SESL

Imagine you’re a scientist looking for information on disease-causing genes. To find this information in published literature or biological databases, you currently have to search each source separately. It’s assumed that you—the scientist—will know what sources are available and where to look to find the information you need.

Now imagine you’re that same scientist, later in the day, and you want to buy a toaster or find the cheapest fare for your upcoming vacation. You plug in your criteria in Amazon.com or Expedia and these sites—not you—aggregate the information from the available sources and display them conveniently for you to browse.

Why should scientific information be handled differently from retail goods or travel products? The SESL project has explored the feasibility of an Amazon.com-like "brokering service" that would help scientists rapidly gather information on disease-causing genes. The service envisioned by the SESL team "pushes" appropriate information to scientists based on a single query, rather than requiring scientists to "pull" information from often disconnected databases and literature sources possessing a multiplicity of different user interfaces.

The SESL public demonstrator for brokering gene data associated with Type 2 diabetes was completed in 2011. The demonstrator will ultimately include content from numerous bioinformatics databases (Uniprot, OMIM, and ArrayExpress) and five publishers (Nature Publishing Group, Oxford University Press, the Royal Society of Chemistry, UK Pubmed Central, and Elsevier). The SESL team is also publishing the concepts underpinning knowledge brokering and the cultural and technical achievements of this pilot work. Wendy Filsell and Ian Harrow, the lead authors, expect to have a paper ready for publication by the end of 2011. A technical paper describing the architecture and components used to build the knowledge broker is being developed by Dietrich Rebholz-Schuhmann of EMBL-EBI. Watch this space for links to the papers when they are completed.

The SESL team expected the project to evolve into a second phase exploring the business models for sustainably delivering a knowledge brokering service. In the interim, however, SESL’s learnings have begun influencing other semantics-based projects. An important and well-funded example of this is the Innovative Medicines Initiative Open PHACTS consortium, which is building a semantics-based Open Pharmacological Space. The SESL team has determined that the best way to progress life-science knowledge brokering is to support and drive these other semantics-based initiatives.