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monarch-initiative / monarch-disease-ontology-RETIRED

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Review classification of X-linked intellectual disability - hypotonic face in MonDO #87

Closed nicolevasilevsky closed 6 years ago

nicolevasilevsky commented 8 years ago

image

http://purl.obolibrary.org/obo/Orphanet_93971

nicolevasilevsky commented 8 years ago

image

I think the problematic part is with these terms.

All of these orphanet terms are synonyms of the OMIM term, so I think the three orphanet terms are equiv?

http://www.omim.org/entry/309580 Synonyms: SMITH-FINEMAN-MYERS SYNDROME 1; SFM1 SFMS XLMR-HYPOTONIC FACIES SYNDROME CARPENTER-WAZIRI SYNDROME CHUDLEY-LOWRY SYNDROME JUBERG-MARSIDI SYNDROME; JMS HOLMES-GANG SYNDROME MENTAL RETARDATION, X-LINKED, WITH GROWTH RETARDATION, DEAFNESS, AND MICROGENITALISM

cmungall commented 8 years ago

how it looks in the latest

img-orphanet_93971

clearly the link with p=0.02 is wrong, should be equivalent. It's being forced to make this due to a high weighting between the ordo and the mesh due to the ordo assignment being E. See #139 - we should downweight these ordo xref categories.

For now we just override it - force equivalence between the mesh and omim with p=1