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James Malone

Homepage of Dr James Malone, Lead Ontologist at the European Bioinformatics Institute, Cambridge, UK.

Contact me at malone@ebi.ac.uk



Ontologies, Bioinformatics, Artificial Intelligence, Data Mining

My research is underpinned by the hypothesis that computational techniques can offer novel insights into biomedical problems by data integration and large scale data anlysis. My work has covered a wide range of techniques and technologies in applying this work to bioinformatic data. I am presently very active in the bio-ontology community where I work on knowledge representation for experimental variable data, such as those found in ArrayExpress. This has resulted in the Experimental Factor Ontology (EFO), though I have also worked on communnity efforts such as the Ontology for Biomedical Investigation as part of my work on EMERALD for producing data standards across the European Microarray Community. I have also been working with Semantic Web groups and I am involved in developing the EBI RDF Platform and built an R package that can query this resource. I also co-wrote the recently awarded SWORD Software Ontology project, funded by JISC. My work also touches on aspects of data integration, such as RDF triple representation of data and natural language extraction and text mining from which a set of tools have been developed. I have previously worked with industry and academia in applying AI techniques such as automated ontology construction, decision support, text mining at Edinburgh University and my PhD work concnered the use of neural networks and fuzzy learning in identifying interesting proteins from 2-D electrophoresis gel data. I am currently based in the Samples, Phenotypes and Ontologies group at EBI, Cambridge. I jointly organised the first UK Ontology Network Workshop in 2012, click here for more information on UKON. As a proud native of Newcastle I also provide a Geordie version>> I also write a blog.