Chado Comparative Schema

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

Click the link above 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.