Visualising a scientific article

Abstract

This paper describes my entry in the Elsevier Grand Challenge "Knowledge Enhancement in the Life Sciences" contest. The entry takes 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 typed 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":http://bioguid.info, a tool I constructed to resolve globally unique identifiers and return associated metadata.