Chado
Chado copied to clipboard
Changes to feature_stock, featuremap_stock, featureinterval and linkers
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)
- with these fields:
- 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?