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Handle transcipt stable IDs - #43
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Changes
Make the transcript stable IDs findable in
/id/{stable_id}endpointBefore
Query
Response
{"status_code": 404, "details": "Not Found"}After
Query
Response
[ { "assembly": { "name": "iyAndPrae1.1", "accession_id": "GCA_963932275.1" }, "scientific_name": "Andrena praecox", "common_name": null, "type": null, "is_reference": false, "stable_id_type": "transcript", "feature_explorer_url": "http://www.ensembl.org/feature-explorer/0a222fd5-5452-4530-b439-fdcbfb984ae1/transcript:ENSTJET00000010396", "genome_browser_url": "http://www.ensembl.org/genome-browser/0a222fd5-5452-4530-b439-fdcbfb984ae1?focus=transcript:ENSTJET00000010396", "release_type": "integrated", "release_name": "2026-07" } ]Also
Returns
{"status_code": 404, "details": "Not Found"}JIRA Ticket
https://embl.atlassian.net/browse/ENSPLAT-287
Questions
Interestingly the code changes assume the protein feature explorer and genome browser links are similar to gene and transcript (which I know it's not correct), for example:
Query:
Returns:
[ { "assembly": { "name": "iyPimRufi1.1", "accession_id": "GCA_963932165.1" }, "scientific_name": "Pimpla rufipes", "common_name": null, "type": null, "is_reference": false, "stable_id_type": "protein", "feature_explorer_url": "http://www.ensembl.org/feature-explorer/010ac724-e482-4d86-b40c-c756b2ed2271/protein:ENSWGJP00000002679", "genome_browser_url": "http://www.ensembl.org/genome-browser/010ac724-e482-4d86-b40c-c756b2ed2271?focus=protein:ENSWGJP00000002679", "release_type": "integrated", "release_name": "2026-07" } ]fm_stable_ids_extractoras well as re-indexingTo construct an appropriate destination URL, the Resolver needs to know the transcript associated with the protein.
The proposed solution as mentioned in JIRA ticket is to extend
/idto resolve protein stable IDs, including the required changes to the MongoDB extraction and redb generation process.For example adding which transcript is associated to each protein, for example this:
Eventually becomes
That will work probably fine though I don't like it tbh, also this raises the question of how we would like to extend it later to include exons?