Tip of the Week: PLAN2L for Arabidopsis literature

plan2L_jingFor this tip of the week we look at a text-mining tool for the Arabidopsis literature, Plan2L, or PLant ANnotation to Literature.  It has a very straightforward interface that permits searching of the paper space, and you can do that with a variety of focal points: the bibliome as a whole, or with emphasis on interactions, regulation, cell cycle, and more.  The results offer links to the PubMed abstracts, and tabular results of the statistics of the term occurance in that area of focus.  Green results indicate positive scores and likely relevance, red are likely to be non-relevant, a graphical guide to quickly finding the data of interest. Links to other resources including the BioCreative server, WikiGenes, iHOP and TAIR are provided as well.

The current emphasis for this resource is Arabidopsis, but it would be quite useful for other species too.  If you are interested in text mining Arabidopisis I would also encourage you to compare the results with the Textpresso installation at TAIR to see what you discover in a different text miner interface as well.

Plan2L site: http://zope.bioinfo.cnio.es/plan2l/plan2l.html

For their recent paper on Plan2L see: http://www.ncbi.nlm.nih.gov/pubmed/19520768 or the full article freely available in PubMedCentral:  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=19520768

3 thoughts on “Tip of the Week: PLAN2L for Arabidopsis literature

  1. Martin Krallinger

    Nice presentation, actually in case of the basic search it is possible to re-rank the sentence hits for each of the supported biological topics (regulation, interaction development sub-types,…). We are planning to improve the interface and also some of the specific text mining modules. We want to construct a similar system for muscle (development, regeneration) relevant genes, as well as genes relevant for specific cancer types. In case you have some suggestions, just send me an e-mail. It would be nice to put a copy of this video on the plan2l web, but I do not know how to contact the author of the video. Regards, Martin Krallinger (PLAN2L author)

  2. Mary

    Oh, hi Martin–thanks for coming by. And thanks for the additional tips.

    Delighted to hear about the expansion to other topics. I studied muscle development for my PhD so that’s a particular favorite of mine! I’d be happy to do another “tip” then.

    I’ll write you to on the video.

  3. Pingback: Tip of the Week: Year of Tips, part deux | The OpenHelix Blog

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