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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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synpolydactyly same as Polysyndactyly ? #3919

Closed kanems closed 2 years ago

kanems commented 3 years ago

Mondo term (ID and Label) synpolydactyly MONDO:0021651

Synonym to be added Polysyndactyly (Maybe?? the definitions seem to be the same, but maybe I am missing some nuance.) Synonym subtype: ie, broad/exact/narrow/related exact

Database cross reference for the synonym Such as PubMed ID (in the format PMID:XXXXXX) or a cross-reference to another ontology, like OMIM or Orphanet.

NCI, Polysyndactyly (C125597) "DEFINITION: A rare anatomical malformation characterized by polydactyly (extra fingers or toes) and syndactyly (webbed fingers or toes)."

Also SNOMED_CT 84598000 and UMLS CUI C0265553 map with the NCI code and definition above in Metathesaurus.

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nicolevasilevsky commented 3 years ago

Let's ask @pnrobinson and @ahamosh.

These seem to be synonymous to me too but there are separate Wikipedia pages for these terms (https://en.wikipedia.org/wiki/Polysyndactyly and https://en.wikipedia.org/wiki/Synpolydactyly) and I can't find any reference to these being used synonymously.

ahamosh commented 3 years ago

So synpolydactyly is used more frequently. The separate entity in Wikipedia for polysyndactyly is used for crossed polysyndactyly where it is one family with post-axial polydactyly of the hands and pre-axial polydactyly of the feet. That is null entry in OMIM. The other polysyndactyly entries in OMIM are syndromic.

kanems commented 3 years ago

Just adding this for reference... NCI seems to distinguish between these two terms with regard to 1. cause and 2. disease vs. phenotype. So these are not equivalent it seems. MedGen will have to make CN identifier for synpolydactyly parent concept, UMLS has no appropriate CUI for it.

https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=21.10d&ns=ncit&code=C75003&key=n115691217&b=1&n=null "Preferred Name: Synpolydactyly

Definition: A rare genetic disorder characterized by malformations in the hands and feet. The abnormalities include increased number of fingers and toes and fusion of digits into one large digit." (Genetic variation causes this, subtypes are listed in OMIM associated with HOXD13, FBLN1, etc) NCI points to UMLS C2699746, but this is the entry for the syndromic type 1 form. UMLS does not appear to have a separate cui for the concept of synpolydactyly that isn't linked to a specific gene.

https://ncithesaurus.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&version=21.10d&code=C125597&ns=ncit&type=properties&key=null&b=1&n=0&vse=null "Preferred Name: Polysyndactyly

Definition: A rare anatomical malformation characterized by polydactyly (extra fingers or toes) and syndactyly (webbed fingers or toes)." (Agnostic of cause, just the clinical finding/observation) Maps to UMLS C0265553 but NCIT points to C3808274 (UMLS merged that into the other CUI in 2020 release)

nicolevasilevsky commented 2 years ago

Thanks @kanems. I will look at this more closely asap.

sabrinatoro commented 2 years ago

@nicolevasilevsky looking at Mondo, things are slightly more complicated... So I want to double check: 1) adding synonym and references: NCIT C125597 ("Preferred Name: Polysyndactyly") SNOMED_CT 84598000 UMLS CUI C0265553 → all of these are Mondo:equivalentTo to polysyndactyly 4 (MONDO:0008272)

Should I

2) classification:

pnrobinson commented 2 years ago

The two terms are synonymous, but I would suggest that we revise the primary labels in MONDO. For instance, now the names of the children of this term in the definition are not the same as the names of the child terms https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0017425&viewMode=PreferredRoots&siblings=false

Also, I think it is not accurate that these diseases are "just" hands, as suggested by "preaxial polydactyly of fingers"

nicolevasilevsky commented 2 years ago

@sabrinatoro I agree with your plan of action, please go ahead.

Also, could you look at 'synpolydactyly type 1' and 'synpolydactyly type 3', they are children of 'syndactyly type 2', which seems odd.

sabrinatoro commented 2 years ago

I think syndactyly type 2 (MONDO:0019683) - (has_exact_synonym : synpolydactyly) should be merged into synpolydactyly (MONDO:0021651)

New issue: #4285