BioDataFuse / BioDataFuse/pyBiodatafuse

StringDB not working with non-human data anymore

Open
#237 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
15
Forks
14
PR merge metrics
No merged PRs in 30d

Description

**Describe the bug**
The StringDB annotator used to be able to work with non-human data, but since recently it only returns the error 'UserWarning: There is no interaction between your input list based on StringDB.', even when using data that used to work before.

**To Reproduce**
These are the identifiers I used to test the annotator.
ENSMUSG00000067274 - (rplp0)
ENSMUSG00000003429 - (rps11)
ENSMUSG00000000740 - (rpl13)
ENSMUSG00000017548 - (rpl19)

Then regularly call the function:
ppi_df, ppi_metadata = stringdb.get_ppi(bridgedb_df=bridgedb_df, species="Mouse")

This will produce the error mentioned above, even though when viewed in the online String database, there should be ppi's here.

![Image](https://github.com/user-attachments/assets/314e3ed6-4f02-4eba-95b5-d47a47db8fe9)

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.