Use ontology term for gene symbol search

[Relequestual]

A few times in the Schemas, a gene is mentioned, and it is implied the HGNC name is used, however it is not explicitly stated. I, and I think others, are not especially confident in using HGNC names as the defacto standard. One immediate problem is that you now cannot query HGNC for genes on grch37, and only grch38 genes are returned. (I mean, a gene that is valid in 37 will redirect to a gene in 38, which is not in 37. Obviously a problem for those not using 38).

In the Matchmaker Exchange group, I have just brought this to our attention, and we've had some discussions on this. HGNC genes are updated with the "whenever" release cycle methodology. Ensembl has a regular 2-3 monthly release. There are problems with both data sources, but we're already in a non ideal situation. (It's difficult to get gene names for grch37 only genes from HGNC, as far as I am able to tell) _I elaborate on this more in the following issue in the MME repo:_

_ga4gh/mme-apis#113_

There was a previous parrallel discussion regarding how to represent phenotypes. The main problem raised with HPO is the lack of stable releases. We couldn't agree on this being a problem or not, but personally I feel that expecting everyone to update reference data on a nightly cycle is unreasonable. /sidebar

I struggle to believe this is a problem that someone else hasn't thought about and at least attempted to solve. I'd like thoughts and comments on this, even if suggestions are not 100% solid, to generate discussion.

A polite reminder to please try to stay on topic with your replies, and not diverge from the issue at hand.

[david4096]

The genesymbol search in sequence annotations currently accepts a string. This should be upgraded to an ontology term so that a constrained vocabulary can be used.