Wrong gene annotation for ENSG00000135070 (ISCA1)

[h-escoffier]

Description

The annotation of gene ENSG00000135070 (ISCA1, iron-sulfur cluster assembly 1) appears to contain incorrect field values for uniprot, hgnc.symbol, and ncbigene. The UniProt accession Q9BUE6 has been placed under the ensembl list, and the uniprot, hgnc.symbol and ncbigene fields contain swapped/incorrect values.

This appears to be present across the files: genes.tsv, Human-GEM.xml, Human-GEM.xlsx.

---

Current annotation

{
  'sbo': 'SBO:0000243',
  'ensembl': ['ENSG00000135070', 'ENST00000375991.9', 'ENST00000326094.4', 'ENST00000311534.6', 'ENST00000637705.1', 'Q9BUE6'],
  'uniprot': 'ISCA1',
  'hgnc.symbol': '81689',
  'ncbigene': 'iron-sulfur cluster assembly 1'
}

Expected annotation

{
  'sbo': 'SBO:0000243',
  'ensembl': ['ENSG00000135070', 'ENST00000375991.9', 'ENST00000326094.4', 'ENST00000311534.6', 'ENST00000637705.1'],
  'uniprot': 'Q9BUE6',
  'hgnc.symbol': '28660',
  'ncbigene': '81689'
}

---

Changes

Field	Before	After
ensembl	included Q9BUE6 (UniProt accession)	transcript IDs only
uniprot	ISCA1	Q9BUE6
hgnc.symbol	81689	28660
ncbigene	iron-sulfur cluster assembly 1	81689

---

References: UniProt | HGNC | NCBI

I have already applied the fix across affected files in a dedicated branch on my fork and can open a pull request if that would be helpful.

Best,
Hugues

[edkerk]

Thank you for reporting and resolving the issue as well. Please open a PR so this can be applied directly.

[h-escoffier]

I've opened a PR (#1018)
Please let me know if anything needs to be changed or if there are any issues with it !

The PR is targeting the main branch instead of develop (as recommended in the contributing guidelines), as the files I modified (genes.tsv, Human-GEM.xml, Human-GEM.xlsx) don't seem to exist in the develop branch. I hope this is not an issue !

[edkerk]

In #1018 it appears that you worked on a branch coming from main, but it really should be coming from develop. I noticed that you forked only the main branch in your personal repo, you can add the develop branch this way (run in your local human-GEM folder):

git remote add upstream https://github.com/SysBioChalmers/human-GEM.git
git fetch upstream develop
git checkout -b develop upstream/develop
git push origin develop

While being in the develop branch you can then create a new branch. In #1018 I suggested to rebase, but I actually suggest you to make a new branch for the following reason:

The XLSX and XML files are only generated in the main branch, during development we only have one model version (YAML) to make sure that we don't forgot making edits in one model file and not the other. But the changes you suggest are actually on annotations, which are not stored in the YAML file but in the genes.TSV file. This file you can find in the develop branch (and therefore also in your new branch that comes from develop): https://github.com/SysBioChalmers/Human-GEM/blob/develop/model/genes.tsv. So please make the edit there and then open a new PR.

Thank you for your help!

[h-escoffier]

I've opened a new PR (#1019) targeting the develop branch this time. I hope everything is good now :)

Feel free to reach out if anything needs to be adjusted, I'm happy to help !