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geneontology / panther-enrichment

One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.
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How to keep the genomes consistent in the drop-down menu #7

Open huaiyumi opened 6 years ago

huaiyumi commented 6 years ago

Between each release, PANTHER add/delete genomes for various reasons. In our next release, 18 more plant genomes will be added. Currently the drop-down menu contains the list of organisms from PANTHER12 while the current release is v.13.1. We need to work out a way to keep them consistent. The easiest is probably to retrieve the list from our database through webservice.

huaiyumi commented 5 years ago

I opened this ticket. It is a question to the GO website, because it has a different list of organism that those in the PANTHER site.

huaiyumi commented 5 years ago

@cmungall Please have someone in your group contact Dustin or Anushya about how to retrieve the list of organisms correctly from PANTHER so that they are consistent.

cmungall commented 5 years ago

@lpalbou did you write the code that provides the list?

lpalbou commented 5 years ago

There were two tickets about the go site species dropdown list: https://github.com/geneontology/go-site/issues/963 and https://github.com/geneontology/go-site/issues/966.

I used Anushya API call to get the current list of PANTHER species and updated the HTML page accordingly (Seth original list was static, so I just updated the species name & links). There should be no difference today between PANTHER species and those shown in this dropdown list, except if they have been updated in the past few days.

But this is indeed not an automated approach and I thought those species only changed once a year for PANTHER release. If it changes every month, the site must do an API call to fetch the list and populate the dropdown list every time it loads. @huaiyumi @cmungall please confirm that's what you want ?

Note that as discussed, I would prefer to avoid any dynamic data / UI manipulation on a site without framework.