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ga4gh / va-spec

An information model for representing variant annotations.
Apache License 2.0
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Oncogenicity mechanism value set #28

Open mbrush opened 5 years ago

mbrush commented 5 years ago

In recent calls, we decided that the mechanism by which an oncogenic variant contributes to disease should be captured as a qualifier on a Variant Oncogenicity Annotation. There was much debate about the choice of terms to use to capture the mechanism. This ticket will hold discussion on this topic.

To summarize briefly: we initially started with the set of terms CIViC uses to capture the outcome of a Biological Assertion: gain of function, loss of function, neomorphic, unaltered function, other . However there is additional nuance/granularity that may be useful to capture that is not reflected in this list. The concepts outlined in Muller's morph classification were highlighted in particular

@arpaddanos agreed to take a pass at defining a set/hierarchy of terms based on these and other sources (e.g. it may be worth looking across existing knowledgebases and cataloging the terms/concepts they use).

mbrush commented 5 years ago

Terms in this space used by a couple model organism databases are referenced in the GENO ontology ticket here: https://github.com/monarch-initiative/GENO-ontology/issues/3. May or may not be useful for this work.