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Minor BBS and PXE changes #1047

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Dec 19, 2019
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Minor BBS and PXE changes #1047

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af7ec1d
BBS text def, see https://github.com/monarch-initiative/hpo-annotatio…
cmungall Dec 5, 2019
3e24b89
PXE minor changes (see also #1046 for other PXE changes)
cmungall Dec 18, 2019
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35 changes: 20 additions & 15 deletions src/ontology/mondo-edit.obo
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Expand Up @@ -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"}
Expand Down Expand Up @@ -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"}
Expand Down Expand Up @@ -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"}
Expand Down Expand Up @@ -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"}
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -279792,13 +279793,13 @@ 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]
Expand All @@ -279815,6 +279816,7 @@ 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
Expand Down Expand Up @@ -300826,13 +300828,13 @@ 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"}
Expand Down Expand Up @@ -319990,9 +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
Expand Down Expand Up @@ -352571,6 +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
Expand Down Expand Up @@ -407484,11 +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]
Expand Down