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