The Arabidopsis information resource (TAIR)

The Arabidopsis information resource (TAIR) provides a curated genome database for Arabidopsis thaliana to support gene function, expression, and genome annotation studies.

Key Features:

• Genome Assembly and Annotation: Maintains and updates A. thaliana genome assemblies and annotations (TAIR8, TAIR9, TAIR10), including re-annotated pseudogenes and transposon genes and integration of proteomics and next-generation transcriptome sequencing data.
• Functional Annotation: Provides functional annotation of A. thaliana genes to support interpretation of gene roles and biological processes.
• Controlled Vocabulary Terms: Annotates gene function and expression using controlled vocabulary terms to standardize annotations.
• Visualization and Analysis Tools: Includes visualization and analysis tools for interpretation of genomic and expression data.
• Textpresso for Arabidopsis: Implements Textpresso for Arabidopsis to enable full-text literature searches across A. thaliana publications.

Scientific Applications:

• Gene Function and Expression Analysis: Supports discovery and interpretation of gene function and expression patterns in A. thaliana.
• Genome Assembly and Annotation Improvement: Enables assembly updates and re-annotation of gene models including pseudogenes and transposon genes (TAIR8–TAIR10).
• Integration of Transcriptomics and Proteomics Data: Facilitates incorporation of next-generation transcriptome sequencing and proteomics data for evidence-based annotation.
• Standardized Annotation and Comparative Studies: Uses controlled vocabularies to standardize annotations for comparative and functional genomics studies.
• Literature Mining: Supports full-text literature mining and retrieval of A. thaliana research via Textpresso.

Methodology:

Updated genome assemblies and annotations (TAIR8, TAIR9, TAIR10); re-annotation of pseudogenes and transposon genes; integration of proteomics and next-generation transcriptome sequencing data; and full-text indexing/search via Textpresso for Arabidopsis.