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The Arabidopsis Information Resource in 2024
Leonore Reiser1, Erica Bakker1, Sabarinath Subramaniam1
1Phoenix Bioinformatics, Newark, CA 94560, USA.
Genetics
|March 8, 2024
Summary
The Arabidopsis Information Resource curates gene function data for Arabidopsis thaliana, with 74% of its proteome annotated. This highlights knowledge gaps for unannotated genes, guiding future research.
Area of Science:
- Plant genomics
- Bioinformatics
- Functional genomics
Background:
- The Arabidopsis Information Resource (TAIR) has curated Arabidopsis thaliana genome data since 1999.
- TAIR integrates experimental gene function information from literature into controlled vocabulary annotations.
- The resource aims to be a "gold standard" for functional annotation and a hub for community collaboration.
Purpose of the Study:
- To provide an update on TAIR's biocuration and modernization efforts.
- To assess the current state of Arabidopsis gene function knowledge using Gene Ontology (GO) annotations.
- To identify and highlight "unknown" genes with no functional annotation or experimental support.
Main Methods:
- Utilizing Gene Ontology (GO) annotations to evaluate known and unknown Arabidopsis gene functions.
- Reviewing ongoing biocuration work and infrastructure modernization, including the implementation of JBrowse2.
- Tracking community activities, such as genome structural reannotation efforts.
Main Results:
- Currently, 74% of the Arabidopsis thaliana proteome is annotated with at least one GO term.
- Half of the annotated loci have experimental support for molecular function, biological process, or cellular component.
- A significant portion of the genome remains functionally unannotated, representing knowledge gaps.
Conclusions:
- TAIR continues to be a vital resource for Arabidopsis research, providing curated functional annotations.
- The assessment of GO annotations reveals the extent of current knowledge and identifies areas for future investigation.
- Highlighting unannotated genes serves to direct research efforts towards novel discoveries and understanding gene function.
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