Difference between revisions of "Chado Natural Diversity Module/natdiv schema changes call"
From GMOD
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== Agenda == | == Agenda == | ||
| − | + | # Triage proposed changes into the following categories: | |
| − | * implement before paper publishing | + | #* implement before paper publishing |
| − | * implement after paper publishing | + | #* implement after paper publishing |
| − | * do not implement | + | #* do not implement |
| + | # Bio::Chado::Schema update | ||
| + | #* can someone do one after the changes have been made? [[User:Maccallr|Maccallr]] 14:37, 26 May 2011 (UTC) | ||
== Proposed changes == | == Proposed changes == | ||
Revision as of 14:37, 26 May 2011
Conference call to resolve the latest proposed changes to natdiv module.
Contents
Date
Thursday, May 26, 6pm BST / 1pm EST / 10am PST
Participants
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.
- nd_experimentprop.value is NOT NULL while all others (in NatDiv) allow NULL (rest of chado is mixed). Propose all allow NULL.
