Functionome site: add or change a few hyperlinks

[thomaspd]

• 1. Links to help. These appear in two places: 1) in the top of the page, after the search box, with the text "Let us know", and 2) in the footer, with the text "Contact us". The link should be to the Google form-- @suzialeksander can you please add the link to this ticket?
• 2. On the gene page, add a few more links to external resources.
• • HGNC. This was in the previous version but lost in the update.
• • Alliance of Genome Resources. This was in the previous version but lost in the update.
• • NCBI Gene. The hyperlink can be made from the UniProt ID, for example: https://www.ncbi.nlm.nih.gov/gene/?term=Q9H568
• 3. On the gene page, next to the "Function details" header, add the text "PAN-GO evolutionary model for this family", and link to PanTree, e.g. https://pantree.org/tree/family.jsp?accession=PTHR12563
• 4. On the menu, clicking on Downloads currently shows two choices: as CSV, as JSON. The menu should have more choices:
• • all data as CSV (link is same as current "as CSV")
• • all data as JSON (link is same as current "as JSON")
• • annotations as GAF (link to http://data.pantherdb.org/ftp/downloads/paint/pango/... - @dustine32 will make the file by concatenating the GAFs that are already there
• • evolutionary models as GAF (link to http://data.pantherdb.org/ftp/downloads/paint/pango/IBD.gaf)

[tmushayahama]

Added #2413 (comment), so all the links issues are in one issue cc @kltm @thomaspd

[tmushayahama]

Now the changes are up and ready for testing. Check if the all the links dont have typo (so far its manual hardcoded) cc @thomaspd @kltm

Todo:

Will wait for @suzialeksander contact us form and @dustine32 GAF (the link is pointing above, you can lemme know if any changes

[thomaspd]

I did some testing, and checked off completed items above.
For item 2, the NCBI link is using the gene symbol instead of the UniProtID in the URL, so it isn't working. Please fix.
For item 3, I realize that having the link in the Function details heading is confusing. Can you please move it to the Gene Information section at the top of the page?

[thomaspd]

For NCBI, please try this link formulation instead, using the gene name together with the taxonomy ID for human:
https://www.ncbi.nlm.nih.gov/gene?term=(ABCD3%5BPreferred%20Symbol%5D)%20AND%209606%5BTaxonomy%20ID%5D

[tmushayahama]

Thanks @thomaspd for the links, this works. I have updated the site. also removed the KB and font size consistency

[dustine32]

@tmushayahama I just put up the "annotations as GAF" file here:
http://data.pantherdb.org/ftp/downloads/paint/pango/functionome_release.gaf.gz

[suzialeksander]

@tmushayahama are you looking for the responder's link to the feedback survey?

https://docs.google.com/forms/d/e/1FAIpQLScX_caoY-mqsyK5Y6M2bof7EXVG0UY5DhOQ67zBMoAKKlRF4Q/viewform?usp=sharing

[tmushayahama]

Thanks @suzialeksander added the contact us
@dustine32 do you have http link, it seems not to work (it works if coming from http)

[dustine32]

@tmushayahama Just made some symlinks for you. These HTTPS URLs should work now:
https://functionome.org/download/functionome_release.gaf.gz
https://functionome.org/download/IBD.gaf

[tmushayahama]

Thanks @dustine32 these are working. I also changed pantree, @mugitty can you check if links working

[mugitty]

@tmushayahama I tested and the link to https://pantree.functionome.org works

[mugitty]

@tmushayahama , the link for the Tree Viewer should go to https://enrichment.functionome.org/treeViewer/treeViewer.jsp? instead of https://www.pantherdb.org/treeViewer/treeViewer.jsp?

[tmushayahama]

thanks @mugitty , the links are now updated on the site