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PreprintCited by 208Biomedical Text Mining and OntologiesGenomics and Phylogenetic StudiesBioinformatics and Genomic Networks

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The Arabidopsis Information Resource in 2024

Open access
Reiser, Leonore, Bakker, Erica, Subramaniam, Sabarinath, Chen, Xingguo, Sawant, Swapnil, Khosa, Kartik, Prithvi, Trilok, Berardini, Tanya Z.·2023·Genetics
DOI 10.1101/2023.11.06.565838PMC PMC11075553

Preprint — published as 10.1093/genetics/iyae027 · Paper page

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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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Figures

Fig. 1. Histogram showing the annotation status of the Arabidopsis proteome by GO aspect and GO evidence class. The unknown set includes proteins with annotations to the root ontology term using the evidence code ND. The experimental set includes proteins with at least one annotation using one of these evidence codes: Inferred from Direct Assay, Inferred from Expression Pattern, Inferred from Genetic Interaction, Inferred from Mutant Phenotype, Inferred from Physical Interaction, inferred from High-throughput Direct Assay, inferred from High-throughput Expression Pattern, or inferred from EXPeriment (EXP). The non-experimental set includes proteins ONLY having annotations of at least one of the following evidence codes: IEA, Inferred from Sequence or Structural Similarity, Non-traceable Author Statement, Traceable Author Statement, Inferred by Curator, Inferred from Reviewed Computational Analysis, IBA, and Inferred from Sequence Model.
Fig. 1. Histogram showing the annotation status of the Arabidopsis proteome by GO aspect and GO evidence class. The unknown set includes proteins with annotations to the root ontology term using the evidence code ND. The experimental set includes proteins with at least one annotation using one of these evidence codes: Inferred from Direct Assay, Inferred from Expression Pattern, Inferred from Genetic Interaction, Inferred from Mutant Phenotype, Inferred from Physical Interaction, inferred from High-throughput Direct Assay, inferred from High-throughput Expression Pattern, or inferred from EXPeriment (EXP). The non-experimental set includes proteins ONLY having annotations of at least one of the following evidence codes: IEA, Inferred from Sequence or Structural Similarity, Non-traceable Author Statement, Traceable Author Statement, Inferred by Curator, Inferred from Reviewed Computational Analysis, IBA, and Inferred from Sequence Model.CC BY · PubMed Central
Fig. 2. Venn diagram illustrating the overlap among proteins having ND annotations to each aspect. Files containing Arabidopsis Genome Initiative (AGI) locus IDs for each aspect (MF_UNK, unknown molecular functions; BP_UNK, unknown biological process; CC_UNK, unknown cellular component; INSERT REF for files) were uploaded to the Vlaams Instituut voor Biotechnologie (VIB) Venn Diagram Generator (http://bioinformatics.psb.ugent.be/webtools/Venn/).
Fig. 2. Venn diagram illustrating the overlap among proteins having ND annotations to each aspect. Files containing Arabidopsis Genome Initiative (AGI) locus IDs for each aspect (MF_UNK, unknown molecular functions; BP_UNK, unknown biological process; CC_UNK, unknown cellular component; INSERT REF for files) were uploaded to the Vlaams Instituut voor Biotechnologie (VIB) Venn Diagram Generator (http://bioinformatics.psb.ugent.be/webtools/Venn/).CC BY · PubMed Central
Fig. 3. Histogram displaying the distribution of PANTHER 17 gene families containing Arabidopsis unknown proteins grouped by highest taxonomic classification. Plant-specific families are indicated by green bars.
Fig. 3. Histogram displaying the distribution of PANTHER 17 gene families containing Arabidopsis unknown proteins grouped by highest taxonomic classification. Plant-specific families are indicated by green bars.CC BY · PubMed Central
Fig. 4. Screenshot of GOAT data submission interface after logging in via ORCiD. a) Users add DOI or PubMed ID for the paper they are curating. b) Users enter locus identifiers and any gene names/symbols. Users can add more genes by clicking the “Add Another Gene” button. c) Users must enter at least one annotation for at least one gene (specified in the above list). d) Users can add as many annotations as desired. e) They can choose different types of annotations from the drop down menu. The type of annotation determines the set of GO or PO terms available as well as the types of evidence (Method). Once all annotations are entered, the user is prompted to review the submission (F) before submitting. Submissions are then reviewed by a TAIR curator before being imported into TAIR and integrated to the GO database on a quarterly basis.
Fig. 4. Screenshot of GOAT data submission interface after logging in via ORCiD. a) Users add DOI or PubMed ID for the paper they are curating. b) Users enter locus identifiers and any gene names/symbols. Users can add more genes by clicking the “Add Another Gene” button. c) Users must enter at least one annotation for at least one gene (specified in the above list). d) Users can add as many annotations as desired. e) They can choose different types of annotations from the drop down menu. The type of annotation determines the set of GO or PO terms available as well as the types of evidence (Method). Once all annotations are entered, the user is prompted to review the submission (F) before submitting. Submissions are then reviewed by a TAIR curator before being imported into TAIR and integrated to the GO database on a quarterly basis.CC BY · PubMed Central
Fig. 5. JBrowse2 interface showing the locus At1g31860, the structure of the three different gene models, locations of T-DNA insertions, supporting cDNAs, and one some mRNA-seq expression data as a coverage track.
Fig. 5. JBrowse2 interface showing the locus At1g31860, the structure of the three different gene models, locations of T-DNA insertions, supporting cDNAs, and one some mRNA-seq expression data as a coverage track.CC BY · PubMed Central
Fig. 6. JBrowse 2 visualization of syntenic comparison between genomic regions of A. thaliana and A. lyrata. Individual tracks show A. lyrata protein coding genes (version 1.0), “Connectors” indicating syntenic regions between A. thaliana and A. lyrata, and A. thaliana protein coding genes (Araport11 release). Syntenic comparison was performed using MC-Scan and the output PAF file was uploaded into JBrowse2 to create the above syntenic panel.
Fig. 6. JBrowse 2 visualization of syntenic comparison between genomic regions of A. thaliana and A. lyrata. Individual tracks show A. lyrata protein coding genes (version 1.0), “Connectors” indicating syntenic regions between A. thaliana and A. lyrata, and A. thaliana protein coding genes (Araport11 release). Syntenic comparison was performed using MC-Scan and the output PAF file was uploaded into JBrowse2 to create the above syntenic panel.CC BY · PubMed Central
Fig. 7. Phases of genome reannotation.
Fig. 7. Phases of genome reannotation.CC BY · PubMed Central

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Research works printed but not linked: 1

  1. Saha S. , S. Cain , E. K. S. Cannon , N. Dunn , A. Farmer , et al., 2022 Recommendations for extending the GFF3 specification for improved interoperability of genomic data. arXiv [q-bio.OT].

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Metadata

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.
ORCID
Venue
Genetics
Publisher
openRxiv
Published
2023-11-07
Volume
227
Issue
1
ISSN
0016-6731 (ISSN-L)
DOI
10.1101/2023.11.06.565838
PMC
PMC11075553
OpenAlex
W4392600686
Cited by
202
References
43
Citations by year
2026: 79 · 2025: 59 · 2024: 29
FWCI
22.73
Type
journal article
Language
en
Open access
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
  • Health Sciences › Medicine › Health Informatics › 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

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