Publication trends in Arabidopsis

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Published on: September 18, 2014

Pete McQuilton and Richard Smith of Nowomics have pulled a load of information on Arabidopsis trends for us to write this fascinating guest blog post. Nowomics is a new website that fetches data from many biological databases every day and works out what’s changed, and finds genes and species names mentioned in new PubMed abstracts. This lets users (this can be anyone – it’s free!) to follow genes and gene ontology terms to create a personalised news feed of new papers and data. 

Arabidopsis thaliana, the humble model organism for flowering plants, has been studied for over 140 years. Discovered by Johannes Thal (hence the name thaliana), the mouse-ear cress is a member of the mustard family (Brassicaceae), alongside such luminaries as cabbage and radish. With it’s relatively small sequenced genome (114.5mb/125Mb total), rapid life cycle (about 6 weeks from germination to mature seed), prolific seed production and many genetic tools and mutants, Arabidopsis is a wonderful model organism for basic research in genetics and molecular biology.

As part of a series of blog posts at Nowomics we have examined the publication trends in Arabidopsis-related research. We’ve extracted data on primary research papers from PubMed (excluding reviews and clinical trials) for a ten year range from 2004-2013 and have identified those that mention Arabidopsis in the title or abstract. These papers are defined as Arabidopsis papers (further details of the method are given below).

From this analysis, it is clear that the Arabidopsis community is thriving, having produced just over 3500 papers in 2013, up from 1847 in 2004. This represents a 91% increase in article number, keeping pace with the overall rise in number of journal articles published, which has grown by 95% since 2004.

Journals

Figure 1. The top Arabidopsis-publishing journals 2004-2013.
Figure 1. The top Arabidopsis-publishing journals 2004-2013.

From 2004 to 2011, Plant Physiology (Plant Physiol.), Plant Journal (Plant J.) and Plant Cell made up the top three journals publishing Arabidopsis research (see figure 2). Plant Signal Behaviour (Plant Signal Behav.) has risen rapidly from it’s inception in 2006 to join the top five in 2008. By far the strongest trend, however, is the rise of PLoS ONE from outside the top ten in 2010 with just 66 Arabidopsis papers, to topping the chart with 315 in 2013. That figure represents 9% of all Arabidopsis articles in 2013. The meteoric rise of PLoS ONE can be seen for other organisms, such as in Drosophila, as described in a previous blog post. (more…)

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