Abstract
The NCBI Taxonomy underpins many bioinformatics and phyloinformatics databases, but by itself provides limited information on the taxa it contains. One readily available source of information on many taxa is Wikipedia. This paper describes iPhylo Linkout, a Semantic wiki that maps taxa in NCBI's taxonomy database onto corresponding pages in Wikipedia. Storing the mapping in a wiki makes it easy to edit, correct, or otherwise annotate the links between NCBI and Wikipedia. The mapping currently comprises some 53,000 taxa, and is available at http://iphylo.org/linkout. The links between NCBI and Wikipedia are also made available to NCBI users through the NCBI LinkOut service.
Highlights
One of the great challenges of phyloinformatics is linking together information on phylogenies, taxa, genomes, specimens, and publications [1]
There are a plethora of biodiversity databases [2], but a dearth of services that map identifiers across these databases
This paper describes the construction one such tool, a biodiversity knuckle that maps identifiers between two major resources, the NCBI taxonomy database [6] and Wikipedia [7]
Summary
One of the great challenges of phyloinformatics is linking together information on phylogenies, taxa, genomes, specimens, and publications [1]. Given a mapping from NCBI tax_ids to Wikipedia pages, it would be straightforward to extract taxon images from Wikipedia and create illustrations of phylogenies from, for example, TreeBASE, annotated with images of the taxa contained in those phylogenies. The initial mapping was constructed by extracting the scientific name of the taxon that was the topic of each Wikipedia page, finding a match for this in the NCBI taxonomy database.
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