Mikel Egaña Aranguren
Position: M. Sc. student.
I obtained a Biology degree from the University of the Basque Country (UPV/EHU) (Spain) in 2003, then completed a Bioinformatics MSc (2004) and Computer Science PhD (2009) at the University of Manchester, UK. This included a Marie Curie placement at the Vlaams Institute for Biotechnology (VIB) in Belgium, and a placement at the European Bioinformatics Institute (EBI), UK. I undertook a post-doctoral fellowship at the University of Murcia in Spain and currently am funded for three years by the Marie Curie program at the Universidad Politecnica Madrid, with my first year in the Ontology Engineering Group (OEG) of the Computer Science department, followed by my current position in the Biological Informatics Group (BIG) of the Centre for Plant Biotechnology and Genomics, lead by Mark Wilkinson.
My research interest lies in the exploitation of Semantic Web technology to answer cutting-edge life science questions, particularly at the molecular level, including automated generation of hypotheses «hidden» in the current «data tsunami». I have implemented this research agenda through investigations at the interface between Computer Science and Life Sciences, including:
- Models: I have participated in the development of semantic resources used for knowledge integration and inference of meaningful scientific facts, including Cell Cycle Ontology, Orthologous Genes Ontology Linked Open Data, and BioGateway.
- Tools: I contributed to the development of the Ontology Pre Processor Language (OPPL), a scripting language for OWL ontologies; Onto-Perl, a Perl API for managing biomedical ontologies; and OPPL-Galaxy and NCBO-Galaxy, Galaxy tools for exploiting ontologies as part of bioinformatics workflows.
- Methodologies: I have defined, collected and documented Ontology Design Patterns as ready-to-use but expressive blocks, reducing the effort for biologists to build rich and rigorous bio-ontologies.
Through my experiences, I have gained a broad scientific perspective, with insights into the technology required to manage diverse biomedical tasks. Also, having developed such resources and tools, I have obtained a thorough technical experience, resulting in a considerable flexibility with regards to confronting technical problems and developing and maintaining systems: I can develop software (mainly Java and Perl but also Python and Bash), build solid knowledge models (OWL and RDF) including Knowledge Bases and Linked Data datasets, and administer UNIX systems. This technical flexibility allows me to oversee most technical aspects of even the most complex biomedical problem-spaces such as metagenome analyses. My technical skills are supported by my broad domain knowledge – at the University of Manchester I worked with Knowledge Representation (KR) experts; in the EBI I collaborated with bioinformaticians; in the VIB I worked with bioinformaticians and biologists; at the OEG I worked with KR experts, and now, at the BIG, I primarily collaborate with biologists.
I have a notable publication record, including high impact journals such as Genome Biology and BMC bioiformatics; Life Sciences conferences such as ISMB; and Computer Science conferences including EKAW.