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multi-allele genotypes and phenotypes #42

Closed ValWood closed 2 years ago

ValWood commented 2 years ago

Is there a way to load multi-allele genotypes and phenotypes? We have glossed over this data so far in our discussions but I am assuming that it is done for some other species?

It isn't a high priority but it is something we would probably ly want to do if it were available.

kimrutherford commented 2 years ago

PombeMine loads our PHAF file: https://curation.pombase.org/dumps/latest_build/pombase-latest.eco.phaf.gz which only contains single allele phenotypes.

Multi allele/locus export isn't implemented yet: https://github.com/pombase/curation/issues/693

ValWood commented 2 years ago

Yes we need a suitable exchange format for multi-gene genotypes. I would like to speak to @cmungall about this because we don't want to roll our own.

kimrutherford commented 2 years ago

We'll need to implement stable IDs for alleles and genotypes before we can export multi- locus/allele genotypes and phenotypes.

This is related: pombase/pombase-chado#840

ValWood commented 2 years ago

Until a format exists, this is impossible. Also not high-priority. Closing