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monarch-initiative / deprecated-human-disease-ontology

Deprecated, see README
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add medgen disease id mappings #4

Closed nlwashington closed 9 years ago

nlwashington commented 9 years ago

please add medgen ids to the uberdisease ontology for xrefs. these will be useful for linking with clinvar data. http://www.ncbi.nlm.nih.gov/medgen/docs/faq/#rel

also found this possibly relevant: ftp://ftp.ncbi.nih.gov/pub/medgen/MedGen_HPO_OMIM_Mapping.txt.gz

ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen

also see related https://github.com/monarch-initiative/disease-miner/issues/5 and https://support.crbs.ucsd.edu/browse/NIF-11766

nlwashington commented 9 years ago

Also note that the medgen-to-omim (and other vocab) mappings here can't be trusted as equivalence classes. For example, for Hermasky-Pudluck syndrome, http://beta.neuinfo.org/mynif/search.php?q=DOID_3753&dis=Hermansky-Pudlak%20syndrome&t=indexable&nif=nlx_151671-4&b=0&r=20 it has several subtypes; each one maps to GeneReviews:NBK1287, which is for a general type of Hermansky-Pudlak.

mellybelly commented 9 years ago

yeah i think i would want to manually review all medgen xrefs...

cmungall commented 9 years ago

This issue was moved to monarch-initiative/monarch-disease-ontology#8