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PHI-base / PHI5_web_display

PHI5_web_display will allow to display PHI-Canto data
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Wild type host genotypes should be displayed as 'wild type' #52

Closed jseager7 closed 2 years ago

jseager7 commented 2 years ago

Host section

In the latest version of PHI-base 5, in the Host section of the gene page, host genotypes with no genes are wrongly displayed using their internal identifier from the PHI-Canto JSON export. For example:

Arabidopsis-thaliana-wild-type-genotype-ecotype-Landsberg-erecta

In these cases, the string "wild type" should be used instead of the internal identifier. Here's a mockup:

image

(Note that I'm not sure whether we originally planned to include wild type host genotypes in the Host section, since they cannot be linked to any host gene page. I will confirm this with the rest of the PHI-base team.)

Metagenotype display names

Also, in the display names for metagenotypes, hosts with no genes are displayed with the string "(wild_type)", which is an allele type instead of a genotype name. For example:

TRI5+ (wild_type) [Wild type product level] F. graminearum (PH-1) | (wild_type) T. aestivum (cv. Bobwhite)

The correct display is simply "wild type", followed by the scientific name.

TRI5+ (wild_type) [Wild type product level] F. graminearum (PH-1) | wild type T. aestivum (cv. Bobwhite)

Note also that there should only be one space between the string "wild type" and the scientific name: the current display has two spaces.

jseager7 commented 2 years ago

Unless this is already done, I'm going to close this as not planned since we've changed our mind on what information should be shown in the Pathogen and Host sections: we just want to show the interacting gene(s) instead of the genotype. I'll open a new issue for the new design.