The Arabidopsis Information Resource (TAIR): gene structure and function annotation

By D. Swarbreck, C. Wilks, Philippe Lamesch, T. Berardini, M. Garcia-Hernandez, Hartmut Foerster, Donghui Li, T. Meyer, Robert J. Muller, Larry Ploetz and 6 more. Nucleic Acids Res., 2007

1,093 citations recorded by the source corpus.

The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research community. New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007. A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models). A total of 681 new genes and 1002 new splice variants were added. Overall, 10 098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d419cae6d64e1304a07a7b152c8a84e971a16fca

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Citations in the corpus

GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database (2011, background): “An important goal is to saturate the A. thaliana genome with T-DNA insertion lines for each (or at least most) of the 27 206 nuclear protein-coding genes that are currently annotated (3).”
Modelling and simulating generic RNA-Seq experiments with the flux simulator (2012, background): “the SGD annotation for yeast (31), the TAIR annotation for cress (32) and the murine as well as the human RefSeq annotation (33).”
The Universal Protein Resource (UniProt) 2009 (2008, methodology): “It includes not only UniProtKB but also translations from the EMBL-Bank/DDBJ/GenBank Nucleotide Sequence Databases, the Ensembl database of eukaryotic genomes, the H-Invitational Database (H-Inv), the Vertebrate Genome Annotation Database (VEGA), the International Protein Index (IPI), Protein Resear”
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data (2010, methodology): “We consider only those sequence reads that perfectly matched the Arabidopsis genome as defined by The Arabidopsis Information Resource (TAIR) [22] (version 9).”
The Universal Protein Resource (UniProt) in 2010 (2009, background): “in the EMBL/GenBank/DDBJ Nucleotide Sequence Databases (7) and sequences from TAIR Arabidopsis thaliana (8), SGD (9) and Ensembl Homo sapiens (10) with some defined exclusions.”
The Amborella Genome and the Evolution of Flowering Plants (2013, background): “Irish, The flowering of Arabidopsis flower development, Plant J 61, 1014–1028 (2010).”
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium (2009, background): “Arabidopsis thaliana ARATH TAIR (11) Dicot plant Caenorhabditis elegans CAEEL WormBase (12) Nematode worm Danio rerio DANRE Ensembl, ZFIN (13) Zebrafish Dictyostelium discoideum DICDI DictyBase (14) Cellular slime mold Drosophila melanogaster DROME FlyBase (15) Fruit fly Escherichia coli ECOLI EcoCy”
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools (2011, methodology): “As with the previously described TAIR6 and TAIR7 releases (21), PASA was used to incorporate all available A.”
Metabolomics for functional genomics, systems biology, and biotechnology. (2010, background): “0 contains 2,632 compound entries already, which is presumed from the documentated Arabidopsis metabolites, as well as that in manually curated metabolic pathways (13, 37, 191).”
Literature-curated protein interaction datasets (2009, methodology): “The improved results for Arabidopsis likely reflect a smaller research community whose members can maintain uniformity in gene and protein names 15 .”
PlnTFDB: updated content and new features of the plant transcription factor database (2009, neutral): “7 81 2162 Arabidopsis thaliana 6 8 (18) 30 707 125 81 2451 Populus trichocarpa 2 1.”
Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, background): “Even for the very compact Arabidopsis genome that only contains 21% of repetitive sequences including 7% LTR-RTs (4,24,25), assembling a continuous genome using NGS reads is still challenging.”
The BioGRID Interaction Database: 2011 update (2010, methodology): “BioGRID data are also available through partner model organism databases (MODs) including SGD (8), FlyBase (21), TAIR (10) and GeneDB (9), through external resources such as NCBI Entrez-Gene, DroID (22) and GermOnline (23), and through meta-databases such as STRING (24), iRefIndex (25) and Pathway C”