ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB imports published gene symbol names from Gramene’s GenesDB via BioMart’s RESTful web service for Gramene release 35 (June 2012) for MSU6 loci. The external_gene_id field for Gramene GenesDB is extracted from Biomart with following XML query:

<Query formatter="CSV" header="1" uniqueRows="0"
    virtualSchemaName="default" datasetConfigVersion="0.7">
    <Dataset name="osativa_eg_gene" interface="default">
        <Filter name="with_gramene_genesdb" excluded="0"/>
        <Attribute name="ensembl_gene_id" />
        <Attribute name="ensembl_transcript_id" />
        <Attribute name="gramene_genesdb" />
        <Attribute name="external_gene_id" />
        <Attribute name="external_gene_db" />
    </Dataset>
</Query>

From Gramene's website:

The purpose of Gramene is to work in collaboration with others on database software and planning, and to integrate contributions from researchers with publicly available genomic data to make a comprehensive cereal genomic and comparative resource available to the scientific community. The information and software used in the development and building of the Gramene database and web site is available from various sources within the public domain. Permission for reproduction has been given or implied by the researchers/institutes who contributed or published the original materials. However, there may be patents, copyrights or intellectual property rights associated with the original data, and users of the Gramene database contents are solely responsible for compliance with original restrictions and acknowledgement requirements when using original data.

Citations:

Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research, 34: D717-723.

Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 30, 103-105.

Usage When Searching Rice DB Usage Viewing Rice DB Results
  • Can search for published gene symbols.
  • Can search for GenesDB IDs.
  • Gene symbol names and Gramene citations can be shown.
Example: iaa9
Example: GR:0020013
Example: GR:0020210
Example: show gene symbols for LOC_Os02g56120, LOC_Os02g17680
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System Information

Transcript of last update

Took 2 seconds, 381 millis starting Wed, 20 Feb 2013 14:11:07 GMT:
Using /tmp/RiceDB/GrameneGenesDBSymbols_
Using /var/www/ricedb/Data/downloaded/GrameneGenesDBSymbols_
Updating column and identifier names