bridgedb / bridgedb/datasources

Unclear origin of the UCSC genome browser "uc\d{3}[a-z]{3}\.\d" type identifier

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Dominant language
Python
Stars
4
Forks
8
PR merge metrics
No merged PRs in 30d

Description

Following up from https://github.com/bridgedb/datasources/issues/2 and [consulting the UC genome browser team](https://twitter.com/GenomeBrowser/status/1392173934250913793) ("I cannot find any gene with that identifier, so that may be the problem"), it is unclear what the correct fix is for the issue. The link out points out the browser directly, but either takes a gene name (like TP53) or a chromosal position. See also http://genome.ucsc.edu/FAQ/FAQlink.html#genes

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with the linked BridgeDb issue, the UC Genome Browser team's response, and the UCSC gene-linking FAQ to establish what the identifier represents and which target format is supported. Done means the expected identifier and correct UCSC link behavior are confirmed, with an agreed fix identified for the data source.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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