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Changes to feature_stock, featuremap_stock, featureinterval and linkers

Open spficklin opened this issue 6 years ago • 3 comments

This issue imported from the Chado v1.4 requested changes google doc:

Requests by Ethy Cannon / Naama Menda / Steve Cannon

http://gmod.827538.n3.nabble.com/Opening-up-comments-on-changes-to-Chado-tc4036098.html#a4039144

  • feature_stock with a type_id is used to associate a QTL feature with the parent with the favorable allele. (v1.3)
  • featuremap_stock with a type_id is used to associate a genetic map with a stock record describing its mapping population.
  • Do other linker tables have types? If so, should we make this a standard for all linker tables to have a type, but let it be non-required? (v1.4, get some more use cases)

http://gmod.827538.n3.nabble.com/Proposed-changes-to-map-module-tc4031971.html

  • Change featureloc.fmin and featureloc.fmax to a float. Something to do with featuremap but I don’t understand….
  • Add a type field to the featurepos table to indicate the “type” of the position (e.g. start or end).
  • Add a new ‘featureinterval’ table
    • with these fields:
      • featureinterval_id
      • featuremap_id (map set, to get coordinate units)
      • feature_id (object feature being placed)
      • srcfeature_id (target feature)
      • startpos (double precision)
      • endpos (double precision)
  • Stephen Ficklin (1/14/15): In the email it says this would help newbies but duplicates some information already in the featurepos table. Not sure if we should add tables that duplicate info. I got slapped around once for suggesting such a thing.
  • Scott Cain (1/14/15): As well you should! Perhaps featureinterval should be a view?

spficklin avatar Jan 10 '18 18:01 spficklin