959 Nematode Genomes: a semantic wiki for coordinating sequencing projects

Abstract

Genome sequencing has been democratized by second-generation technologies, and even small labs can sequence metazoan genomes now. In this article, we describe '959 Nematode Genomes'--a community-curated semantic wiki to coordinate the sequencing efforts of individual labs to collectively sequence 959 genomes spanning the phylum Nematoda. The main goal of the wiki is to track sequencing projects that have been proposed, are in progress, or have been completed. Wiki pages for species and strains are linked to pages for people and organizations, using machine- and human-readable metadata that users can query to see the status of their favourite worm. The site is based on the same platform that runs Wikipedia, with semantic extensions that allow the underlying taxonomy and data storage models to be maintained and updated with ease compared with a conventional database-driven web site. The wiki also provides a way to track and share preliminary data if those data are not polished enough to be submitted to the official sequence repositories. In just over a year, this wiki has already fostered new international collaborations and attracted newcomers to the enthusiastic community of nematode genomicists. www.nematodegenomes.org.

Figure 1.

Systematic tree of Nematoda, with a few taxonomic nodes expanded to show how the Blaxter and Helder classifications were incorporated into the tree.

Figure 2.

Species page for C. elegans displaying information for the species as well as the status of strains that have been sequenced.

Figure 3.

Page for the taxonomic node Enoplia, showing NCBI Taxonomy and NCBI EST link-outs, as well as the results of the query ‘Species and strains under this taxon with their sequencing status set to anything other than “None”’.