Difference between revisions of "Chado Comparative Schema"
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==[[Sybil Chado Comparative Genomics Data|Sybil/IGS]]== | ==[[Sybil Chado Comparative Genomics Data|Sybil/IGS]]== | ||
− | + | See [[Sybil Chado Comparative Genomics Data]] to see a description of the [[Sybil]]/IGS way of storing comparative data. | |
== [[FlyBase Comparative Genomics Data|FlyBase]] == | == [[FlyBase Comparative Genomics Data|FlyBase]] == | ||
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− | + | This [[FlyBase Comparative Genomics Data|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. | |
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+ | == [[Media:ParameciumDB_synteny.pdf|ParameciumDB]] == | ||
+ | [[ParameciumDB]] [[Media:ParameciumDB_synteny.pdf|working document]] heavily inspired by the [[FlyBase Comparative Genomics Data|FlyBase comparative implementation standard]]. This document describes how ParameciumDB models paralogy and synteny within a genome that has undergone whole genome duplications. | ||
− | [[Category: | + | [[Category:Comparative Genomics]] |
Latest revision as of 20:01, 12 April 2008
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.