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Allow combining single-allele genotypes from different organisms #1826

Closed kimrutherford closed 5 years ago

kimrutherford commented 5 years ago

From #1818:

Every now and then there are multi-allele genotypes that combine genes/alleles of different species.

Canto will need to know which organism to attach to the new multi-organism genotype. eg. was a fly gene inserted into cerevisiae or vice versa?

Let's chat about this next time.

kimrutherford commented 5 years ago

I think this has a lot of overlap with #826. Am I understanding that correctly?

vmt25 commented 5 years ago

From #1818:

Every now and then there are multi-allele genotypes that combine genes/alleles of different species.

Canto will need to know which organism to attach to the new multi-organism genotype. eg. was a fly gene inserted into cerevisiae or vice versa?

The host organism is always Drosophila melanogaster.

Let's chat about this next time.

Sounds good

vmt25 commented 5 years ago

I think this has a lot of overlap with #826. Am I understanding that correctly?

It is related but different.

Anyways, at a first glance it seems to have been fixed by the original #1818 ticket - I managed to make a phenotype annotation to a mixed species genotype (https://curation.pombase.org/flybase-test/curs/33dac4236dd1bfdb/feature/genotype/view/14) (apologies - working on Kim's test sessions and pretending to be him)

The way FlyBase handles interspecies complementation is by phenotypic genetic interactions e.g.: a Dmel mutant gives phenotype A, which is suppressed by a mouse/cerevisiae ortholog transgene

This kind of relational genetic interactions is complicated and should be discussed and left for later discussion/ticket

FlyBase also includes intra-species complementation which, from reading #826, seems to be the same as PHI-Base's complementation annotation. Again, this should prob be left for later discussion/ticket.

kimrutherford commented 5 years ago

I managed to make a phenotype annotation to a mixed species genotype

At the moment it's not always going do the right thing. The organism referenced by the new multi-allele genotype won't be consistent.

kimrutherford commented 5 years ago

We decided the solution is to set the organisms of all genotypes to Dmel while loading. Then we don't have to worry about mixing organisms.

kimrutherford commented 5 years ago

We decided the solution is to set the organisms of all genotypes to Dmel while loading. Then we don't have to worry about mixing organisms.

That's done now. The load script ("canto_add.pl") now has a taxon ID argument to set the organism of all genotypes.