Chado Natural Diversity Module/natdiv schema changes call

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

Date

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

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

Hackathon changes

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

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.
  • Chado has some way to post-compose cvterms which Maccallr 11:56, 17 May 2011 (UTC) doesn't understand.

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