Andrea Splendiani Current position: Postdoc on EU Project Bootstrep, at University of Rennes 1, Medical Informatics Department (FR) Former positions: Stagiaire Scientifique at Institut Pasteur, Systems Biology Unit (FR) PhD student (ex) in Computer Science, Univ. of Milano-Bicocca (IT) Research assistant at Genopolis Consortium (IT)

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Research interests:


I'm intersted in the organization of knowledge in the Life Science domain, and in its exploitation in functional evaluation of high-throughput data.
Can the web be a distributed knowledge base that can be used directly to interpret the results of high-throughput experiments ?
My primary focus is in ontologies represented in the Semantic Web framework, in particular pathway ontologies (BioPAX), and I make an heavy use of Cytoscape and Jena.
In the past, I have been active on microarray database design and development.
More can be found in these project descriptions or related documents.

Some projects of mine:

The Genopolis Microarray Database
MIAME compliant, controlled vocabularies, distributed annotation	visual context-based browsing of microarray data
The Genopolis Microarray Database originated as custom microarray database project for Affymetrix GeneChip data, supporting an homogeneous community studying dendritic cells differentiation. It is based on an object model MAGE compliant, and provides support for MIAME annotation, export to ArrayExpress as well as many search and visualization features (including browsing of data based on related/similar samples of genes). Group of users and the microarray facilty staff can build toghether experimental descriptions, with supports for controlled vocabularies and consistency controls. Access management support restricted access to unpublished data within groups of users. The Genopolis Microarray Database is currently deployed at Genopolis. It was described in this paper, and its code base is publicly available on bioinformatics.org.

RDFScape
RDFScape aims at making the Semantic Web available for Systems Biology, and at improving the using on ontologies for functional evaluation of experimental data. It is an ongoing project. In its current release, it empowers Cytoscape with the possibility to read owl/rdf ontologies, and to reason on them through standard and custom inference rules. Results can be used to generate semantic-based transformations of the original information, that can queried, browsed or overlayed to other data within Cytoscape. In its future versions, it will include the ability to score "ontology patterns" based on actual experimental data (this will be the basis to extend Pathway Scoring methods, and to assess the correspondence between information content in ontology and in actual data). More information about RDFScape can be found on this working paper (soon to appear a paper in BMC), while the current codebase is on bioinformatics.org.

A platform for ontology alignment/enrichment (work in progress)
This work originated within the Bootstrep project. It aims at providing a platform where several tasks related to ontology alignment/enrichment can be modularly composed. At the same time this platform will act as an "ontology information server" (performing reasoning on demand, answering queries). A new method for ontology alignment that makes use of the flexibility of this platform is also under development.

Other projects of mine:

I'm collaborating with Leaf Bioscience s.r.l. and in the DC-THERA NoE. In particular, part of the development of RDFScape is financed by dc-thera through Leaf Bioscience s.r.l.. I'm also assisting Leaf Bioscience s.r.l. in the development of a knowledge resource for the dc-thera community based on ontologies.