Chado Natural Diversity Module/natdiv schema changes call

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Revision as of 17:19, 26 May 2011 by RobertBuels (Talk | contribs)

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Conference call to resolve the latest proposed changes to natdiv module.

Date

Thursday, May 26, 6pm BST / 1pm EST / 10am PST

Participants

  • Seth
  • Bob
  • Scott
  • Rob
  • Naama
  • Lukas
  • Sook
  • Yuri
  • Maren
  • Lacey

Agenda

  1. Triage proposed changes into the following categories:
    • implement before paper publishing
    • implement after paper publishing
    • do not implement
  2. Bio::Chado::Schema update
    • can someone do one after the changes have been made? Maccallr 14:37, 26 May 2011 (UTC)

Proposed changes

Prop table in genotype module

  • change: addition of (vanilla) prop table to genotype module [cvterm_id, value, rank]
    • proposer: Seth Redmond / Vectorbase
    • reason: enables us to store ontology terms for current genotypes, e.g. presence/absence of specific inversions - impossible under current schema
    • Did I understand correctly that for a genotypeprop table that cvterm_id would allow NULL? Scott 17:17, 26 May 2011 (UTC)

Hackathon changes

  • phenotype
  • phenotypeprop (Can somebody add the reason for adding this table?)

SF.net SVN: gmod:[24128] schema/trunk/chado/modules/phenotype/phenotype.sql

Commit message
GMOD Evo Hackathon changes to phenotype module: 1) Removed UNIQUE and NOT NULL constraints on phenotype.uniquename. 2) Added phenotype.units_id. 3) Added phenotypeprop table. 4) Deprecated phenotype_cvterm table.
Diff
http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/modules/phenotype/phenotype.sql?r1=24128&r2=24127&pathrev=24128

Yuri's proposals

  • Add environmentprop. This is useful when creating phenstatements.
  • Add phenstatementprop. This is useful when creating phenstatements.
  • Add nd_experiment_protocolprop. I use this to store protocol values specific to an nd_experiment.
  • Add nd_experiment_phenotypeprop. I use this to store phenotype observations specific to an nd_experiment.
  • Add cvalue_id to NatDiv property tables and related property tables like projectprop. This allows for postcomposition of cvterms like units to the property type_id.

Bob's proposals

Just looking at the NatDiv prop tables, saw some inconsistencies:

  • nd_geolocationprop.value is varchar(250) while others in NatDiv are 255. Rest of chado is type 'text'. Propose change to text.

this means we need to change the value type in all nd prop tables to text (Naama)

  • nd_experimentprop.value is NOT NULL while all others (in NatDiv) allow NULL (rest of chado is mixed). Propose all allow NULL.

This was already fixed. I committed the SQL a couple of weeks ago (Naama)

    • I just haven't rolled it into the default_schema.sql yet Scott 17:10, 26 May 2011 (UTC)