title: Ontology-based federated data access to human studies information.
abstract: Human studies are one of the most valuable sources of knowledge in biomedical research, but data about their design and results are currently widely dispersed in siloed systems. Federation of these data is needed to facilitate large-scale data analysis to realize the goals of evidence-based medicine. The Human Studies Database project has developed an informatics infrastructure for federated query of human studies databases, using a generalizable approach to ontology-based data access. Our approach has three main components. First, the Ontology of Clinical Research (OCRe) provides the reference semantics. Second, a data model, automatically derived from OCRe into XSD, maintains semantic synchrony of the underlying representations while facilitating data acquisition using common XML technologies. Finally, the Query Integrator issues queries distributed over the data, OCRe, and other ontologies such as SNOMED in BioPortal. We report on a demonstration of this infrastructure on data acquired from institutional systems and from ClinicalTrials.gov.
authors.affiliation: University of California, San Francisco, CA, USA.
authors.forename: Ida
authors.initials: I
authors.lastname: Sim
authors.forename: Simona
authors.initials: S
authors.lastname: Carini
authors.forename: Samson W
authors.initials: SW
authors.lastname: Tu
authors.forename: Landon T
authors.initials: LT
authors.lastname: Detwiler
authors.forename: James
authors.initials: J
authors.lastname: Brinkley
authors.forename: Shamim A
authors.initials: SA
authors.lastname: Mollah
authors.forename: Karl
authors.initials: K
authors.lastname: Burke
authors.forename: Harold P
authors.initials: HP
authors.lastname: Lehmann
authors.forename: Swati
authors.initials: S
authors.lastname: Chakraborty
authors.forename: Knut M
authors.initials: KM
authors.lastname: Wittkowski
authors.forename: Brad H
authors.initials: BH
authors.lastname: Pollock
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Johnson
authors.forename: Vojtech
authors.initials: V
authors.lastname: Huser
mesh_terms: D002986:Clinical Trials as Topic; D003628:Database Management Systems; D016208:Databases, Factual; D006805:Human Experimentation; D006801:Humans; D011381:Programming Languages; D018875:Vocabulary, Controlled