title: Toward an ontology-based framework for clinical research databases.
abstract: Clinical research includes a wide range of study designs from focused observational studies to complex interventional studies with multiple study arms, treatment and assessment events, and specimen procurement procedures. Participant characteristics from case report forms need to be integrated with molecular characteristics from mechanistic experiments on procured specimens. In order to capture and manage this diverse array of data, we have developed the Ontology-Based eXtensible data model (OBX) to serve as a framework for clinical research data in the Immunology Database and Analysis Portal (ImmPort). By designing OBX around the logical structure of the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI), we have found that a relatively simple conceptual model can represent the relatively complex domain of clinical research. In addition, the common framework provided by BFO makes it straightforward to develop data dictionaries based on reference and application ontologies from the OBO Foundry.
authors.affiliation: Department of Pathology, U.T. Southwestern Medical Center, Dallas, TX 75390-9072, United States.
authors.forename: Y Megan
authors.initials: YM
authors.lastname: Kong
authors.forename: Carl
authors.initials: C
authors.lastname: Dahlke
authors.forename: Qun
authors.initials: Q
authors.lastname: Xiang
authors.forename: Yu
authors.initials: Y
authors.lastname: Qian
authors.forename: David
authors.initials: D
authors.lastname: Karp
authors.forename: Richard H
authors.initials: RH
authors.lastname: Scheuermann
mesh_terms: D035843:Biomedical Research; D019295:Computational Biology; D003628:Database Management Systems; D016208:Databases, Factual; D008490:Medical Informatics; D008962:Models, Theoretical; D012107:Research Design
references.citation: Nat Biotechnol. 2007 Nov;25(11):1251-5
references.pmid: 17989687
references.citation: J Am Med Inform Assoc. 2008 Mar-Apr;15(2):130-7
references.pmid: 18096907
references.citation: Stud Health Technol Inform. 2004;102:20-38
references.pmid: 15853262
references.citation: J Am Med Inform Assoc. 2007 Sep-Oct;14(5):662-73
references.pmid: 17600107
references.citation: J Biomed Inform. 2009 Apr;42(2):327-33
references.pmid: 19026765
references.citation: J Am Med Inform Assoc. 2010 Mar-Apr;17(2):131-5
references.pmid: 20190054
references.citation: J AHIMA. 2009 Jul;80(7):44-50; quiz 51-2
references.pmid: 19663144
references.citation: Acad Med. 2010 Mar;85(3):457-62
references.pmid: 20182118
references.citation: Nat Biotechnol. 2008 Aug;26(8):889-96
references.pmid: 18688244
references.citation: Methods Inf Med. 2009;48(5):408-13
references.pmid: 19621114
references.citation: Cytometry A. 2008 Oct;73(10):926-30
references.pmid: 18752282