GMOD
Chado Group 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