wild type[WT level] alleles should only be allowed in diploid genotypes

[manulera]

@ValWood @kimrutherford

I was doing a CC today and the author has annotated double mutants cdc15+[wt level] pom1-as1[wt level] to capture the fact that in pom1-as1 you have abnormal protein localisation of cdc15. They have used the assayed_using cdc15 extension, so they are aware of it. I guess they wanted to be explicit or did not realise that you can use any gene in the session for assayed_using, even if it's not in the genotype.

In any case, preventing the creation of a double mutant genotype including a wt allele with wt expression in the genotype management window + a good error message might prevent this in the future, and is a good way to show users how the annotation should be done in Canto.

I propose the following error message:

Wild type alleles where expression has not been altered cannot be included in double mutant genotypes. It is implied that all loci that are not mentioned in a genotype contain the wild type allele expressed at the wild type level. To use a gene name in an assayed_using extension, you only need to add the gene to the curation session. For instance, if you want to indicate that deletion of ase1 results in abnormal localisation of peg1, you do not need to include peg1 in the genotype, you can annotate ase1delta -> abnormal protein localisation (assayed_using peg1).

Even more so, I guess we should not allow phenotypes of single allele mutants with wild type[WT level], or diploid loci with both wild type[WT level]? I don't think there is a use case for this, what do you think @ValWood?

[manulera]

Oh I see there is already a warning in the genotype management page:

A wild type allele with wild type product level is only valid in a genotype that has another allele of the same gene.

I guess they ignored it, but should we just not allow it at all?