The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

By Philippe Lamesch, T. Berardini, Donghui Li, D. Swarbreck, C. Wilks, Rajkumar Sasidharan, Robert J. Muller, Kate Dreher, Debbie L. Alexander, M. Garcia-Hernandez and 7 more. Nucleic Acids Res., 2011

2,247 citations recorded by the source corpus.

The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is a genome database for Arabidopsis thaliana, an important reference organism for many fundamental aspects of biology as well as basic and applied plant biology research. TAIR serves as a central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation. TAIR also provides researchers with an extensive set of visualization and analysis tools. Recent developments include several new genome releases (TAIR8, TAIR9 and TAIR10) in which the A. thaliana assembly was updated, pseudogenes and transposon genes were re-annotated, and new data from proteomics and next generation transcriptome sequencing were incorporated into gene models and splice variants. Other highlights include progress on functional annotation of the genome and the release of several new tools including Textpresso for Arabidopsis which provides the capability to carry out full text searches on a large body of research literature.

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Citations in the corpus

De novo assembly of haplotype-resolved genomes with trio binning (2018, unknown): “To demonstrate this approach and the accuracy of the TrioCanu haplotypes, we used Nucmer 33 and Assemblytics 34 to identify a total of 4,828 structural variants (SVs) between the Col-0 reference genome (TAIR10 35 ) and a de novo assembly of the Cvi-0 genome 20 .”
The BioGRID interaction database: 2013 update (2012, methodology): “2 supports 28 million systematic names, aliases, official symbols and external identifiers from Ensembl (30), UniprotKB (31), NCBI Entrez-Gene (32), Genbank (33), SGD (13), WormBase (23), FlyBase (26), HGNC (34), MGD (27), TAIR (15), VectorBase (35), BeeBase (36), ZFIN (25) and HPRD (37), among othe”
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations (2016, methodology): “A smaller fraction of manual subcellular curations were derived from TAIR (8), AmiGO and Swissprot.”
The BioGRID interaction database: 2015 update (2014, background): “…also accessible to the individual researcher indirectly through a number of other biological databases including NCBI Entrez-Gene (48), Uniprot (49), DroID (80), GermOnline (81), FlyBase (42), TAIR (73), SGD (41), PomBase (43), STRING (47), iRefIndex (82), GeneMania (83) and Pathway Commons (50).”
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies (2018, background): “Furthermore, the chromosome-resolved assembly for Col-0 (TAIR10) was also available to enable detailed chromosome-scale comparisons [30].”
The BioGRID interaction database: 2019 update (2018, methodology): “The GIST has been designed to precisely specify genetic interactions using a universal genetic interaction terminology and is supported by other MODs, including SGD (19), CGD (26), PomBase (25), ZFIN (29), FlyBase (27) and TAIR (28).”
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants (2015, methodology): “In PlantPAN 2.0, gene information of Arabidopsis , rice, and maize were updated according to the latest version of TAIR (TAIR10 genome release), RAP-DB and MaizeGDB (21– 23).”
PsRobot: a web-based plant small RNA meta-analysis toolbox (2012, methodology): “The Arabidopsis thaliana genome was downloaded from the Arabidopsis Information Resource (TAIR) (24) and the rice genome was from Rice Genome Annotation Project (RGAP) (25) and the Rice Annotation Project Database (RAP-DB) (26) databases.”
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] (2013, methodology): “We chose to benchmark MAKER-P using Arabidopsis because it has a well-assembled reference genome and its genome annotations have been subject to extensive computational and manual curation (Lamesch et al., 2012).”
FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana (2015, background): “org) (26), PubMed and Google Scholar (http: //scholar.”
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants (2016, methodology): “Taking an integrative strategy by combining sequencebased prediction (29), orthologous-based projection, and collection of existing annotation in canonical sources (25,26), we successfully annotated 93.”
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis (2012, methodology): “This was achieved using a protein ‘reference set’ (RS) compiled by manual analysis of TAIR10 annotation and MapMan (41) evaluation of biochemical pathways and functional groups.”
PGDD: a database of gene and genome duplication in plants (2012, background): “List of 26 plants currently served by PGDD Species name Common name Release version Gene number Arabidopsis lyrata Lyrate rockcress Version 1.0 (April 2011) 32 670 Arabidopsis thaliana Arabidopsis TAIR 9.0 (June 2009) 27 379 Brachypodium distachyon Purple false brome Phytozome v6.”
FlyBase: establishing a Gene Group resource for Drosophila melanogaster (2015, background): “These are generally either inter-species databases that are focused on a particular functional attribute (e.g. kinase.com (7), Ribosomal Protein Gene database (8)), or are organism-specific databases that include discrete lists of related genes (e.g. HGNC (9), The Arabidopsis Information Resource (T”
The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome (2015, methodology): “…meth-ods and manual review, TAIR produced a total of ﬁve genome releases with the most recent (TAIR10) made public in November 2010 (https://www.arabidopsis. org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp#data) (Lamesch et al ., 2012; Swarbreck et al ., 2008;).”