Include species and strain in Pathogen Phenotype and Host Phenotype

[jseager7]

I've noticed that the genotype names in the Pathogen Phenotype and Host Phenotype sections do not include the species name or strain name. The strain name can't be seen in the pop-up details either.

It's technically redundant to include the species name (since the gene page can only contain one pathogen or host species), but I still think it would be better to include the species name because it makes the meaning of the strain name more obvious.

To illustrate, here's a Pathogen Phenotype example from PHIG:255.

I'm suggesting we include the species name and strain name in the genotype name…

…and also in the details pop-up.

We'd also want to do the same for Host Phenotype annotations. Here's an example for PHIG:276.

Before:

After:

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@CuzickA @martin2urban Do you agree with this?

[jseager7]

Also, I think the details pop-up should really include the strain name as well, but since this problem also affects other sections like PHI Phenotype, it would be better placed in a separate issue. Here's a mockup anyway:

[CuzickA]

I agree with this. We definitely need to show the strain in the genotype and I'm happy to include the species name to make the entries more uniform. I was also going to point out that it seems odd not to have the strain in the pop-up.

[jseager7]

This has been fixed by issue #79.

[jseager7]

@jashobanta-mcpl I'm reopening this issue since the genotype display names in the pathogen and host sections are still not showing the species and strain names. For example, on PHIG:255:

We expected the genotypes to be displayed as follows:

noxA::pAN7-1 (disruption) E. festucae (Fl1) noxA::pAN7-1 (disruption) [Not assayed] E. festucae (Fl1) noxAdelta (deletion) E. festucae (Fl1)

As a reminder, the general pattern is:

allele_name (allele_type) [expression] species_name (strain)

And expression may be optional.

The species and strain are already shown in the genotype details popup, so hopefully it should be possible to show them in the genotype display name.

[jseager7]

This is now fixed for pathogen phenotypes:

(See also: PHIG:258 and PHIG:264)

Also fixed for host phenotypes:

(See also: PHIG:276)