Cowpea consensus map update

[adf-ncgr]

Tim Close emailed about getting this into LIS. Have followed up with him and will start reviewing the files associated with his submitted manuscript to assess next steps.

[LEGUME-586] created by adf_ncgr

[adf-ncgr]

The paper associated with this has just been accepted and the data for the map are available early-access
in the supplementary materials referenced below; I could certainly munge these into a cmap-loadable file, but this would be a good opportunity for me to learn about the process being used for common bean/peanut and see what would make sense here. Note that there are no QTLs defined in this info, but I believe that previous papers associate them with markers that will have updated positions on this map, so we can presumably use that info to get them also (eventually). In parallel, have been working (sporadically) on getting some of the data into flapjack-compatible files, for possibly hosting in the data store.

supplementary data here:
http://onlinelibrary.wiley.com/wol1/doi/10.1111/tpj.13404/suppinfo

main data of interest for starters would probably be these:

Filename Format Size Description

tpj13404-sup-0008-TableS4.xlsx application/msexcel 10K Table S4. Information on the individual mapping population data used for consensus map construction.

tpj13404-sup-0012-DataS2.xlsx application/msexcel 6953K Data S2. Information of SNPs included in the final Cowpea iSelect Consortium Assay.
tpj13404-sup-0013-DataS3.xlsx application/msexcel 31529K Data S3. Five individual genetic maps (each sheet) and the genotype dataset used for their construction.
tpj13404-sup-0014-DataS4.xlsx application/msexcel 814K Data S4. iSelect SNP consensus genetic map for cowpea.

by adf_ncgr

[adf-ncgr]

Note that this map will need to be added to the traits & maps page (/traits_maps) when it is loaded, and loaded into Chado so that it can be searched via the map search page.

by ecannon

[adf-ncgr]

Hi-
this map has been loaded into CowpeaMine. I'm not clear on the process for getting it in on the chado side
(is there a SOP somewhere that describes this?)

with respect to /traits_maps I am not sure how this is currently maintained, but I suspect it is "hand-crafted with love";
looks like it might be a good candidate to transition to an approach like what Sudhansu Dash created for the genomes page (ie drive the content from a spreadsheet that contains the needful)? Alternatively, driving from the db itself might be a possibility, though I guess many of these maps are not in the chado db so perhaps that's why we have the page in the first
place...

by adf_ncgr

[adf-ncgr]

No SOP. We need one: GH-723 To Do

Yes, the Traits&Maps page is hand-crafted with love. Switching to a spreadsheet-based page would be wonderful: GH-724 To Do .

The downloads on the Traits&Maps page are badly out of date, but now that we have our Data Store, this old approach to downloads should probably be abandoned and the downloads modified for the Data Store. To be discussed.

by ecannon