Research Projects

Current Projects

• e-LICO is an EU funded FP7 project that aims to provide a "data mining assistant" to scientists. It will use both the myExperiment and the Utopia tools to help in this task.
• The Semantic Web Authoring Tool (SWAT) project is funded by the EPSRC. It is a colaboration between the Open University and the University of Manchester. The aim is to use natural language generation techniques to facilitate the building of OWL Tbox and ABox, as well as RDF vocabularies.
• The Ontogenesis network is an EPSRC funded network that brings together life scientists, computer scientists and bioinformaticians interested in the application of Semantic Web technologies. along with David Shotton, who runs the network with me, we've been using the network to do a series of experiments in ontology building. See the project Web site for details.
• BioCatalogue is a project funded by the Tools and Resources theme of the BBSRC. In collaboration with the European bioinformatics Institute, biocatalogue seeks to create a repository of semantically described bioinformatics services.
• ONDEX is a BBSRC funded projectin systems biology.
• myExperiment is a sibling project to myGrid and provides an environment through which scientists can find, exchange, enact workflows and all that entails in terms of description, recommendation, etc.
• myGrid platform grant has a second EPSRC platform grant to sustain the core myGrid team.
• collaborative Open Ontology Development Environment (CO-ODE) is a collaboration with Stanford University to develop the Protege ontology development environment for OWL.

Past Projects

• Open Middleware Infrastructure Instituteis funded by the EPSRC to provide longevity to the software delivered by the UK e-Science programme.
• Sealife is an EU funded project that aims to create user orientated browsers for Semantic Webs of life science. This project employs Simon Jupp and Dmitry Tsarcov.
• ComparaGRID is a BBSRC funded e-Science project that aims to integrate distributed, heterogeneous genomic map resources using semantic technologies based on ontologies.
• Computational Exploration of Molecules in the Context of Biological Pathway Networks (EMPWR) was an NSF funded project that used the BioPAX ontology and a reasoner to explore pathway data.
• The myGrid project was an EPSRC e-Science pilot project. It has created upper middleware services for supporting in silico experiments -- especially in bioinformatics. the myGrid project continues as part of OMII-UK
• < a href="http://mytea.org.uk/">the myTea project was an EPSRC Best Practice project that sought to transfer user interface design from the CombeChem project to the In Silico Proteome Integrated Data Environment Resource (ISPIDER) was a BBSRC funded e-Science project to create a Grid enabled proteomics informatics environment.
• Gene Ontology Next Generation (GONG) developed a methodology for migrating the axiomatically lean Gene Ontology to an axiomatically rich DAML+OIL or OWL description logic version.
• Gene Ontology Annotation Tool (GOAT) used DAML+OIL versions of the Gene Ontology enriched with axioms cross-linking the three GO ontologies to guide annotators to choose GO terms that made biological sense.
• Reconcile And SHare (RASH) was an EPSRC/BBSRC joint bioinformatics initiative funded project that investigated methodologies for sharing the outcomes of reconciling bioinformatics resources.
• Information Retrieval for biology and Nothing Else (IRBANE) sought to use simple information retrieval techniques to gather information helpful to annotators of biological data.
• The original TAMBIS Web pages are available, even though the application itself no longer runs.