The OpenHelix Blog

For 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

There is plenty of buzz out there for the big data biology projects–but usually the focus is the human data (with a few token model organisms thrown in).  But this week plant researchers renewed the call for big plant data.  I’m totally on board with that.

The 1000 Genomes project to obtain more human variation information is well underway, funded, and has companies supporting it.  And that’s great–I’m all for this too!  But as someone who survives largely on the kindness of plants I want more plant research going on.  I want to see this funded and supported.  And as we face increasing stresses on resources from limitations like oil and water supplies to wacky climate conditions and environmental consequences I think we could well afford to spend less time gazing at our human genomic navels and devote more attention to the plants.

There is already some work on this Arabidopsis project.  The first paper with data on this effort came out last fall.  But the researchers are still having to go out and lobby for this project.  A new opinion piece in Genome Biology calls out for awareness and support for this effort.

They have already done a first generation green HapMap.  The paper last fall illustrated the feasibility of the project by looking at the reference Col-O (Columbia) and Bur-O and Tsu-1 strains.  The paper presents the process, compares their pipeline software with another package (SHORE that they developed and MAQ), They have a GBrowse installation that presents the data  (and you can get free training on GBrowse here to effectively use the site).  They also provide data to TAIR.

I think this is important and I hope it gets the same level of support and respect that 1000 humans will get.

1001 Genomes main site: http://1001genomes.org/

1001 Genomes GBrowse: http://gbrowse.weigelworld.org/cgi-bin/gbrowse/ath_reseq_1001/

References:
Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Scholkopf, B., Nordborg, M., Ratsch, G., Ecker, J., & Weigel, D. (2007). Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science, 317 (5836), 338-342 DOI: 10.1126/science.1138632

Ossowski, S., Schneeberger, K., Clark, R., Lanz, C., Warthmann, N., & Weigel, D. (2008). Sequencing of natural strains of Arabidopsis thaliana with short reads Genome Research, 18 (12), 2024-2033 DOI: 10.1101/gr.080200.108

Weigel, D., & Mott, R. (2009). The 1001 Genomes Project for Arabidopsis thaliana Genome Biology, 10 (5) DOI: 10.1186/gb-2009-10-5-107

At the recent ICSB conference I attended a terrific talk by Esther Schmidt. The focus of the talk was Reactome, which is an old favorite of ours. It has great high-quality curated data on biological pathways and has some fun tools to go beyond browsing around. But during the talk I learned about a new aspect of Reactome that I didn’t know about before: Arabidopsis Reactome!

Arabidopsis Reactome is based on the same Reactome software framework, but it is very very green . The focus of the site is, of course, Arabidopsis pathways. In fact, in the paper that describes the resource says that this database covers about 8% of the Arabidopsis proteome at this time. But in addition they have “electronically projected” (aka inferred orthologous events) among 5 other plant species as well. Rice, poplar, a moss and 2 of the grapes have been completed, so they use those 6 species to provide the view of the plant pathway systems that you’ll find at the site.

In this ~3min movie I give you a quick look at the green pathways–but you should go over and have a look yourself as well: http://arabidopsisreactome.org/

Also, check out their paper: http://www.plantcell.org/cgi/content/full/20/6/1426
Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology. Nicolas Tsesmetzis et al. The Plant Cell 20:1426-1436 (2008) DOI: 10.1105/tpc.108.057976