title: Integrating clinical, gene expression, protein expression and preanalytical data for in silico cancer research.
abstract: We present the phase I development of an integrative platform for the analysis of clinical, gene expression, protein expression and pre-analytical data. The platform is aimed at providing transparent access and analysis tools to researchers investigating new biomarkers and prognosis factors in the particular field of lymphoma diseases. In this article, we report on the data integration phase. The platform's principal advantage is its completeness as it integrates in a single environment clinical, genomic and proteomic data, allowing for their combined analysis. The architecture consists in a data warehouse including data on patients, clinical trials and array platforms and a DeMilitarized Zone for data exchange. A secure web-based platform allows any collaborative team to request the data warehouse and access basic statistics on integrated data. The presented system is currently in use.
authors.affiliation: UPRES EA3888 Conceptual Modeling of Biomedical Knowledge, Rennes University, France. delphine.rossille@chu-rennes.fr
authors.forename: Delphine
authors.initials: D
authors.lastname: Rossille
authors.forename: Anita
authors.initials: A
authors.lastname: Burgun
authors.forename: Céline
authors.initials: C
authors.lastname: Pangault-Lorho
authors.forename: Thierry
authors.initials: T
authors.lastname: Fest
mesh_terms: D014408:Biomarkers, Tumor / Q000097:blood*; D002986:Clinical Trials as Topic; D015331:Cohort Studies; D003199:Computer Systems; D003628:Database Management Systems; D030541:Databases, Genetic; D005602:France; D015972:Gene Expression Regulation, Neoplastic / Q000502:physiology*; D036281:Genetic Research; D006801:Humans; D016247:Information Storage and Retrieval; D008223:Lymphoma / Q000097:blood / Q000235:genetics*; D016403:Lymphoma, Large B-Cell, Diffuse / Q000097:blood / Q000175:diagnosis / Q000235:genetics*; D008491:Medical Informatics Applications; D016347:Medical Records Systems, Computerized / Q000458:organization & administration*; D011379:Prognosis; D040901:Proteomics; D012984:Software
chemical_list: D014408:Biomarkers, Tumor