title: Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research.
abstract: OBJECTIVE
  To review and evaluate available software tools for electronic health record-driven phenotype authoring in order to identify gaps and needs for future development.
  
  
  METHODS
  Candidate phenotype authoring tools were identified through (1) literature search in four publication databases (PubMed, Embase, Web of Science, and Scopus) and (2) a web search. A collection of tools was compiled and reviewed after the searches. A survey was designed and distributed to the developers of the reviewed tools to discover their functionalities and features.
  
  
  RESULTS
  Twenty-four different phenotype authoring tools were identified and reviewed. Developers of 16 of these identified tools completed the evaluation survey (67% response rate). The surveyed tools showed commonalities but also varied in their capabilities in algorithm representation, logic functions, data support and software extensibility, search functions, user interface, and data outputs.
  
  
  CONCLUSIONS
  Positive trends identified in the evaluation included: algorithms can be represented in both computable and human readable formats; and most tools offer a web interface for easy access. However, issues were also identified: many tools were lacking advanced logic functions for authoring complex algorithms; the ability to construct queries that leveraged un-structured data was not widely implemented; and many tools had limited support for plug-ins or external analytic software.
  
  
  CONCLUSIONS
  Existing phenotype authoring tools could enable clinical researchers to work with electronic health record data more efficiently, but gaps still exist in terms of the functionalities of such tools. The present work can serve as a reference point for the future development of similar tools.
authors.affiliation: Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA jie.xu@northwestern.edu.
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.affiliation: Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
authors.forename: Luke V
authors.initials: LV
authors.lastname: Rasmussen
authors.affiliation: Galter Health Science Library, Clinical and Translational Sciences Institute (NUCATS), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
authors.forename: Pamela L
authors.initials: PL
authors.lastname: Shaw
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
authors.forename: Guoqian
authors.initials: G
authors.lastname: Jiang
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Kiefer
authors.affiliation: Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA.
authors.forename: Huan
authors.initials: H
authors.lastname: Mo
authors.affiliation: 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: Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Speltz
authors.affiliation: Department of Information Systems, University of Maryland, Baltimore County (UMBC), Baltimore, MD, USA.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA.
authors.forename: Joshua C
authors.initials: JC
authors.lastname: Denny
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
authors.forename: Jyotishman
authors.initials: J
authors.lastname: Pathak
authors.affiliation: Center for Biomedical Research Informatics, NorthShore University Health System, Evanston, IL, USA.
authors.forename: William K
authors.initials: WK
authors.lastname: Thompson
authors.affiliation: Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
authors.forename: Enid
authors.initials: E
authors.lastname: Montague
mesh_terms: D000465:Algorithms; D035843:Biomedical Research; D057286:Electronic Health Records; D006801:Humans; D012984:Software; D057170:Translational Research, Biomedical
keywords: clinical research; electronic health records; phenotype algorithm authoring tool; phenotyping; review