https://www.ncbi.nlm.nih.gov/medgen/docs/help/
MedGen aggregates multiple disease vocabularies.
UMLS CUIs are used as primary IDs, except where no UMLS concept exists. In these cases, a CN ID is provided.
MedGen does not add new classification (is_a). The UMLS hierarchy is used (there is no hierarchy for CN IDs).
As such, MedGen inherits the issues of the UMLS hierarchy, e.g.
UMLS:C1335042 ! Non-Neoplastic Skin Disorder
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UMLS:C0037274 ! Disease, Skin
With the standard OWL interpretation of SubClassOf, this renders the two concepts equivalent. As our computations use OWL semantics, we can't incorporate UMLS links as axioms without causing collapsing of the graph.
This also means we cannot incorporate the UMLS axioms as hard links into the kBOOM process. One area to explore would be to translate the UMLS links into probabilistic links.
However, this is currently out of scope. For now we cross-reference UMLS IDs (we get these from DOID).
We could add additional xrefs for the CNs. However, these seem to recapitulate what we already have IDs for via OMIM etc. If these CNs are being actively used to annotate useful information we will consider adding these.