title: ePhenotyping for Abdominal Aortic Aneurysm in the Electronic Medical Records and Genomics (eMERGE) Network: Algorithm Development and Konstanz Information Miner Workflow.
abstract: OBJECTIVE
  We designed an algorithm to identify abdominal aortic aneurysm cases and controls from electronic health records to be shared and executed within the "electronic Medical Records and Genomics" (eMERGE) Network.
  
  
  METHODS
  Structured Query Language, was used to script the algorithm utilizing "Current Procedural Terminology" and "International Classification of Diseases" codes, with demographic and encounter data to classify individuals as case, control, or excluded. The algorithm was validated using blinded manual chart review at three eMERGE Network sites and one non-eMERGE Network site. Validation comprised evaluation of an equal number of predicted cases and controls selected at random from the algorithm predictions. After validation at the three eMERGE Network sites, the remaining eMERGE Network sites performed verification only. Finally, the algorithm was implemented as a workflow in the Konstanz Information Miner, which represented the logic graphically while retaining intermediate data for inspection at each node. The algorithm was configured to be independent of specific access to data and was exportable (without data) to other sites.
  
  
  RESULTS
  The algorithm demonstrated positive predictive values (PPV) of 92.8% (CI: 86.8-96.7) and 100% (CI: 97.0-100) for cases and controls, respectively. It performed well also outside the eMERGE Network. Implementation of the transportable executable algorithm as a Konstanz Information Miner workflow required much less effort than implementation from pseudo code, and ensured that the logic was as intended.
  
  
  CONCLUSIONS
  This ePhenotyping algorithm identifies abdominal aortic aneurysm cases and controls from the electronic health record with high case and control PPV necessary for research purposes, can be disseminated easily, and applied to high-throughput genetic and other studies.
authors.affiliation: The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA, USA.
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Borthwick
authors.affiliation: The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA, USA.
authors.forename: Diane T
authors.initials: DT
authors.lastname: Smelser
authors.affiliation: The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Bock
authors.affiliation: Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Elmore
authors.affiliation: Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA, USA.
authors.forename: Evan J
authors.initials: EJ
authors.lastname: Ryer
authors.affiliation: Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
authors.forename: Zi
authors.initials: Z
authors.lastname: Ye
authors.affiliation: Divisions of General Internal Medicine and Preventive Medicine, and the Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Pacheco
authors.affiliation: Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Carrell
authors.affiliation: Patient-Centered Research, Aurora Research Institute™, Aurora Sinai Medical Center, Milwaukee, WI, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Michalkiewicz
authors.affiliation: Divisions of General Internal Medicine and Preventive Medicine, and the Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
authors.forename: William K
authors.initials: WK
authors.lastname: Thompson
authors.affiliation: Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
authors.forename: Jyotishman
authors.initials: J
authors.lastname: Pathak
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA.
authors.forename: Suzette J
authors.initials: SJ
authors.lastname: Bielinski
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.
authors.forename: Joshua C
authors.initials: JC
authors.lastname: Denny
authors.affiliation: Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA.
authors.forename: James G
authors.initials: JG
authors.lastname: Linneman
authors.affiliation: Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA.
authors.forename: Peggy L
authors.initials: PL
authors.lastname: Peissig
authors.affiliation: Divisions of General Internal Medicine and Preventive Medicine, and the Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
authors.forename: Abel N
authors.initials: AN
authors.lastname: Kho
authors.affiliation: The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
authors.forename: Omri
authors.initials: O
authors.lastname: Gottesman
authors.affiliation: Patient-Centered Research, Aurora Research Institute™, Aurora Sinai Medical Center, Milwaukee, WI, USA.
authors.forename: Harpreet
authors.initials: H
authors.lastname: Parmar
authors.affiliation: Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
authors.forename: Iftikhar J
authors.initials: IJ
authors.lastname: Kullo
authors.affiliation: Essentia Institute of Rural Health, Duluth, MN, USA.
authors.forename: Catherine A
authors.initials: CA
authors.lastname: McCarty
authors.affiliation: The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
authors.forename: Erwin P
authors.initials: EP
authors.lastname: Böttinger
authors.affiliation: Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA.
authors.forename: Eric B
authors.initials: EB
authors.lastname: Larson
authors.affiliation: Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA.
authors.forename: Gail P
authors.initials: GP
authors.lastname: Jarvik
authors.affiliation: Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
authors.forename: John B
authors.initials: JB
authors.lastname: Harley
authors.affiliation: Patient-Centered Research, Aurora Research Institute™, Aurora Sinai Medical Center, Milwaukee, WI, USA.
authors.forename: Tanvir
authors.initials: T
authors.lastname: Bajwa
authors.affiliation: Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA, USA.
authors.forename: David P
authors.initials: DP
authors.lastname: Franklin
authors.affiliation: The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Carey
authors.affiliation: The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA, USA; Department of Surgery, Temple University School of Medicine, Philadelphia, PA, USA.
authors.forename: Helena
authors.initials: H
authors.lastname: Kuivaniemi
authors.affiliation: The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA, USA.
authors.forename: Gerard
authors.initials: G
authors.lastname: Tromp
keywords: Aortic aneurysm; Case-Control study; Computing methodologies; Electronic health records; Electronic medical record; ICD-9; KNIME