intermine / intermine/pombemine

Enrichment should be on genes rather than alleles (required for demo)

Open
#65 0 comments 1 reaction 0 assignees View on GitHub
Dominant language
Java
Stars
0
Forks
1
PR merge metrics
No merged PRs in 30d

Description

Hi,

It isn't useful to do enrichment on alleles, phenotype enrichment should be on genes.
Annotations are made to alleles, but alleles are connected to genes, and enrichment of phenotypes is only useful at the gene level.

I thought this was fixed, and in most cases I think it was by this ticket,
https://github.com/intermine/pombemine/issues/30

but for this query template
Genes-> alleles and phenotypes
i) the enrichment ~is~ uses alleles instead of ~phenotypes~ genes
ii) the GO enrichment is missing

For all lists containing gene lists GO and phenotype enrichment should be present.
Enrichment is not required at all for alleles (it would be misleading).

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with the Genes -> alleles and phenotypes query template and compare its enrichment behavior with issue #30. Done means gene lists provide GO and phenotype enrichment, while allele lists provide neither, and phenotype enrichment uses genes rather than alleles.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.