Ontology based analysis of experimental data Andrea Splendiani Institute Pasteur, Unité de Biologie Systémique, rue du dr. Roux 25-28, 75015 Paris, France University of Milano-Bicocca, DISCO, via Bicocca degli Arcimboldi 8, 20126 Milano, Italy
[email protected] Abstract relating such a large scale experimental evidence to the exist- ing biological knowledge is essential in order to understand We address the problem of linking observations the phenomenon under study. from reality to a semantic web based knowledge Given the vast amount of data generated by high through- base. Concepts in the biological domain are in- put technologies, this necessitates automated support. creasingly being formalized through ontologies, At the same time there is an increasing availability of struc- with an increasing adoption of semantic web stan- tured biological information, in the semantic web framework dards. Atthe same time biologyis becominga data- in particular. The Gene Ontology[Ashburner et al., 2000] ini- centric science, since the increasing availability of tiative provides ontologies describing functions of gene prod- high throughput technologies yields a humanly in- ucts. It currently encompasses more than 17000 terms linked tractable amount of data describing the behavior by relations of inheritance and containment and it is avail- of biological systems at the molecular level. This able in RDF. MGED-ontology1 provides an ontology to de- creates the need for automated support to interpret scribe attributes relevant to mRNA experiments in OWL, and biological data given the pre-existing knowledge the BioPAX[The BioPAX workgroup] initiative is defining a about the biological systems under study. While common standard to represent biological pathways and inter- this is currently addressed through the analysis of action networks in OWL.