Germplasm Page

[sdash-github]

Being constructed along the line of classic site. Catalogs page is separate. Keep refining page.

[svengato]

The Germplasm page already existed, but I cleaned it up a bit. https://dev.peanutbase.org/germplasm

Issues:

• [x] 1. The Gigwa link is still under peanutbase.org.
• [x] 2. NIFA-PCCGP link is under Germplasm, is that correct?
• [x] 3. What is aradu1_araip1_gnm1.div.HK28.sub10k.vcf? I see other diversity files in the data store, but not that one.
• [ ] 4. Interactive pedigree chart has gone missing does not work.
• [x] 5. Image Collection: work in progress.

[svengato]

Interactive pedigree chart has gone missing.

I found the old one, not under germplasm but https://peanutbase.org/pedigree2000 It does not work though.

[svengato]

By analogy with the Catalogs page, should we have separate pages for Seed Images, Pod Images, and Plant Images?

[svengato]

I went ahead and made them, https://dev.peanutbase.org/germplasm/seed (issue #30) https://dev.peanutbase.org/germplasm/pod (issue #31) https://dev.peanutbase.org/germplasm/plant (issue #32) https://dev.peanutbase.org/germplasm/catalogs (already exists)

SD added(2023-04-26):

34 applies to #30 , #31, #32

[svengato]

I made a new page for the interactive pedigree chart. However,

• [ ] The map links look like https://peanutbase.org/stock/Arachis/hypogaea/Cultivar/Basse but no longer exist. Where might they be?
• [ ] The default behavior is to automatically reduce the image size to fit in the browser window, but this invalidates the coordinates of the image map elements. Using a <div> with style tags forces the image to remain full size, solving the coordinate problem, but horizontal scrolling still does not work as expected.

[adf-ncgr]

regarding the first point, I believe those pages are all victims of the php upgrade that broke a lot of the version of tripal we're using on the site. It may be difficult to find alternative places to link that use the same naming, since I'd guess most of the data for them went into Chado and isn't in datastore files that would be loaded into the mine (for example). Probably our best bet will be to try converting the "friendly names" into PI numbers and link them to either GRIN or ArachisPheno or the GIS app or something like that. Such a conversion can probably make use of the db that is behind the GIS app or the GRIN dump from which it was derived (or perhaps using BrAPI service calls against GRIN in the modern way...)

[svengato]

Somewhere like https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1225751 (for Basse)?

[adf-ncgr]

That is the GRIN option, although personally I'd rather use something we can get to with identifiers that are more stable (like PI numbers). I guess another option would be to dump the relevant info out of Chado and try to get it loaded into ArachisMine.

[adf-ncgr]

I guess https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?accid=PI%20298858 works if we decide to go that way.

[adf-ncgr]

https://germplasm-map.legumeinfo.org/#?accessionIds=PI%20298858 would be another option. Perhaps a germplasm linkout service will exist someday

[svengato]

Updated in commit 8ae23fe.

Known issues: (from above)

• [x] Does a link to aradu1_araip1_gnm1.div.HK28.sub10k.vcf exist? I see other diversity files in the data store, but not that one.

Interactive pedigree chart: added in commit f96441e.

• [ ] Need to add links from GRIN or whatever.
• [ ] Again, the image must be full size in order for the image map coordinates to be valid, but this may be larger than most users' browser window. Therefore, it would be nice to wrap the image in a scroll bar.

[adf-ncgr]

I'd guess that aradu1_araip1_gnm1.div.HK28.sub10k.vcf has become https://data.legumeinfo.org/Arachis/hypogaea/diversity/aradu1_araip1.gnm1.div.Otyama_Kulkarni_2020/aradu1_araip1.gnm1.div.Otyama_Kulkarni_2020.sub10k.vcf.gz

although I think that the "sub10k" may indicate that it is just a subsampling from the main file (I think this was done to support https://peanutbase.org/germplasm/gcvit but not sure if that is still functional given the renaming). Maybe a good question for others more familiar with the history of these data at the Wednesday meeting...

[svengato]

The Otyama_Kulkarni_2020 CHANGES file confirms that it used to be HK28. Good catch!