Chado Natural Diversity Module/natdiv schema changes call
From GMOD
Conference call to resolve the latest proposed changes to natdiv module.
Contents
Date
Thursday, May 26, 6pm BST / 1pm EST / 10am PST
Participants
- Seth, Bob
- Scott
- Rob
- Naama
- Sook
- Yuri
- Maren, Lukas
Agenda
- Triage proposed changes into the following categories:
- implement before paper publishing
- implement after paper publishing
- do not implement
- 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.
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)