allele synonyms are not loaded

[ValWood]

The allele synoyms column is currrently empty.

Please ping @kimrutherford if you need any info.

[kimrutherford]

The allele synonyms aren't in the PHAF file. I've opened an issue: pombase/pombase-chado#966

[ValWood]

ACTIONS

• [x] @kimrutherford add synonyms to PHAF
• [x] @danielabutano load synonyms
• [ ] @ValWood add synonym field to (some) allele query tables.
• Useful test gene cut12 (See "All alleles of a gene" template) stf1-1 is a synonym of cut12.s11 (G71V).
• [ ] @ValWood Also in current load cut12-G71V also exists. I have standardized on cut12.s11 which is the most common usage. check.

[kimrutherford]

@kimrutherford add synonyms to PHAF

The PHAF files now have synonyms in the Allele synonym column: https://curation.pombase.org/dumps/latest_build/pombase-latest.eco.phaf.gz

[kimrutherford]

The PHAF files now have synonyms in the Allele synonym column:

I forgot to say: if there are multiple synonyms for an allele, they are pipe ("|") separated. We chose pipes because some synonyms contain commas.

[danielabutano]

Hi @kimrutherford, the data downloader script uses this file https://www.pombase.org/data/annotations/Phenotype_annotations/phenotype_annotations.pombase.phaf.gz DO you think it's possible to update this file too? Thnaks!

[kimrutherford]

Ah, sorry. I thought you we getting the phenotype annotations from https://curation.pombase.org/dumps/latest_build/pombase-latest.eco.phaf.gz because of this issue: https://github.com/pombase/pombase-chado/issues/869

I've now updated: https://www.pombase.org/data/annotations/Phenotype_annotations/phenotype_annotations.pombase.phaf.gz

[ValWood]

I see the allele synonyms loaded OK.