A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of postgenomic clinical trials on cancer.
This paper reports on original results of the Advancing Clinico-Genomic Trials on Cancer integrated project focusing on the design and development of a European biomedical grid infrastructure in support of multicentric, postgenomic clinical trials (CTs) on cancer. Postgenomic CTs use multilevel clinical and genomic data and advanced computational analysis and visualization tools to test hypothesis in trying to identify the molecular reasons for a disease and the stratification of patients in terms of treatment. This paper provides a presentation of the needs of users involved in postgenomic CTs, and presents such needs in the form of scenarios, which drive the requirements engineering phase of the project. Subsequently, the initial architecture specified by the project is presented, and its services are classified and discussed. A key set of such services are those used for wrapping heterogeneous clinical trial management systems and other public biological databases. Also, the main technological challenge, i.e. the design and development of semantically rich grid services is discussed. In achieving such an objective, extensive use of ontologies and metadata are required. The Master Ontology on Cancer, developed by the project, is presented, and our approach to develop the required metadata registries, which provide semantically rich information about available data and computational services, is provided. Finally, a short discussion of the work lying ahead is included.
Tsiknakis
Manolis
M
Foundation for Research and Technology-Hellas, Institute of Computer Science, GR-71110 Heraklion, Greece. tsiknaki@ics.forth.gr
Brochhausen
Mathias
M
Nabrzyski
Jarek
J
Pucacki
Juliusz
J
Sfakianakis
Stelios G
SG
Potamias
George
G
Desmedt
Cristine
C
Kafetzopoulos
Dimitris
D
D002986:Clinical Trials as Topic; D019295:Computational Biology / Q000379:methods*; D003299:Cooperative Behavior; D003628:Database Management Systems; D023281:Genomics / Q000379:methods; D006801:Humans; D033181:Information Dissemination / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D009369:Neoplasms / Q000175:diagnosis / Q000378:metabolism* / Q000628:therapy*; D012107:Research Design; D012660:Semantics; D018511:Systems Integration; D014481:United States