Changes to the Project and Biomaterial table

[spficklin]

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

Requests by Andrew Farmer

http://gmod.827538.n3.nabble.com/RFC-Chado-relase-v1-3-tp4048655p4048675.html

• Add a biomaterial_project table (v1.4)
  • Stephen says (4/24/2015). because the biomaterial, protocol, study, treatment are not specific to just MAGE data perhaps they should be moved out of the MAGE module into a new ‘Experiment’ module? The assay, array and element tables would also apply to SNP assays as well, so perhaps MAGE is no longer a good name for this module?
• Other Customization to tables:
  • project table
    • add dbxref_id => dbxref (supports NCBI BioProject ids, for example) (v1.4)
      • Stephen says (3/9/2015): Perhaps a project_dbxref table should be used instead.
      • Stephen says (4/24/2015): adding a dbxref_id to the project table can be discussed for v1.4
    • add type_id => cvterm (supports classification of projects, initially using cv derived from NCBI's BioProject vocabulary) (v1.4)
    • ALTER COLUMN description TYPE text (BioProject descriptions can be long)
      • Stephen says (3/9/2015): a few other tables have a ‘description’ field that is too short (e.g pub, library). We end up storing longer descriptions in the associated prop table. Should we extend the description fields of all tables to be of type ‘text’?
  • biomaterial table
    • add stock_id => stock (allows tracking cultivar, etc. for samples; but this may be unnecessary if subspecies info is now going to be included in organism) (v1.4)
      • Stephen says (3/9/2015): Perhaps a stock_biomaterial table should be used instead.
    • add project_id => project (links samples to primary projects, as is done in NCBI) (v1.4)
      • Stephen says (3/9/2015): This should be handled by the suggested biomaterial_project table?