Introduction to Medical Informatics for Informaticians Fall 2015 BMSC-GA 4455
Course Description:
This course will serve as an introduction to Biomedical Informatics, which is the interdisciplinary science of information management in Medicine. The focus of the course will be on areas of Biomedical Informatics relevant to clinical research in medicine and public health. Innovative methods to capture, store, and retrieve clinical and population level data as well as ways in which information systems which can support research interventions will be reviewed. We will also examine the ways in which Informatics can initiate, facilitate, and enable clinical and translational research.
The course will run simultaneously with the MSCI students. Assignments / Evaluation:
- Homeworks - 50%
- Paper/ Proceedings Review - 5% - AMIA Review/ Preparation - 5% - Term Project - 30%
- Term Project Presentation - 10% Objectives:
By the end of the course, student will be able to:
1. Define the major topics within Medical Informatics
2. Understand how Medical Informatics can initiate, facilitate, and enable research in medicine and public health. 3. Understand how clinical information systems can enhance or limit the ability to conduct such research.
4. Understand why Informatics standards and Controlled Vocabularies are important for research.
5. Understand the difference between adverse events and medical errors and their relationship to computer-based systems. Paper Review
In this course, we will monthly immerse ourselves in the informatics literature. We will review papers from the Journal of the
American Medical Informatics Association and proceedings from the American Medical Informatics Association. Students will select a paper from this journal to write a comprehensive review (as if you were a referee) for the paper. Students will work in pairs and review the same paper individually. The review should be about 2 to 3 pages and follow guidelines as per: Alexandrov, A. V., Hennerici, M. G., & Norrving, B. (2009). Suggestions for Reviewing Manuscripts. Cerebrovascular Diseases, 28(3), 243–246. doi:10.1159/000228588.
The fall AMIA symposium will occur during this course. We will require students to write a one page summary of sessions that they will attend and a debrief of sessions they attended. Student responses to certain topics will be published in a class blog that is published on the web. We will also ask the students to read and review the student paper finalists to select a best paper. Term Project
The term project will revolve around a theme in medical informatics. This semester will be a clinical decision support tool. Students will implement a clinical decision support tool for use in the clinical workspace. The project will include project specification and feedback from physicians in the MSCI program. The student will be expected to deliver an interface that allows clinical input and a recommendation for support. Students will work in pairs and follow all recommended guidelines.
Students may also analyze a publicly available dataset for a project of interest. Term Project Presentation
Just as important as doing a project is packaging the project and presenting the idea to others. Students will give a 15 minute presentation with 5 minutes for questions. We will invite physicians and other local entrepreneurs to listen to your ideas and presentations. You will give the whole class a short summary and then just the PhD students a detailed technical presentation. PhD Students
We will meet for an additional hour per week to discuss weekly readings. And there is an additional hour for group programming time. Homeworks
Homework #1 - Representing/ Summarizing Clinical Data
Homework #2 - Natural Language Processing/ Ontologies/ Consumer Informatics Homework #3 - Information Retrieval/ Translational Informatics
Date Title Instructor Readings
Sept 9 Introduction to Biomedical Informatics Aphinyanaphongs (1 hour) Ch 1 (pages 3-35) Video
Sept 16
Data Driven Medicine Aphinyanaphongs Ch 2
Mimic 2 Database
Paper - Finding the Missing Link for Big Biomedical Data
Paper - Evidence Based Medicine in the EHR data. Paper - Technical Challenges for Big Data in
Biomedicine and Health: Data Sources, Infrastructure, and Analytics
Paper - Big Data in Science and Healthcare: A Review of Recent Literature and Perspectives
Paper - Big Data in Medicine Is Driving Big Changes Sept
23
Health Information Exchange Aphinyanaphongs Sept
30
Clinical Information Systems/ Data Warehousing
Chelico (Webex) Ch 12
Paper - An Evidence-Based Approach to Activating Your EMR
Paper - Leadership and Governance for IT Projects Oct 7 Biomedical Informatics
Vocabularies / Meaningful Use Cantor/ Julia Comments on project proposal where you are not familiar. Questions for MDs on project.
Ch 7
Short, more in-depth descriptions of some of the standards databases.
Oct 14
Clinical Decision Support Swartz Ch 22 Oct
23
Oct 30
Entrepreneural Efforts in Consumer Informatics
None Nov 4 NLP / Text Categorization /
Information Extraction
Aphinyanaphongs Ch 8, NLP An Introduction (Chapman), Review of approaches to identifying phenotype cohorts using EHR (Lai).
Nov 11
Information Retrieval / Library / Data Resources
Aphinyanaphongs Ch 21 Nov
18
mHealth/ Patient Centered Portals
Nov 25
Off for Thanksgiving Dec 2 Public Health Informatics
Health Information Exchange / Registries
Scott? or Armine? or Cantor?
Ch 16
Dec 9 Educational Informatics Ch 23
Dec 16
Student Presentation Day
Course Schedule
1 Introduction to Biomedical Informatics Chelico/Yin Online Lecture (Shortliffe) Ch 1 Shortliffe
2 Biomedical Data in the Clinic Yin Ch 2 Shortliffe
3 Clinical Information Systems/ Data Warehouses Chelico Ch 10, 12, 14 Shortliffe 4 Biomedical Informatics Vocabularies/ Meaningful Use/
Ontologies
Cantor Ch 7, Ch 9 Shortliffe 5 Health Information Exchange / Registries Kuperman Online Lecture (Frisse)
Paper (PMID: 20823361)
6 Using EHR Data for Research Yin PMID: 1044898 , 2584185, 20473190 7 Data Management Principles in Clinical Research Robinson PMID: 3326906
8 Research IT Demo on Data Managment Tools @ NYU Speakman Online Lectures (http://www.project-redcap.org/) 9 NLP / Text Categorization / Information Extraction Yin Ch 8 Shortliffe
10 Educational Informatics Triola Ch 21 Shortliffe
11 Entrepreneurial Efforts in Consumer Health Ch 14 Shortliffe 12 Clinical Decision Support Chelico Ch 20 Shortliffe
13 Public Health Informatics Armine Ch 15 Shortliffe
13 Information Retrieval and Digital Libraries Yin Ch 19 Shortliffe 13 International Perspectives of Medical Informatics (Cantor /
Bates)
PMID: 22146917
Ch 1: International Perspectives in Health Informatics
14 Translational Bioinformatics and Personalized Medicine Yin PMID: 20824471, 15 Student presentation day.
Other Potential Topics Patient Monitoring Systems
Entrepreneural Efforts in Informatics Public Health Informatics
Consumer Health Informatics
Information Retrieval and Digital Libraries Protection and Analytics Use of Data EHR Implementation and Evaluation Meaningful Use of the EHR
Standards and Interoperability
Electronic and Personal Health Records Biomedical Computing
Telemedicine
International Perspectives of Medical Informatics Translational Bioinformatics and Personalized Medicine Idea
Reviewing papers in JAMIA
Reviewing accepted papers in AMIA Open source project/ contribution
Programming Project with theme (Teams of 2) - ala Intro to Engineering from RPI
