The Arabidopsis Information Resource in 2024
Open accessPreprint — published as 10.1093/genetics/iyae027 · Paper page
Abstract
Since 1999, The Arabidopsis Information Resource ( www.arabidopsis.org ) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a ‘gold standard’ functional annotation set that reflects the current state of knowledge about the Arabidopsis genome. At the same time, the resource serves as a nexus for community-based collaborations aimed at improving data quality, access and reuse. For the past decade, our work has been made possible by subscriptions from our global user base. This update covers our ongoing biocuration work, some of our modernization efforts that contribute to the first major infrastructure overhaul since 2011, the introduction of JBrowse2, and the resource’s role in community activities such as organizing the structural reannotation of the genome. For gene function assessment, we used Gene Ontology annotations as a metric to evaluate: (1) what is currently known about Arabidopsis gene function, and (2) the set of ‘unknown’ genes. Currently, 74% of the proteome has been annotated to at least one Gene Ontology term. Of those loci, half have experimental support for at least one of the following aspects: molecular function, biological process, or cellular component. Our work sheds light on the genes for which we have not yet identified any published experimental data and have no functional annotation. Drawing attention to these unknown genes highlights knowledge gaps and potential sources of novel discoveries. Article Summary: The Arabidopsis Information Resource (TAIR, www.arabidopsis.org ) is a comprehensive website about Arabidopsis thaliana , a small plant that’s very easy to grow and analyze in the laboratory and is used to understand how many other plants function. We share our progress in data collection and organization, website and tool improvement, and our involvement in community projects.
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- Authors
- Reiser, L., Bakker, E., Subramaniam, S., Chen, X., Sawant, S., Khosa, K., Prithvi, T., & Berardini, T. Z.
- Affiliations
- Phoenix Bioinformatics (US)
- Corresponding author
- Reiser, Leonore
- Berardini, Tanya Z.
- Venue
- Genetics
- Publisher
- openRxiv
- Published
- 2023-11-07
- Volume
- 227
- Issue
- 1
- ISSN
- 0016-6731 (ISSN-L)
- PMC
- PMC11075553
- OpenAlex
- W4392600686
- Cited by
- 202
- References
- 43
- Citations by year
- 2026: 79 · 2025: 59 · 2024: 29 · 2022: 4 · 2021: 1 · 2020: 2 · 2019: 1 · 2018: 1 · 2017: 1 · 2016: 1 · 2014: 2 · 2013: 1
- FWCI
- 22.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute (U24HG012212)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- Arabidopsis thaliana, gene function annotation, controlled vocabulary, Gene Ontology, biocuration, genome reannotation, unknown genes
- MeSH terms
- Arabidopsis, Genome, Plant, Arabidopsis Proteins, Databases, Genetic, Molecular Sequence Annotation, Gene Ontology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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