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Plant Physiol. Mar 2008; 146(3): 1022–1023.
PMCID: PMC2259079

Plant Physiology and TAIR Partnership

Donald R. Ort
Editor-in-Chief

We are pleased to announce a unique partnership between Plant Physiology and The Arabidopsis Information Resource (TAIR) that we anticipate will increase the annotation of Plant Physiology in the TAIR database to nearly 100%. This partnership is the first of its kind, and, if successful, we hope this model can be extended to other journals, organisms, and databases.

TAIR was created in 1999 with the goal “to provide an integrated, up-to-date view of Arabidopsis biology from genome to phenome from various sources of information ranging from personal communication with researchers to published literature” (Rhee et al., 2003, p. 224). Since its inception, TAIR has grown and now includes the complete genome sequence, along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, as well as information about the Arabidopsis research community.

For sometime now, TAIR has been curating data from published literature, adding any new or additional information relating to Arabidopsis genetic and molecular biology data to the database. Curation is a labor-intensive process, but it makes certain that the information included in the database is high quality and as accurate as possible. By focusing on previously published literature, the widest possible coverage of annotations of the genome has been achieved. However, due to the high number of Arabidopsis-related publications and the relatively small number of TAIR curators, keeping on top of current literature is proving to be problematic. To help with this, TAIR implemented a cutoff using journal impact factor and focus was shifted to curate papers from the top of the ranked list. Plant Physiology was just at this cutoff and, due to the high volume of Arabidopsis articles that we publish, the Journal dropped from TAIR's list of top priority journals. TAIR noted that for 2006 and 2007 they were only able to curate 25% (50/200) of the Arabidopsis papers that Plant Physiology published.

In May 2007, Sue Rhee, Principal Investigator, and Eva Huala, Director of TAIR, approached us with the idea of Plant Physiology partnering with TAIR to increase the curation of Arabidopsis gene function data from our journal to as close to 100% as possible. The idea behind this is that once a manuscript has been accepted, the author submits all the relevant information to Plant Physiology, which will then submit the information in bulk to TAIR for vetting and addition to the database. Since then we have been working with the Lead Scientific Curator of Functional Genomics, Tanya Berardini, to devise the best possible way to do this and have come up with a Web-based interface (Fig. 1) for authors to enter their information to be sent to TAIR. A link to this site will be included in the manuscript acceptance letter, and we are anticipating that this will make it even easier for authors to submit their Arabidopsis gene function data to TAIR. We are excited by this new collaboration and are pleased that TAIR selected us for what we think will be a successful partnership that other biological databases and journals can emulate to increase the flow of information and data dissemination within the research community.

Figure 1.
Screen shot of Plant Physiology's TAIR submission page (http://www.aspb.org/publications/tairsubmission.cfm).

References

  • Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31 224–228 [PMC free article] [PubMed]

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