[bilalebi]

Changes

Make the transcript stable IDs findable in /id/{stable_id} endpoint

Before

Query

https://resolver.ensembl.org/id/ENSTJET00000010396

Response

{"status_code": 404, "details": "Not Found"}

After

Query

http://localhost:8001/id/ENSTJET00000010396

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

http://localhost:8001/id/ENSTJET00000010396?type=gene

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:

http://localhost:8001/id/ENSWGJP00000002679?type=protein

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"
  }
]

1. Will we ever have such views?

• http://www.ensembl.org/feature-explorer/010ac724-e482-4d86-b40c-c756b2ed2271/protein:ENSWGJP00000002679
• http://www.ensembl.org/genome-browser/010ac724-e482-4d86-b40c-c756b2ed2271?focus=protein:ENSWGJP00000002679

2. This PR doesn't handle proteins yet because it requires changes in the fm_stable_ids_extractor as well as re-indexing

To 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 /id to 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:

ENSWGJP00000002679
Hit! ENSWGJP00000002679
Value: 010ac724-e482-4d86-b40c-c756b2ed2271|protein

Eventually becomes

ENSWGJP00000002679
Hit! ENSWGJP00000002679
Value: 010ac724-e482-4d86-b40c-c756b2ed2271|protein|TRASCRIPT_ID_GOES_HERE

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?