Welcome to my Elsevier Challenge entry

This web site is part of my entry in Elsevier's Grand Challenge "Knowledge Enhancement in the Life Sciences".My original proposal (rather grandly titled "Towards realising Darwin’s dream: setting the trees free") is available from Nature Precedings (doi:10.1038/npre.2008.2217.1). A paper describing the actual entry is also available ("Visualising a scientific article", doi:10.1038/npre.2008.2579.1).

My project uses a collection of fulltext issues of Molecular Phylogenetics and Evolution as the starting point, then extracts citation links to both papers and data, such as Genbank sequences and specimens, together with geotagged localities, and builds a "web" of objects linked by relationships. Each object (such as a publication, a sequence, a specimen, a taxon name, etc.) is treated equally, so that you can take a publication and see what taxa it refers to, or take the taxon and find all the publications that refer to the taxon. Although the database has been seeded with some articles from Molecular Phylogenetics and Evolution, much of the data comes from GenBank, PubMed, and specimen databases. These are accessed through bioguid.info, a tool I constructed to resolve identifiers and return associated metadata.


You can find background on this project on my blog. In many ways the inspiration for this project is SiloBreaker. I will post a more detailed description of the project (and what goes on under the hood) shortly. You can also see my earlier attempt. Meantime, some starting points (not all from Molecular Phylogenetics and Evolution) are:


As it stands the demo has some glaring limitations, particularly regarding the lists of studies that are geographically overlapping. The lack of phylogenetic trees is also frustrating. In the absence of an automated way to extract trees from images, I may add some trees from TreeBASE and disaply them using my tvwidget. There are also likely to be some errors in the underlying data, or in how it has been parsed. Meantime I welcome any feedback or comments.

Rod Page

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Video about the challenge

What is a study about?

Visual summary of the organisms included in a Molecular Phylogenetics and Evolution article.


Example of a map automatically constructed from geotagged specimens cited by a Molecular Phylogenetics and Evolution article (the map requires a browser that can display SVG, Internet Explorer users will need a plugin such as RENESIS).

Error, browser must support "SVG"