At the end of this course, students will be able to • Define medical informatics • Define information management, information technology and informatics • Define concepts of medical informatics • Selecting best techniques to manage a medical informatics project.

1. BYM 516 E
Basics of Biomedical Informatics
2014-2015
Dr. Serkan Türkeli

2. Dr. Serkan Türkeli
E-posta: serkanturkeli@yahoo.com/
sturkeli@itu.edu.tr
Internet: serkanturkeli.minmba.com

3. Scope, Purpose and
Description
This course is designed to provide the
student an overview of the medical
informatics and how it relates to
healthcare operations. This course
introduces students to the procedures,
tools, and techniques used in planning
and managing medical informatics
projects. Students will learn computer-
based tools in health care, human
computer interfaces, an introduction to
computer applications in medicine,
electronic health record, database,
knowledge-based systems, medical
decision and analysis, introduction to
health information systems:
communication and networks,
telemedicine and Internet applications,
advance topics in biomedical informatics.

4. Required Readings Tim Benson, Principles of Health
Interoperability: HL7 and SNOMED, Springer
2009 978-1-84882-802-5.
Joseph Tan, Healthcare Information Systems
and Informatics: Research and Practices

5. Grading
Criteria
Students will be evaluated using the following criteria:
Active, Meaningful Participation 25%
Midterm Project
Written Deliverable and Presentation 35%
Final Project
Written Deliverable and Presentation 40%

6. Course Schedule
Week 1: Introduction and Overview
Course Introduction
Student Introduction
What is Medical Informatics?
Week 2: Data, Information, Knowledge, Wisdom
Hierarchy
Week 3: Electronic Medical (Health) Records
Week 4: Hospital information systems
Week 5: Interoperability (HL7, Medical Terminology… )
Week 6: Clinical support systems
Week 7: Midterm1

7. Week 8: Modeling of HIS (health information system)
Week 9: Standards in medical informatics
Week 10: Medical Decision Support Systems
What makes an organization intelligent?
Week 11: Telemedicine
Week 12: Privacy and security in healthcare
Week 13: Final Projects Presentation
Week 14: Final

8. Objectives and Goal
At the end of this course, students will be able to
• Define medical informatics
• Define information management, information
technology and informatics
• Define concepts of medical informatics
• Selecting best techniques to manage a medical
informatics project.

9. Resources 1: Online resources
1. AHRQ National Resource Center for Health IT
http://healthit.ahrq.gov/
2. National Coordinator for Health Information Technology
http://healthit.hhs.gov/
3. Health IT Stimulus News
http://www.ihealthbeat.org/
4. OpenClinical
http://www.openclinical.org/
5. CPOE.org
http://www.cpoe.org/
6. Certification Commission for Health Information Technology (CCHIT)
http://www.cchit.org/

10. Resources 2: Major professional
organizations
1. American Medical Informatics Association (AMIA)
http://www.amia.org/
2. Health Information and Management System Society (HIMSS)
http://www.himss.org/
3. International Medical Informatics Association (IMIA)
http://www.imia.org/
4. Certi
cation Commission for Healthcare Information Technology (CCHIT)
http://www.cchit.org/
5. Health Level 7 (HL7)
http://www.hl7.org/

11. Resources 3: Academic journals
1. Journal of the American Medical Informatics Association (JAMIA)
http://www.jamia.org/
2. Journal of Medical Internet Research (JMIR)
http://www.jmir.org/
3. Journal of Biomedical Science (JBS)
http://www.springerlink.com/content/112912/
4. International Journal of Medical Informatics (IJMI)
http://www.intl.elsevierhealth.com/journals/ijmi/
5. Methods of Information in Medicine (MIM)
https://www.schattauer.de/index.php?id=704

12. First assignment
Bernstam, E. V., Smith, J. W., & Johnson, T. R. (2010).
What is Biomedical Informatics? Journal of Biomedical
Informatics, 43(1), 104-110.
Write a two-pages paper about « the future of medical
informatics».

13. Articles 1: Introduction to
Medical Informatics
1) Haux R. Medical informatics: past, present, future. Int J Med
Inform. 2010; 79(9): 599-610
2) Hersh, W. (2009). A Stimulus to Define Informatics and Health
Information Technology. BMC Medical Informatics and Decision
Making, 9, 24.
3) Himmelstein DU, Wright A, Woolhandler S. Hospital Computing and
the Costs and Quality of Care: A National Study. Am J Med 2009;
123(1):40-46
4) Shcherbatykh I, Holbrook A, Thabane L et al. Methodologic Issues
In Health Informatics Trials: The Complexities of Complex
Interventions. JAMIA 2008; 15:575-580
5) J. Walker, P. Carayon, N. Leveson, R. Paulus, J. Tooker, H. Chin, A.
Bothe, and W. Stewart, “EHR Safety: The Way Forward to Safe and
Effective Systems,” Journal of the American Medical Informatics
Association 15 (2008): 272-277.

14. Articles 2: EHR
1) Fernandopulle, R. and N. Patel (2010). "How The Electronic Health
Record Did Not Measure Up To The Demands Of Our Medical Home
Practice." Health Affairs 29(4): 622-628.
2) O’Malley, A., J. Grossman, et al. (2009). "Are Electronic Medical
Records Helpful for Care Coordination? Experiences of Physician
Practices." Journal of General Internal Medicine 25(3): 177-185.
3) Bates, D. W. and A. Bitton (2010). "The Future Of Health Information
Technology In The Patient-Centered Medical Home." Health Affairs
29(4): 614-621.
4) Bates, D. W. & Gawande, A. A.(2003). Patient Safety: Improving
Safety with Information Technology. The New England Journal of
Medicine, 348, 2526-2534
5) Gans, D., Kralewski, J., Hammons, T., & Dowd, B. (2005). Medical
Groups’ Adoption of Electronic Health Records And Information
Systems. Health Affairs, 24(5) 1323-1333.

15. Articles 3: Electronic Health
Record Safety and Regulation
1) Koppel R, Metlay JP, Cohen A, Abaluck B, Localio AR, Kimmel SE, Strom BL. Role of
computerized physician order entry systems in facilitating medication errors. JAMA 293(10): 1197-203,
2005 Mar 9. http://jama.ama-assn.org/content/293/10/1197.full
2) Han YY, Carcillo JA, Venkataraman ST, et al. Unexpected increased mortality after implementation
of a commercially sold computerized physician order entry system. Pediatrics 2005;116:1506-1512.
http://pediatrics.aappublications.org/content/116/6/1506.full
3) H. Singh, S. Mani, D. Espadas, N. Petersen, V. Franklin, and L. A. Petersen, “Prescription Errors
and Outcomes Related to Inconsistent Information Transmitted through Computerized Order Entry,”
Archives of Internal Medicine 169, no. 10 (2009): 982-989.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919338/pdf/nihms131429.pdf
4) J. Walker, P. Carayon, N. Leveson, R. Paulus, J. Tooker, H. Chin, A. Bothe, and W. Stewart, “EHR
Safety: The Way Forward to Safe and Effective Systems,” Journal of the American Medical Informatics
Association 15 (2008): 272-277. http://171.67.114.118/content/15/3/272.full.pdf
5) F. Schulte and E. Schwartz, “FDA, Obama Digital Medical Records Team at Odds over Safety
Oversight,” Huffington Post, August 3, 2010. http://huffpostfund.org/stories/2010/08/fda-obama- digital-
medical-records-team-odds-over-safety-oversight

16. Articles 4: Meaningful Use of Electronic
Health Records and Impact on the EHR
Market
1) Blumenthal, D. (2010). "Launching HITECH." N Engl J Med 362(5): 382-385.
http://proquest.umi.com.proxy.lib.umich.edu/pqdweb?did=1955840561&Fmt=7&clientI
d=17822 &RQT=309&VName=PQD
2) Blumenthal, D. and M. Tavenner (2010). "The "Meaningful Use" Regulation for
Electronic Health Records." N Engl J Med: 1006-1114.
http://proquest.umi.com.proxy.lib.umich.edu/pqdweb?did=2102399491&Fmt=7&clientI
d=17822&RQT=309&VName=PQD
3) Tai, Betty, et al. "Meaningful use of electronic behavioral health data in primary health
care." Science translational medicine 4.119 (2012): 119mr3-119mr3.
4) Jha AK. Meaningful Use of Electronic Health Records: The Road Ahead. JAMA.
2010. http://jama.ama-assn.org/content/304/15/1709.full
5) Maxson, E., S. Jain, et al. (2010). "The Regional Extension Center Program: Helping
Physicians Meaningfully Use Health Information Technology." Annals of Internal
Medicine 153(10): 666- 670

17. Articles 5: Health Information
Technology and Health Reform
1) Fisher, E. S., M. B. McClellan, et al. (2009). "Fostering Accountable Health Care:
Moving Forward In Medicare." Health Affairs 28(2): w219-231.
http://proquest.umi.com.proxy.lib.umich.edu/pqdweb?did=1865634431&sid=6&F
mt=4&clientId=17822&RQT=309&VName=PQD
2) Landon, B. E., J. M. Gill, et al. (2010). "Prospects For Rebuilding Primary Care
Using The Patient-Centered Medical Home." Health Affairs 29(5): 827-834.
http://proquest.umi.com.proxy.lib.umich.edu/pqdweb?did=2037442611&Fmt=7&c
lientId=1782 2&RQT=309&VName=PQD
3) Bates, D. W. and A. Bitton (2010). "The Future Of Health Information Technology
In The Patient-Centered Medical Home." Health Affairs 29(4): 614-621.
http://proquest.umi.com.proxy.lib.umich.edu/pqdweb?did=2013981611&Fmt=7&c
lientId=1782 2&RQT=309&VName=PQD
4) Bitton A, Flier LA. Jha AK. (2012). "Health information technology in the era of
care delivery reform: To what end?" JAMA: The Journal of the American Medical
Association 307(24): 2593- 2594.

18. Articles 6: Interoperability
1) Kuperman, G. J. Health-information exchange: why are we doing it, and what are we doing?
J Am Med Inform Assoc. 2011.
http://jamia.bmj.com.proxy.lib.umich.edu/content/18/5/678.full.pdf
2) Williams, C., F. Mostashari, et al. (2012). "From The Office Of The National Coordinator: The
Strategy For Advancing The Exchange Of Health Information." Health Affairs 31(3):527-536.
3) Lenert, L., D. Sundwall, et al. (2012). "Shifts in the architecture of the Nationwide Health
Information Network." Journal of the American Medical Informatics Association.
4) Adler-Milstein J, J. A. K. (2012). "Sharing clinical data electronically: A critical challenge for
fixing the health care system." JAMA: The Journal of the American Medical Association
307(16): 1695-1696.
5) Micky Tripathi. The Dangers of Too Much Ambition in Health Information Exchange.
Ihealthbeat. June 22, 2012. http://m.ihealthbeat.org/perspectives/2012/the-dangers-of-too-
much-ambition- in-health-information-exchange.aspx
6) Frisse, M. E., K. B. Johnson, et al. (2011). "The financial impact of health information
exchange on emergency department care." Journal of the American Medical Informatics
Association.

19. Articles 7: Process and Workflow
1) Zheng K, Haftel HM, Hirschl RB, O'Reilly M, Hanauer DA. Quantifying the impact of
health IT implementations on clinical workflow: a new methodological perspective. J Am
Med Inform Assoc. Jul-Aug 2010;17(4):454-461.
2) Rebuge, Álvaro, and Diogo R. Ferreira. "Business process analysis in healthcare
environments: A methodology based on process mining." Information Systems 37.2
(2012): 99-116.
3) Niazkhani Z, Pirnejad H, Berg M, Aarts J. The impact of computerized provider order
entry systems on inpatient clinical workflow: a literature review. J Am Med Inform Assoc.
Jul-Aug 2009;16(4):539-549.
4) Lanham HJ, Leykum LK, McDaniel RR, Jr. Same organization, same electronic health
records (EHRs) system, different use: exploring the linkage between practice member
communication patterns and EHR use patterns in an ambulatory care setting. J Am Med
Inform Assoc. Aug 24 2011.
5) Unertl, K. M., L. L. Novak, et al. (2010). "Traversing the many paths of workflow
research: developing a conceptual framework of workflow terminology through a
systematic literature review." Journal of the American Medical Informatics Association
17(3): 265-273.

20. Article 7: Natural Language
Processing
1) Murff, H. J., F. FitzHenry, et al. (2011). "Automated Identification of
Postoperative Complications Within an Electronic Medical Record Using Natural
Language Processing." JAMA: The Journal of the American Medical Association
306(8): 848-855.
2) Jha, A. K. (2011). "The Promise of Electronic Records." JAMA: The Journal of
the American Medical Association 306(8): 880-881.
3) Hanauer, D. A. (2006). EMERSE: the electronic medical record search engine,
American Medical Informatics Association.
4) Seyfried, L., D. A. Hanauer, et al. (2009). "Enhanced identification of eligibility
for depression research using an electronic medical record search engine."
International Journal of Medical Informatics 78(12): e13-e18.
5) Thomas, Anil A., et al. "Extracting data from electronic medical records:
validation of a natural language processing program to assess prostate biopsy
results." World journal of urology 32.1 (2014): 99-103.

21. Articles 8: mHealth
1) Hawn, C. (2009). "Take Two Aspirin And Tweet Me In The Morning: How Twitter,
Facebook, And Other Social Media Are Reshaping Health Care." Health Affairs
28(2): 361-368.
http://content.healthaffairs.org/content/28/2/361.full.pdf+html?sid=aeb4be03-9e52-
4aff-ace6-34d62eebb6e1
2) Klasnja, P. and W. Pratt (2011). "Healthcare in the pocket: Mapping the space of
mobile-phone health interventions." Journal of Biomedical Informatics.
http://ac.els- cdn.com/S1532046411001444/1-s2.0-S1532046411001444-
main.pdf?_tid=85e90388ad092b496d68c42ebda23d68&acdnat=1343920403_c3a
b4bbc90ea791a95675e8b6550b8c7
3) Feder, J. L. (2010). "Cell-Phone Medicine Brings Care To Patients In Developing
Nations." Health Affairs 29(2): 259-263.
http://proquest.umi.com.proxy.lib.umich.edu/pqdweb?did=1970293501&Fmt=7&cli
entId=17822&RQT=309&VName=PQD
4) Kahn, James G., Joshua S. Yang, and James S. Kahn. "‘Mobile’health needs and
opportunities in developing countries." Health Affairs 29.2 (2010): 252-258.
5) Free, Caroline, et al. "The effectiveness of mobile-health technologies to improve
health care service delivery processes: a systematic review and meta-analysis."
PLoS medicine 10.1 (2013): e1001363.

22. Contact
Contact: Dr. Serkan Türkeli
E-posta: serkanturkeli@yahoo.com
sturkeli@itu.edu.tr
Office hour Wed. 13.30-17.30 (Please send an email for appointment)