CHADO Information

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Question 1: Specification Language Tables of a relational database; concrete implementation in Postgres

Question 2: Scope The core is a representation of biological sequence features (builds from SO) and genetic aspects It has been extended with two modules that are relevant to handle phylogenies

  1. organism module: organism, genus, species
  2. phylogeny module: phylonode, phylotree (linked to organism, with features (e.g., sequence at leaf) and distance, and the ability to have additional relationships between nodes)

Question 3: Case or Frame Dependence Phylogenies module is general and not limited to a specific frame/case. You can attach arbitrary features to nodes (possibly linking to tables that are user-defined and outside of the core of Chado)

Question 4: Extensibility The design of Chado has been proposed with extensibility in mind:

  • modular design (functional modules)
  • ability to add new tables; dbxref to connect different entities across tables
  • discussion of a scheme to encode ontologies as graphs in tables.

Question 5: Open nature The design of Chado is modular and open to addition of modules containing new relational tables. There is no specific discussion in the documentation about publication of new modules to the Chado official distribution.

Question 6: Controlling Authority Chado is part of GMOD, which is an open source project (distributed via sourceforge). GMOD consortium is the controlling authority.

Question 7: Update and Version Policy The distribution of GMOD is through sourceforge; a CVS system keeps track of versioning and updates.

Question 8: Conformance Policy There is no conformance policy described

Question 9: Status Stable distribution; latest release (of the complete GMOD core) is January 2007.

Question 10: How widely is used? GMOD core is the basis of a number of tools (about 20 tools at this time). There is no indication of how widely Chado itself is used (outside of GMOD). FlyBase has been ported to Chado.

Brief Summary

  • Chado is a relational schema that underlies many GMOD installations.
  • It has a modular structure; the basic modules capture similar concepts as SO, publications, and audit
  • Additional modules cover phylogenies, micro-array data, organism data
  • It includes a discussion for mapping ontologies on relational tables
  • It includes a mapping to an XML representation