jseager7
commented
2 years ago We've decided on the following:
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For pathogen gene pages:
- The Pathogen section should show a list of all pathogen strains that have annotations involving the gene of the gene page.
- The Host section should display a list of genes, plus the scientific name and NCBI Taxonomy ID, of any host that interacts with the pathogen (as part of a metagenotype). Wild type host genotypes (genotypes with no genes) will presumably not be included now.
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For host gene pages:
- The Host section should show a list of all host strains that have annotations involving the gene of the gene page.
- The Pathogen section should display a list of genes, plus the scientific name and NCBI Taxonomy ID, of any pathogen that interacts with the host (as part of a metagenotype).
I'll create new mockups and instructions for this change in another issue.
Currently, the host gene pages show a list of genotypes in the Host section. The list includes all genotypes that involve the gene specified on the gene page. For example, the gene page for RPP1 of Arabidopsis thaliana (PHIG:276) shows the following genotypes:
However, on the pathogen gene pages, the Pathogen section does not include a list of pathogen genotypes (as one would expect). Instead, the Host section still includes a list of host genotypes that are involved in interactions that include the pathogen gene.
Shown below is the Pathogen and Host sections for ATR1 of Hyaloperonospora arabidopsidis (PHIG:277), which is involved in interactions with RPP1. Note the lack of pathogen genotypes and the missing host genotype names.
My understanding of the original requirements was as follows:
The pathogen gene pages would contain a list of relevant host genotypes in the Host section. The Pathogen section of pathogen gene pages would show a summary of the pathogen species and strains, but would not show any pathogen genotypes.
The host gene pages would contain a list of relevant pathogen genotypes in the Pathogen section. The Host section of host gene pages would show a summary of the host species and strains, but would not show any host genotypes.
There is no need to summarise the pathogen genotypes on pathogen gene pages (and vice versa for hosts) since they are already listed in the other sections.
I believe the original rationale for including genotypes of the opposite role in their own section was so that links could be added to interacting genes from the other side of the interaction (meaning, pathogen gene pages could link to host gene pages and vice versa).
I'll discuss this with the rest of the PHI-base team.