Research

I’m interested in a variety of subjects, which cross the boundary between Life Sciences and Computer Science.

In an area which is broadly called ``Bioinfomatics” or at times “Computational” or ``Systems Biology”, I’m interested in how to organize knowledge in the Life Science domain, with the goal of providing a computational support to understand the function of biological systems. In very broad terms, I’m interested in what can be a “computational collective scientific intelligence”. In the specifics, I have been active on a variety of projects, many of which are still in progress. I’ve grouped them in four related areas:

Biomedical ontologies and representation of Biological Pathways

The functional evaluation of experimental data relies on ontologies. I’m particularly interested in pathway ontologies, as their information complexity is particularly reach. I’ve been active for some time in the BioPAX workgroup, where I am now an editor, and I’m setting up a workgroup to make BioPAX more Semantic Web friendly.

Biomedical knowledge bases and infrastructures

I’ve been designing a few Life Science information resources, with an emphasis on the consistent annotation of the information content, and its integrability with external resources.

Visualization and User Interaction on the Semantic Web

With its “late semantic binding” , the Semantic Web makes a part of the data integration process easier, but post-pone much of the interpretation work at a later phase (this is an RDF-centric view of the Semantic Web). It makes sense, as the interpretation is closer to the actual usage of the information. However, there is the need for tools which can be used to analyze and extract information from schema-less representations. I’ve been experimenting in this direction with Cytoscape and more recently within the Ondex team.┬áNot surprisingly , I tend to use a lot tools as Jena.

Ontology based data analysis

I have played with a few approaches to bring information from ontologies into the data “analysis process”, meant in its broader term, which include interactive analytical methods. I’ve been experimenting with it both in the context of microarray databases, and pathways/interaction data.

More information on projects falling in these categories can be accessed through the site menu.

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