NOTE: We are working on migrating this site away from MediaWiki, so editing pages will be disabled for now.
Chado Group Module
From GMOD
(Redirected from Chado Groups Module)
This module will facilitate comparative methods and analyses in Chado. It mainly consists of the grp (group) table and supporting tables.
Contents
Discussion
Use cases
- Protein families
- Candidate genes (QTL)
- Coexpression analysis
- Ortholog groups
- Organisms used in a study
- Stocks used in a study
- Metabolic pathways
- Functional sets
- Gene sets (a la MSigDB)
- Collections of genes/organisms (a la Entrez)
Potential issues
You could potentially link an organism and a feature (and anything else with a grpmember linker table) to the same grpmember_id.
Current schema is incompatible with chado-xml.
Should grpmember have a type_id column?
Integration with Chado
Tables in blue would be part of the Comparative module proper, while tables in red would be part of submodules.
Not shown: grp_cvterm, analysisgrpmember
SQL Implementation
Resources
Mailing list discussion
Original discussion
Video of original talk