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This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences, 2008

Open Access Research

Knowledge-driven enhancements for task composition in bioinformatics

Karen Sutherland1*, Kenneth McLeod1, Gus Ferguson1 and Albert Burger12

Author Affiliations

1 Department of Computer Science, Heriot-Watt University, Edinburgh, UK

2 MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, Edinburgh, UK

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BMC Bioinformatics 2009, 10(Suppl 10):S12  doi:10.1186/1471-2105-10-S10-S12

Published: 1 October 2009



A key application area of semantic technologies is the fast-developing field of bioinformatics. Sealife was a project within this field with the aim of creating semantics-based web browsing capabilities for the Life Sciences. This includes meaningfully linking significant terms from the text of a web page to executable web services. It also involves the semantic mark-up of biological terms, linking them to biomedical ontologies, then discovering and executing services based on terms that interest the user.


A system was produced which allows a user to identify terms of interest on a web page and subsequently connects these to a choice of web services which can make use of these inputs. Elements of Artificial Intelligence Planning build on this to present a choice of higher level goals, which can then be broken down to construct a workflow. An Argumentation System was implemented to evaluate the results produced by three different gene expression databases. An evaluation of these modules was carried out on users from a variety of backgrounds. Users with little knowledge of web services were able to achieve tasks that used several services in much less time than they would have taken to do this manually. The Argumentation System was also considered a useful resource and feedback was collected on the best way to present results.


Overall the system represents a move forward in helping users to both construct workflows and analyse results by incorporating specific domain knowledge into the software. It also provides a mechanism by which web pages can be linked to web services. However, this work covers a specific domain and much co-ordinated effort is needed to make all web services available for use in such a way, i.e. the integration of underlying knowledge is a difficult but essential task.