The Arabidopsis Information Resource

The The Arabidopsis Information Resource is a Genomics Database.

• AKA: TAIR.
• See: Genomic Database, Model Organism, Arabidopsis Thaliana, Arabidopsis PPI.

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References

• http://www.arabidopsis.org/
  • The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.

2009

• (Cusick et al., 2009) ⇒ Michael E Cusick, Haiyuan Yu, Alex Smolyar, Kavitha Venkatesan, Anne-Ruxandra Carvunis, Nicolas Simonis, Jean-François Rual, Heather Borick, Pascal Braun, Matija Dreze, Jean Vandenhaute, Mary Galli, Junshi Yazaki, David E Hill, Joseph R Ecker, Frederick P Roth, and Marc Vidal. (2009). “Literature-Curated Protein Interaction Datasets.” In: Nature Methods 6, 39 - 46 (2009)
  • Manual curation of protein interactions from literature began with pioneering curation for the yeast Saccharomyces cerevisiae by the Yeast Proteome Database (YPD)13. Those early efforts demonstrated that effective curation was possible and also broadly aimed to capture all types of functional and genomic information, not only PPIs. Genomic databases dedicated to a single model organism arose in parallel with genome sequencingprojects, for example, the Saccharomyces Genome Database (SGD)14 and The Arabidopsis Information Resource (TAIR)15. Although initially devoted to sequence information, many of these databases eventually added many types of literature-curated information, including PPI data. In time, the publications reporting PPIs exceeded the capacity of specialized genome databases and led to the creation of databases dedicated to PPIs, for example, the Munich Information Center for Protein Sequence (MIPS) protein interaction database16, the Biomolecular Interaction Network Database (BIND)17, the Database of Interacting Proteins (DIP)18, the Molecular Interaction database (MINT)19 and the protein Interaction database (IntAct)20. More recent PPI curation efforts, the Biological General Repository for Interaction Datasets (BioGRID)21 and the Human Protein Reference Database (HPRD)22, have attempted larger-scale curation of data from more manuscripts and more interactions.

2007

• Swarbreck, D. et al. (2007). “The Arabidopsis Information Resource (TAIR): gene structure and function annotation.” In: Nucleic Acids Res. 36, D1009–D1014.

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