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PHI-base / PHI5_web_display

PHI5_web_display will allow to display PHI-Canto data
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Search results table should not use 'Pathogen species' heading #77

Closed jseager7 closed 1 year ago

jseager7 commented 1 year ago

The table on the search results page has a 'Pathogen species' heading, but this column can also contain the species name of the host species, not just the pathogen species. This leads to errors like Homo sapiens being labelled as a pathogen.

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The column heading should be renamed to something generic, like 'Species'.

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(raised by @CuzickA)

jseager7 commented 1 year ago

In today's meeting we confirmed that we only need one column that should show the species of the gene, regardless of whether the species is a pathogen or a host.

That is, we do not need one column for the pathogen species and one column for the host species.

jseager7 commented 1 year ago

Need instructions on how to get the species of the gene from the export, because the column currently only shows the pathogen gene.

jseager7 commented 1 year ago

@jashobanta-mcpl Shown below is an example of a gene object for TPR1 (PHIG:290). The value of the organism property is the species name of the gene, which should be displayed in the 'Species' column. This should work for any gene, pathogen or host.

"genes": {
  "Oryza sativa Q5NBT9": {
    "organism": "Oryza sativa",  // species name
    "uniquename": "Q5NBT9"
  }
}
jashobanta-mcpl commented 1 year ago

Above instructions is followed and species is getting populated from organism key of gene block .

jseager7 commented 1 year ago

Confirmed as fixed for both pathogen and host genes:

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