AMIA 2011 Year in Review Files and Presentation

This page contains information about the 2012 Clinical Research Informatics (CRI) Year-In-Review session that I conducted at the conclusion of the 2011 AMIA Joint Summits on Translational Science. Background information, Files, and Bibliographic details are listed below, as is the slide presentation.


Background:

As with the other sessions, the items presented this year are ultimately selected by the presenter using an informal process, do not represent a systematic or comprehensive review, and certainly do not represent an organizational statement nor position of AMIA. I hope you find this useful. Below is information on this year’s session.

Details of search methodology:
  • Initial search by MESH terms: (("Biomedical Research"[Mesh] NOT "Genetic Research"[Mesh]) NOT "Translational Research"[Mesh]) AND "Informatics"[Mesh] AND "2009/01/10"[PDat] : "2011/03/09"[Pdat]
  • Additional search using keywords including: Clinical Trials; Clinical Research; Informatics; Translational; Data Warehouse
  • Additional article finding: based on recommendations from colleagues including the persons who served on the last two CRI Summit scientific program committees and selected other thought leaders in the CRI domain.


Based on the above methodology, the following articles were ultimately selected by the presenter - Peter Embi, i.e. me, as notable contributions to the CRI literature over the past 1+ years. This included: (a) 22 main finalists and (b) 11 additional articles either briefly mentioned or semi-finalists that are listed below but may not have been discussed in detail during the presentation.


Main Bibliography - 2011 CRI Year-in-Review (Organized by Category):

Defining of CRI (briefly mentioned to set context/scope for review):
  1. Embi P, Payne P. Clinical research informatics: challenges, opportunities and definition for an emerging domain. J Am Med Inform Assoc. 2009 May 1;16(3):316-27.

Data Warehousing & Knowledge Management:
  1. Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, et al. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). Journal of the American Medical Informatics Association : JAMIA. 2010 Jan 1;17(2):124-30.
  2. Sim I, Carini S, Tu S, Wynden R, Pollock BH, Mollah SA, et al. The human studies database project: federating human studies design data using the ontology of clinical research. AMIA Summits Transl Sci Proc. 2010 Jan 1;2010:51-5. 
  3. Crowley RS, Castine M, Mitchell K, Chavan G, McSherry T, Feldman M. caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research. Journal of the American Medical Informatics Association : JAMIA. 2010 May 1;17(3):253-64.
  4. Segagni D, Ferrazzi F, Larizza C, Tibollo V, Napolitano C, Priori SG, et al. R Engine Cell: integrating R into the i2b2 software infrastructure. Journal of the American Medical Informatics Association : JAMIA. 2011 Jan 24.
(Additional, semi-finalist articles in this category referred to briefly during presentation)
  1. Payne PRO, Borlawsky TB, Stephens W, Barrett MC, Nguyen-Pham T, Greaves AW. The TRITON Project: Design and Implementation of an Integrative Translational Research Information Management Platform. AMIA Annu Symp Proc. 2010 Jan 1;2010:617-21.
  2. Wynden R, Weiner M, Sim I, Gabriel D, Casale M, Carini S, et al. Ontology mapping and data discovery for the translational investigator. AMIA Summits Transl Sci Proc. 2010;2010:66-70. 
  3. Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H. Integrating existing natural language processing tools for medication extraction from discharge summaries. Journal of the American Medical Informatics Association : JAMIA. 2010 Jan 1;17(5):528-31.
  4. Szalma S, Koka V, Khasanova T, Perakslis ED. Effective knowledge management in translational medicine. J Transl Med. 2010 Jan 1;8:68.
  5. Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, et al. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. Journal of the American Medical Informatics Association : JAMIA. 2009 Jan 1;16(5):624-30.
  6. Ritchie M, Denny J, Crawford D, Ramirez A, Weiner J, Pulley J, et al. Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. Am J Hum Genet. 2010 Apr 9;86(4):560-72.

Researcher Support & Infrastructure
  1. Harris PA, Swafford JA, Edwards TL, Zhang M, Nigavekar SS, Yarbrough TR, et al. StarBRITE: The Vanderbilt University Biomedical Research Integration, Translation and Education portal. Journal of biomedical informatics. 2011 Feb 15.
  2. Harris P, Taylor R, Thielke R, Payne J, Gonzalez N, Conde J. Research electronic data capture (REDCap)--a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform. 2009 Apr 1;42(2):377-81.
  3. Payne PRO, Borlawsky TB, Rice R, Embi PJ. Evaluating the impact of conceptual knowledge engineering on the design and usability of a clinical and translational science collaboration portal. AMIA Summits Transl Sci Proc. 2010 Jan 1;2010:41-5.
  4. Pulley J, Harris P, Yarbrough T, Swafford J, Edwards T, Bernard G. An informatics-based tool to assist researchers in initiating research at an academic medical center: Vanderbilt Customized Action Plan. Acad Med. 2010 Jan 1;85(1):164-8.
  5. Shi Q, You YN, Nelson H, Allen MS, Winchester D, Stewart A, et al. Cancer registries: a novel alternative to long-term clinical trial follow-up based on results of a comparative study. Clin Trials. 2010 Dec 1;7(6):686-95.
(Additional, semi-finalist article in this category not mentioned during presentation)
  1. He S, Hurdle JF, Botkin JR, Narus SP. Integrating a Federated Healthcare Data Query Platform With Electronic IRB Information Systems. AMIA Annu Symp Proc. 2010 Jan 1;2010:291-5.

Participant Recruitment & Eligibility Criteria:
  1. Weng C, Bigger JT, Busacca L, Wilcox A, Getaneh A. Comparing the effectiveness of a clinical registry and a clinical data warehouse for supporting clinical trial recruitment: a case study. AMIA Annu Symp Proc. 2010 Jan 1;2010:867-71.
  2. Dugas M, Lange M, Müller-Tidow C, Kirchhof P, Prokosch H-U. Routine data from hospital information systems can support patient recruitment for clinical studies. Clin Trials. 2010 Apr 1;7(2):183-9.
  3. Weng C, Tu SW, Sim I, Richesson R. Formal representation of eligibility criteria: a literature review. Journal of biomedical informatics. 2010 Jun 1;43(3):451-67.
(Additional, semi-finalist article in this category not mentioned during presentation)
  1. Spragg RG, Masys DR, Sergeant D, Lawrie T, Taut FJH. An informatics strategy to assure enrollment criteria compliance in studies of the critically ill. Contemp Clin Trials. 2010 Nov 1;31(6):530-5.
  2. Goudie AC, Sutton AJ, Jones DR, Donald A. Empirical assessment suggests that existing evidence could be used more fully in designing randomized controlled trials. J Clin Epidemiol. 2010 Sep 1;63(9):983-91.

Drug and Device Surveillance:
  1. Resnic FS, Gross TP, Marinac-Dabic D, Loyo-Berrios N, Donnelly S, Normand S-LT, et al. Automated surveillance to detect postprocedure safety signals of approved cardiovascular devices. JAMA. 2010 Nov 10;304(18):2019-27.
(Additional, semi-finalist article in this category referred to briefly during presentation)
  1. Platt R, Wilson M, Chan KA, Benner JS, Marchibroda J, McClellan M. The new Sentinel Network--improving the evidence of medical-product safety. N Engl J Med. 2009 Aug 13;361(7):645-7.

Consumer/Patient Engagement issues in CRI:
  1. Pulley J, Hassan N, Bernard G, Jirjis J, Schildcrout J, Robertson D, et al. Identifying unpredicted drug benefit through query of patient experiential knowledge: a proof of concept web-based system. Clin Transl Sci. 2010 Jun 1;3(3):98-103.
  2. Menoni V, Lucas N, Leforestier J, Dimet J, Doz F, Chatellier G, et al. The readability of information and consent forms in clinical research in France. PLoS One. 2010;5(5):e10576.

​Policy and Vision Relevant to CRI:
  1. Gostin L, Nass S. Reforming the HIPAA Privacy Rule: safeguarding privacy and promoting research. JAMA. 2009 Apr 1;301(13):1373-5.
  2. Estrin D, Sim I. Health care delivery. Open mHealth architecture: an engine for health care innovation. Science. 2010 Nov 5;330(6005):759-60.
  3. Friedman CP, Wong AK, Blumenthal D. Achieving a nationwide learning health system. Sci Transl Med. 2010 Nov 10;2(57):57cm29.
  4. Hersh W, Jacko JA, Greenes R, Tan J, Janies D, Embi PJ, et al. (Multiple commentaries indexed under single title): Health-care hit or miss? Nature. 2011 Feb 17;470(7334):327-9.
  5. Stead W, Searle J, Fessler H, Smith J, Shortliffe E. Biomedical Informatics: Changing What Physicians Need to Know and How They Learn. Acad Med. 2010 Aug 12.
  6. Payne PRO, Embi PJ, Niland J. Foundational biomedical informatics research in the clinical and translational science era: a call to action. Journal of the American Medical Informatics Association : JAMIA. 2010 Nov 1;17(6):615-6.

Presentation


Files:


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