adf-ncgr
commented
9 years ago The short answer would be that the grand map overhaul is still a work in progress and that not all issues were resolved before the last rollover.
Allow me to expand...The cMap file for BAT93_x_JALOEEP558_b is the updated replacement map for Pv Freyre integrated linkage map - 1998 (PvFreyre1998). Therefore, the BAT93_x_JALOEEP558_b file should have been uploaded to LIS and the PvFreyre1998 map removed from the system. It appears that this process was not completed before the rollover and that PvFreyre1998 is available through cMap map search, whereas BAT93_x_JALOEEP558_b returns the answer "No maps meet criteria". The graphical display of the traits and maps tab was altered by Scott in preparation for the expected changeover in the map sets, so this is why the BAT93_x_JALOEEP558_b was visible to the user and why the PvFreyre1998 was commented out of view. I did not erase the PvFreyre1998 html links entirely from the html code, both because of the uncertainty over what map files would ultimately be loaded before the deadline, and also because Jugpreet really holds sovereignty over what should appear or not appear for common bean at legumeinfo.
You will also notice in cMap map search for common bean that Phaseolus vulgaris Consensus genetic map 2011 is present in the system, but that it is not linked to the graphical display for easy access by the user. The reason is that Phaseolus vulgaris Consensus genetic map 2011 was functionally replaced by PvConsensus_GaleanoFernandez2011_a, which is the updated common bean consensus map. The PvConsensus_GaleanoFernandez2011_a map is the one hooked up the links at the traits and maps tab. I expect that a newer version of PvConsensus_GaleanoFernandez2011_a will soon appear with the QTLs in higher fidelity positions, as a result of Jugpreet's improvement in the projection methodology. Again, I commented out the viewer experience of the Phaseolus vulgaris Consensus genetic map 2011 in expectation that a final decision as to its fate would be made later.
There are also many deleted cMaps showing up in the cMap map search for Arachis at the moment. Attempts to open them also result in an error message as they do not exist in the database — they have been replaced by newer maps with distinct names. This issue will also be resolved before the next rollover I hope.
Please ask if anything is still not comprehensible. Thank you!
by scottkalberer
Noticed this while addressing issue #343. PvFreyre1998 linkage groups commented out but tested that it works.
Question: What is it's status? Good for display or was it deliberately commented out for some problem? Jugpreet thinks Ethy and Scott should know about it as they were cleaning up some maps. Will activate it after Ethy or Scott's comments.
Note: Has been activated in lis-stage only for the purpose of addressing this issue.
[LEGUME-344] created by sdash-legume