Gene list provision - Githubissues

Antonialock commented 5 years ago

Provide a table of gene lists on the website.

The table should contain relevant metadata explaining what the gene list consists of similar to the track metadata in JBrowse.

kimrutherford commented 5 years ago

This overlaps #585.

kimrutherford commented 5 years ago

I think this is also related: #481

kimrutherford commented 5 years ago

Provide a table of gene lists on the website.

We can sort-of do this already with the predefined queries, but there is no metadata attached. We can add that though.

ValWood commented 4 years ago

Let's also see if Pombemine pans out. Putting to "future"

kimrutherford commented 3 years ago

Let's also see if Pombemine pans out.

We should revisit this issue. :-)

ValWood commented 2 years ago

https://github.com/pombase/website/issues/1249 is essentially the same thing. I will add the contents here:

From the survey

A list of chemical and genetic perturbation sets would be most valuable Gene sets aside from GO terms, in GMT format. (we can think about other useful data subsets)

http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29 I don't think we will provide this format, but I wanted to record requests for "lists of lists". We do this anyway but good to explore what else people need.

For instance, FlyBase do "pathway lists" (Helens talk) which are the same as process lists, but include the MF annotations. I was hoping to deal with that generically this way: http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29

ValWood commented 1 year ago

@manulera I thought we had a ticket about "gene lists" somewhere. Where is your ticket? We can close this one in favour of yours....

manulera commented 1 year ago

This is the issue: https://github.com/pombase/curation/issues/3478

pombase / website

Gene list provision #1403