Ontology-based federated data access to human studies information.

Ida Sim, Simona Carini, Samson W. Tu, Landon T. Detwiler, James Brinkley, Shamim A. Mollah, Karl Burke, Harold P Lehmann, Swati Chakraborty, Knut M. Wittkowski, Brad H. Pollock, Thomas M. Johnson, Vojtech Huser, Studies Database Project Human Studies Database Project

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)856-865
Number of pages10
JournalAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium
Volume2012
StatePublished - 2012
Externally publishedYes

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Semantics
Systematized Nomenclature of Medicine
Research
Databases
Informatics
Evidence-Based Medicine
Biomedical Research
Technology

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Sim, I., Carini, S., Tu, S. W., Detwiler, L. T., Brinkley, J., Mollah, S. A., ... Human Studies Database Project, S. D. P. (2012). Ontology-based federated data access to human studies information. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, 2012, 856-865.

Ontology-based federated data access to human studies information. / Sim, Ida; Carini, Simona; Tu, Samson W.; Detwiler, Landon T.; Brinkley, James; Mollah, Shamim A.; Burke, Karl; Lehmann, Harold P; Chakraborty, Swati; Wittkowski, Knut M.; Pollock, Brad H.; Johnson, Thomas M.; Huser, Vojtech; Human Studies Database Project, Studies Database Project.

In: AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, Vol. 2012, 2012, p. 856-865.

Research output: Contribution to journalArticle

Sim, I, Carini, S, Tu, SW, Detwiler, LT, Brinkley, J, Mollah, SA, Burke, K, Lehmann, HP, Chakraborty, S, Wittkowski, KM, Pollock, BH, Johnson, TM, Huser, V & Human Studies Database Project, SDP 2012, 'Ontology-based federated data access to human studies information.', AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, vol. 2012, pp. 856-865.
Sim, Ida ; Carini, Simona ; Tu, Samson W. ; Detwiler, Landon T. ; Brinkley, James ; Mollah, Shamim A. ; Burke, Karl ; Lehmann, Harold P ; Chakraborty, Swati ; Wittkowski, Knut M. ; Pollock, Brad H. ; Johnson, Thomas M. ; Huser, Vojtech ; Human Studies Database Project, Studies Database Project. / Ontology-based federated data access to human studies information. In: AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 2012 ; Vol. 2012. pp. 856-865.
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