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ga4gh-beacon / beacon-v2-Models

Models that leverage the Beacon Framework v2
Apache License 2.0
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gene and aachange parameters #18

Closed jrambla closed 3 years ago

jrambla commented 3 years ago

So far, we have been looking at Beacon from the genomic allele point of view, but we are having more and more examples of queries based on gene name/symbol and aminoacid substitution. This is in our slide with examples, in the Matchmaker Exchange requests and probably in many rare diseases and oncology use cases. Although the gene name could be addressed by the filtering terms, no so with the aa-change... I've realized that adding both aspects as "named parameters" could make the solution much more straight-forward and, hence, I'm suggesting adding these two parameters in this PR.

antbro commented 3 years ago

Excellent point !

People will definitely want to specify queries via

So I'd like to see this as filter options.

But should the filtering also be required to specify species? I am not sure if Gene Name/Symbol can refer to non-orthologus genes across species, but if they do then we'd need to specify species. Then again, this species filter might be something for the next version?

I am not sure if searching for amino-acid substitution is so urgent. Ot will also be difficult to standardise and implement. Plus do you mean amino acid substitutions anywhere in a gene, or at specific locations? And what about classes of aa change. Or even simple aa presence? This feels like something for next version

Cheers Tony

From: Jordi Rambla @.> Sent: 01 August 2021 08:07 To: ga4gh-beacon/beacon-v2-Models @.> Cc: Brookes, Anthony J. (Prof.) @.>; Review requested @.> Subject: [ga4gh-beacon/beacon-v2-Models] gene and aachange parameters (#18)

So far, we have been looking at Beacon from the genomic allele point of view, but we are having more and more examples of queries based on gene name/symbol and aminoacid substitution. This is in our slide with examples, in the Matchmaker Exchange requests and probably in many rare diseases and oncology use cases. Although the gene name could be addressed by the filtering terms, no so with the aa-change... I've realized that adding both aspects as "named parameters" could make the solution much more straight-forward and, hence, I'm suggesting adding these two parameters in this PR.

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jrambla commented 3 years ago

I was referring to specific locations and changes like BRAF V600E. Although V600* seem viable to me also. I see so many cases where the "user story" starts with such examples that it seems natural to me to have it, although more advanced/sophisticated cases should wait.