Feature/mgi projections

[vinay-ebi]

Summary

PR updates the GeneNameDescProjection_conf pipeline configuration to ensure gene names and descriptions from canonical mouse (mus_musculus) are projected into all mouse strains.

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Changes

• Extended gn_config:
  • Removed mouse strains from anti-species
  • Taxonomy Myomorpha covers all the mouse strains

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Rationale

• Provides consistent gene naming and descriptions across mouse reference and strain assemblies.

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Example

For a gene annotated in mus_musculus with:

• Name: Pten (from MGI)
• Description: phosphatase and tensin homolog

It will now be projected automatically into all configured strains (129s1svimj, balbcj, c57bl6nj, etc.).

[nwillhoft]

Thanks Vinay. Please could I check with the addition of danio rerio to the antispecies - are we wanting to prevent projections onto zebrafish?

[vinay-ebi]

Thanks Vinay. Please could I check with the addition of danio rerio to the antispecies - are we wanting to prevent projections onto zebrafish?

Yes, zebrafish has its own zfin ID. We don't want to override with HGNC ID, We fixed this in release 115 with these changes, but we have not pushed these changes.

Release 114:
+--------------------+-------------+-----------------------+--------------------+
| ensembl_gene_id | gene_symbol | gene_symbol_source_db | gene_symbol_source |
+--------------------+-------------+-----------------------+--------------------+
| ENSDARG00000000563 | TTN | HGNC | HGNC:12403 |
+--------------------+-------------+-----------------------+--------------------+
Release 115:
+--------------------+-------------+-----------------------+---------------------+
| ensembl_gene_id | gene_symbol | gene_symbol_source_db | gene_symbol_source |
+--------------------+-------------+-----------------------+---------------------+
| ENSDARG00000000563 | ttn.1 | ZFIN_ID | ZDB-GENE-030616-413 |
+--------------------+-------------+-----------------------+---------------------+

[nwillhoft]

All looks good for projecting onto mouse strains, and removing projection onto zebrafish.