Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Devise strategy for dealing with deprecated gene identifiers (ENSEMBL) #93

Open
2 tasks
dosumis opened this issue May 13, 2021 · 1 comment
Open
2 tasks
Assignees

Comments

@dosumis
Copy link
Contributor

dosumis commented May 13, 2021

These markers are in the analysis but are deprecated.

see https://github.com/obophenotype/brain_data_standards_ontologies/actions/runs/820006328

These are deprecated
ensembl:ENSMUSG00000100851 couldn't find in ensmusg.tsv
ensembl:ENSMUSG00000096972 couldn't find in ensmusg.tsv

ENSEMBL GUI is not too useful
https://www.ensembl.org/Mouse/Search/Results?q=ENSMUSG00000100851;facet_species=Mouse

  • Is there some way to use ENSEMBL API or some other API to automatically map forwards? - or to suggest mappings?
  • These are not in the ensmusg.tsv - reference from @jeremymiller - investigate whether there is a more up to date analysis corresponding to ensmusg.tsv ? - Also this file should have version metadata (try to dig this out).
@shawntanzk
Copy link
Collaborator

shawntanzk commented May 13, 2021

Found it by googling, but of course doesn't solve the underlying issue

ENSMUSG00000100851 | Gm28928 | http://angiogenes.uni-frankfurt.de/gene/ENSMUSG00000100851
ENSMUSG00000096972 | Gm26883 | http://angiogenes.uni-frankfurt.de/gene/ENSMUSG00000096972

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants