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Breeding by Design for Functional Rice with Genome Editing Technologies
Published on: January 3, 2025
OryGenesDB 2008 update: database interoperability for functional genomics of rice.
Gaëtan Droc1, Christophe Périn, Sébastien Fromentin
1CIRAD Dept BIOS UMR DAP - TA40/03, 34398 Montpellier, France.
Nucleic Acids Research
|November 28, 2008
Summary
OryGenesDB is a rice reverse genetics database featuring 171,000 flanking sequence tags (FSTs). The new Orylink tool enhances rice functional genomics by querying multiple databases, improving data accessibility and interoperability.
Area of Science:
- Agricultural Science
- Bioinformatics
- Genetics
Background:
- Rice reverse genetics research requires integrated data resources.
- Existing databases often lack comprehensive functional genomics data and cross-database querying capabilities.
Purpose of the Study:
- To present OryGenesDB 2008, an updated database for rice reverse genetics.
- To introduce Orylink, a novel tool for accelerating rice functional genomics research.
- To enhance data accessibility and interoperability among rice genomics databases.
Main Methods:
- Consolidation of flanking sequence tags (FSTs) and functional genomics data from diverse sources.
- Development of Orylink for complex cross-database queries and results management.
- Integration of OryGenesDB with Oryza Tag Line and GreenPhylDB via Orylink.
- Provision of Web services for independent use and enhanced interoperability.
Main Results:
- OryGenesDB 2008 release contains 171,000 FSTs across 10 categories and 78 annotation layers.
- Orylink facilitates efficient querying across OryGenesDB, Oryza Tag Line, and GreenPhylDB.
- New tools for FST retrieval and probe design are available.
- Web services enhance the interoperability of bioinformatics applications.
Conclusions:
- OryGenesDB 2008, with the addition of Orylink, provides a powerful virtual workbench for rice functional genomics.
- The integrated approach significantly speeds up research by leveraging multiple databases.
- Enhanced data accessibility and interoperability are key benefits for the rice research community.
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