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Chado Comparative Schema

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Overview

This article will be used to describe strategies to store comparative data within Chado. To kickstart the discussion the ex-TIGR crew will detail their strategy as used in the sybil system. We will discuss/criticize it in the discussion section.

Goal

The goal of this article and the ensuing discussion is to define a usage convention for the storage of comparative data in Chado. These data include: Paralogous and Orthologous Gene clusters and Syntenic Blocks (and potentially more?).

Strategies

Sybil/IGS

See Sybil Chado Comparative Genomics Data to see a description of the Sybil/IGS way of storing comparative data.

FlyBase

This document describes how FlyBase has implemented comparative data for Dmel<->Dpse and also how it plans to implement these analyses for 10 more Drosophila species.

ParameciumDB

ParameciumDB working document heavily inspired by the FlyBase comparative implementation standard. This document describes how ParameciumDB models paralogy and synteny within a genome that has undergone whole genome duplications.