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Chado Group Module

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This module will facilitate comparative methods and analyses in Chado. It mainly consists of the grp (group) table and supporting tables.

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

ChadoComparativeModule.png

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

Source Code

GitHub

Resources

Mailing list discussion

Original discussion

Video of original talk