervertebral disk displacement); or lesions of the cauda equina." [MESH:D012585] synonym: "bilateral sciatica" RELATED [MESH:D012585] -synonym: "bilateral Sciaticas" RELATED [MESH:D012585] +synonym: "bilateral sciaticas" RELATED [MESH:D012585] synonym: "neuralgia, sciatic" RELATED [MESH:D012585] -synonym: "Neuralgias, sciatic" RELATED [MESH:D012585] +synonym: "neuralgias, sciatic" RELATED [MESH:D012585] synonym: "sciatic neuralgia" RELATED [MESH:D012585] synonym: "sciatic Neuralgias" RELATED [MESH:D012585] synonym: "sciatica, bilateral" RELATED [MESH:D012585]