Add endpoint to search for gene(s) given chr/assmebly or accession and start/end coordinates.
Use case
This would be a nice feature to have for VarCat/Variation Normalizer. We need to update Variation Normalizer genomic GRCh38 -> protein endpoint to include the associated gene context. My first approach was to just use MANE data. However, not all genes are included in MANE data.
Proposed solution
Create a GET /gene/search/locations endpoint or something similar that will search for genes given location coordinates.
Alternatives considered
I thought about using UTA, but I think we'd run into issues where genes live in intronic space before first exon and after last exon. I talked with @jarbesfeld and he seems to agree.
Feature description
Add endpoint to search for gene(s) given chr/assmebly or accession and start/end coordinates.
Use case
This would be a nice feature to have for VarCat/Variation Normalizer. We need to update Variation Normalizer genomic GRCh38 -> protein endpoint to include the associated gene context. My first approach was to just use MANE data. However, not all genes are included in MANE data.
Proposed solution
Create a
GET /gene/search/locationsendpoint or something similar that will search for genes given location coordinates.Alternatives considered
I thought about using UTA, but I think we'd run into issues where genes live in intronic space before first exon and after last exon. I talked with @jarbesfeld and he seems to agree.
Implementation details
No response
Potential Impact
I think we'll have to add new GSI in DynamoDB
Additional context
No response
Contribution
Yes, I can create a PR for this feature.