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Mondo Disease Ontology
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SPLIT OMIMPS terms #5619

Closed nicolevasilevsky closed 1 year ago

nicolevasilevsky commented 1 year ago

[Term] id: MONDO:0031329 name: craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome xref: OMIMPS:213980 {source="MONDO:equivalentTo"} ! craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome

[Term] id: MONDO:0031415 name: Carey-Fineman-Ziter syndrome xref: OMIMPS:254940 {source="MONDO:equivalentTo"} ! carey-fineman-ziter syndrome is_a: MONDO:0003847{ source="https://orcid.org/0000-0001-5208-3432"} ! Mendelian disease relationship: has_characteristic MONDO:0021152 {source="OMIMPS:212093"} ! inherited

[Term] id: MONDO:0031632 name: developmental delay with short stature, dysmorphic facial features, and sparse hair xref: OMIMPS:616901 {source="MONDO:equivalentTo"} ! developmental delay with short stature, dysmorphic facial features, and sparse hair relationship: has_characteristic MONDO:0021152 {source="OMIMPS:256550"} ! inherited

see spreadsheet

nicolevasilevsky commented 1 year ago

Note: I updated the IDs for 3 terms on 2022-12-12

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Add new terms

Note: these can just be copied and pasted into the mondo-edit.obo text file. Go to edit mode and copy the text.

[Term] id: MONDO:0031329 name: craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome xref: OMIMPS:213980 {source="MONDO:equivalentTo"} ! craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome is_a: MONDO:0003847{ source="OMIMPS:213980"} ! Mendelian disease property_value: IAO:0000233 https://github.com/monarch-initiative/mondo/issues/5619 xsd:anyURI relationship: has_characteristic MONDO:0021152 {source="OMIMPS:213980"} ! inherited

[Term] id: MONDO:0800436 name: craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1 def: "A rare syndrome characterized by facial dysmorphism, intellectual deficit and costovertebral abnormalities." [Orphanet:1394, https://orcid.org/0000-0001-5208-3432] subset: gard_rare subset: ordo_malformation_syndrome {source="Orphanet:1394"} synonym: "cerebro facio thoracic dysplasia" RELATED [GARD:0001210] synonym: "cerebrofaciothoracic dysplasia" EXACT CLINGEN_PREFERRED [GARD:0001210, OMIM:213980] synonym: "CFSMR" RELATED DEPRECATED [MONDO:Lexical, OMIM:213980] synonym: "CFSMR1" EXACT [MONDO:Lexical, OMIM:213980] synonym: "pascual-Castroviejo syndrome" RELATED [GARD:0001210] synonym: "pascual-Castroviejo syndrome type 1" EXACT [Orphanet:1394] xref: GARD:0001210 {source="MONDO:equivalentTo"} xref: ICD10CM:Q87.5 {source="Orphanet:1394/attributed", source="Orphanet:1394/ntbt", source="Orphanet:1394"} xref: MESH:C565862 {source="MONDO:equivalentTo"} xref: OMIM:213980 {source="GARD:0001210", source="Orphanet:1394/e", source="MONDO:equivalentTo", source="Orphanet:1394"} xref: Orphanet:1394 {source="OMIM:213980", source="MONDO:equivalentTo"} xref: SCTID:720635002 {source="MONDO:equivalentTo"} xref: UMLS:C1859252 {source="OMIM:213980", source="MONDO:ncbi_mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:1394"} relationship: excluded_subClassOf MONDO:0000508 {source="MONDO:Redundant", source="Orphanet:1394"} ! syndromic intellectual disability relationship: excluded_subClassOf MONDO:0015159 {source="Orphanet:1394"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability relationship: excluded_subClassOf MONDO:0018454 {source="MONDO:0019711-obsoleted", source="https://github.com/monarch-initiative/mondo/pull/2571/"} ! dysostosis of genetic origin is_a: MONDO:0031329 {source="OMIM:213980"} ! craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome relationship: has_characteristic MONDO:0021136 {source="MONDO:0015162", source="MONDO:0015983"} ! rare property_value: seeAlso https://rarediseases.info.nih.gov/diseases/1210/cerebro-facio-thoracic-dysplasia xsd:anyURI {source="GARD:0001210"} property_value: IAO:0000233 https://github.com/monarch-initiative/mondo/issues/5619 xsd:anyURI relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql

[Term] id: MONDO:0031415 name: Carey-Fineman-Ziter syndrome xref: OMIMPS:254940 {source="MONDO:equivalentTo"} ! carey-fineman-ziter syndrome is_a: MONDO:0003847{ source="OMIMPS:254940"} ! Mendelian disease relationship: has_characteristic MONDO:0021152 {source="OMIMPS:212093"} ! inherited property_value: IAO:0000233 https://github.com/monarch-initiative/mondo/issues/5619 xsd:anyURI relationship: has_characteristic MONDO:0021152 {source="OMIMPS:254940"} ! inherited

[Term] id: MONDO:0800437 name: Carey-Fineman-Ziter syndrome 1 def: "A rare condition characterized by the association of hypotonia, Moebius sequence (bilateral congenital facial palsy with impairment of ocular abduction), Pierre-Robin sequence (micrognathia, glossoptosis, and high-arched or cleft palate), unusual face, and growth delay." [Orphanet:1358] subset: gard_rare {source="GARD:0003889"} subset: ordo_malformation_syndrome {source="Orphanet:1358"} synonym: "Carey Fineman Ziter syndrome" RELATED [GARD:0003889] synonym: "Carey-Fineman-Ziter syndrome 1" EXACT [OMIM:254940, Orphanet:1358] synonym: "CFZS" RELATED ABBREVIATION [GARD:0003889, OMIM:254940] synonym: "CFZS1" EXACT ABBREVIATION [OMIM:254940] synonym: "congenital nonprogressive myopathy with Moebius and Robin sequences" RELATED [GARD:0003889] synonym: "Moebius sequence, Robin complex, and hypotonia" RELATED [GARD:0003889] synonym: "myopathy, congenital nonprogressive with Moebius and Robin sequences" RELATED [GARD:0003889] synonym: "myopathy, congenital nonprogressive, with Moebius sequence and Robin sequence" EXACT [OMIM:254940] synonym: "myopathy-Moebius-Robin syndrome" EXACT [Orphanet:1358] xref: DOID:0080194 {source="MONDO:equivalentTo"} xref: GARD:0003889 {source="MONDO:equivalentTo"} xref: ICD10CM:Q87.0 {source="Orphanet:1358", source="Orphanet:1358/attributed", source="Orphanet:1358/ntbt"} xref: ICD9:359.89 {source="MONDO:relatedTo", source="MONDO:i2s"} xref: MESH:C536102 {source="MONDO:equivalentTo"} xref: OMIM:254940 {source="MONDO:equivalentTo", source="Orphanet:1358", source="Orphanet:1358/e"} xref: Orphanet:1358 {source="MONDO:equivalentTo", source="OMIM:254940"} xref: SCTID:429753001 {source="MONDO:equivalentTo"} xref: UMLS:C1850746 {source="MONDO:equivalentTo", source="Orphanet:1358", source="MONDO:ncbi_mim2gene_medline", source="OMIM:254940"} relationship: excluded_subClassOf MONDO:0015160 {source="Orphanet:1358"} ! multiple congenital anomalies/dysmorphic syndrome-variable intellectual disability syndrome relationship: excluded_subClassOf MONDO:0015335 {source="Orphanet:1358"} ! orofacial clefting syndrome relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/33778 {source="MONDO:mim2gene_medgen"} ! MYMK is_a: MONDO:0031415 {source="OMIM:254940"} ! Carey-Fineman-Ziter syndrome property_value: seeAlso https://rarediseases.info.nih.gov/diseases/3889/carey-fineman-ziter-syndrome xsd:anyURI {source="GARD:0003889"} property_value: IAO:0000233 https://github.com/monarch-initiative/mondo/issues/5619 xsd:anyURI relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql

[Term] id: MONDO:0031632 name: developmental delay with short stature, dysmorphic facial features, and sparse hair xref: OMIMPS:616901 {source="MONDO:equivalentTo"} ! developmental delay with short stature, dysmorphic facial features, and sparse hair is_a: MONDO:0003847{ source="OMIMPS:616901"} ! Mendelian disease relationship: has_characteristic MONDO:0021152 {source="OMIMPS:256550"} ! inherited property_value: IAO:0000233 https://github.com/monarch-initiative/mondo/issues/5619 xsd:anyURI relationship: has_characteristic MONDO:0021152 {source="OMIMPS:616901"} ! inherited

[Term] id: MONDO:0800438 name: developmental delay with short stature, dysmorphic facial features, and sparse hair 1 subset: ordo_malformation_syndrome {source="Orphanet:459061"} synonym: "DEDSSH1" EXACT ABBREVIATION [OMIM:616901] synonym: "developmental delay with short stature, dysmorphic facial features, and sparse hair" EXACT [OMIM:616901, OMIM:genemap2] synonym: "developmental delay with short stature, dysmorphic features, and sparse hair 1" EXACT [OMIM:616901] synonym: "developmental delay-short stature-dysmorphic features-sparse hair syndrome" EXACT [Orphanet:459061] synonym: "Loucks-Innes syndrome" RELATED [OMIM:616901] synonym: "diphtamide deficiency syndrome" EXACT [OMIM:616901] xref: OMIM:616901 {source="Orphanet:459061", source="MONDO:equivalentTo", source="Orphanet:459061/e"} xref: Orphanet:459061 {source="MONDO:equivalentTo"} xref: UMLS:C4310801 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline"} relationship: excluded_subClassOf MONDO:0000508 {source="MONDO:Redundant", source="Orphanet:459061"} ! syndromic intellectual disability relationship: excluded_subClassOf MONDO:0015159 {source="Orphanet:459061"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability relationship: excluded_subClassOf MONDO:0018454 {source="MONDO:0019710-obsoleted", source="https://github.com/monarch-initiative/mondo/pull/2571/"} ! dysostosis of genetic origin is_a: MONDO:0031415 {source="OMIM:616901"} ! developmental delay with short stature, dysmorphic facial features, and sparse hair relationship: has_characteristic MONDO:0021136 {source="MONDO:0015162", source="MONDO:0015983"} ! rare relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/3003 {source="MONDO:mim2gene_medgen"} ! DPH1 property_value: IAO:0000233 https://github.com/monarch-initiative/mondo/issues/4521 xsd:anyURI relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql

sabrinatoro commented 1 year ago

@nicolevasilevsky be aware that some new IDs have been used for other terms between when this issue was created and now. For instance, MONDO:0800386 was to be used for 'Carey-Fineman-Ziter syndrome 1'. However, it has been used recently for 'organophosphate poisoning'. The main problem is that, when preparing for the obsoletion of MONDO:0009700(Carey-Fineman-Ziter syndrome), users would use the ID shown in the comments, ie MONDO:0031415 or MONDO:0800386 which is not the correct id anymore. Same for :

TO DO: since these ID have already been used for new terms (which were already released), we need to assign new ids for these post-splits terms and update the comments for the obsoletion candidate

PS: I did not update anything at this point, because I don't know where the master for this id range is, and I don't want to add to the confusion.

ValWood commented 1 year ago

It seems that https://monarchinitiative.org/disease/MONDO:0014824 is split into 2 terms. Do both of these terms apply to DPH1? I can't trace this info and the new term is not yet in OLS.

nicolevasilevsky commented 1 year ago

there is: MONDO:0031632 'developmental delay with short stature, dysmorphic facial features, and sparse hair', which is equivalent to OMIMPS:616901

and MONDO:0800438 developmental delay with short stature, dysmorphic facial features, and sparse hair 1, which is equivalent to OMIM:616901 and is associated with the DPH1 gene variation

ValWood commented 1 year ago

right so it shouldn't be replace by ? should be consider ? (I would need MONDO:0800438 not MONDO:0031632 to be specific for DPH1 ortholog.

nicolevasilevsky commented 1 year ago

Good point, I will change this to consider. Thanks!