DC for sensory ataxia?

[nicolevasilevsky]

From @cmungall on March 13, 2015 6:31

Should we have a DC to cluster the two OMIMs (brown) here?

Copied from original issue: monarch-initiative/human-disease-ontology#12

[nicolevasilevsky]

From @mellybelly on March 14, 2015 22:52

I think the 'sensory ataxic neuropathy, dysarthria, and opthalmoparesis' term is a compound term, where we may want a higher level parent, though in this case there might not be one as it isn't necessarily solely nervous system disease.

Orphanet_70595 (yellow to the left) is a superclass of the OMIM term that has almost the same label though, these are likely the same disease and are mutually xrefed. Merge these?

[nicolevasilevsky]

From @pnrobinson on March 15, 2015 9:22

Note that diseases by their very nature are compound terms, so to speak, and so in a disease ontology, http://www.omim.org/entry/607459 is perfectly fine. Not sure whether I understand? -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

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Von: Melissa Haendel [notifications@github.com] Gesendet: Samstag, 14. März 2015 23:52 An: monarch-initiative/human-disease-ontology Betreff: Re: [human-disease-ontology] DC for sensory ataxia? (#12)

I think the 'sensory ataxic neuropathy, dysarthria, and opthalmoparesis' term is a compound term, where we may want a higher level parent, though in this case there might not be one as it isn't necessarily solely nervous system disease.

Orphanet_70595 (yellow to the left) is a superclass of the OMIM term that has almost the same label though, these are likely the same disease and are mutually xrefed. Merge these?

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/human-disease-ontology/issues/12#issuecomment-80751531.

[nicolevasilevsky]

From @mellybelly on March 15, 2015 14:45

only that for these we talked about a higher level subsumer until we can auto classify based upon the phenotypes. I think we should define some manual curation rules for what to do in cases like this one. for now they just hang out at root, basically.

[nicolevasilevsky]

From @cmungall on March 15, 2015 20:39

Orphanet_70595 (yellow to the left) is a superclass of the OMIM term that has almost the same label though, these are likely the same disease and are mutually xrefed. Merge these?

Currently the merge rules are quite conservative. The reason a merge doesn't happen here is because ORDO xrefs the OMIM ID from two distinct classes that are siblings. If we merged the OMIM into one parent, then we either lose the dual classification, or we rewire the hierarchy of ORDO, which would be rude and dangerous.

[Term]
id: Orphanet:254881
name: Spinocerebellar ataxia with epilepsy
synonym: "Mitochondrial spinocerebellar ataxia with epilepsy" EXACT []
synonym: "MSCAE" EXACT []
synonym: "SCAE" EXACT []
***xref: OMIM:607459
is_a: Orphanet:377788 {http://purl.obolibrary.org/obo/ECO_0000218=""} ! disease
relationship: has_AgeOfOnset Orphanet:108943 ! Adolescence / Young adulthood
relationship: has_inheritance Orphanet:108933 ! autosomal recessive
relationship: part_of Orphanet:254818 ! Ataxia neuropathy spectrum

[Term]
id: Orphanet:70595
name: Sensory ataxic neuropathy - dysarthria - ophthalmoparesis
synonym: "SANDO" EXACT []
xref: ICD10:G71.3
xref: MESH:C537583
***xref: OMIM:607459
xref: UMLS:C1843851
is_a: Orphanet:377788 {http://purl.obolibrary.org/obo/ECO_0000218=""} ! disease
relationship: has_AgeOfOnset Orphanet:108944 ! Adulthood
relationship: has_inheritance Orphanet:108933 ! autosomal recessive
relationship: has_prevalence Orphanet:108929 ! Unknown
relationship: part_of Orphanet:206966 ! Mitochondrial myopathy
relationship: part_of Orphanet:225700 ! Mitochondrial disease with epilepsy
relationship: part_of Orphanet:225703 ! Mitochondrial disease with peripheral neuropathy
relationship: part_of Orphanet:254818 ! Ataxia neuropathy spectrum