Leadership in Public Health

Instructor: Russ Waitman, PhD

Office Hours: By Appointment

Office: 3001C Student Center

Telephone: (913)945-7087

E-mail:

Location: 3001D Student Center

Credit hours: 3 credits

Clinical Informatics Coordinator: Tamara McMahon, MA and Maren Wennberg, BS.

Course Description:

This course is tailored towards master of clinical research students but open to all other students as well (health professions, MPH, medical, nursing). It introduces students to biomedical informatics, clinical and administrative information systems and workflows, data warehousing and hypothesis generation using HERON ( and the i2b2 web client( programming using Structured Query Language (SQL), and developing a computable phenotypes and research cohorts for observational research or prospective trial eligibility based on secondary data sources centered on electronic health records. Students will also gain experience developing their cohort, an analytic ready database and filesusing SQLite ( and REDCap ( conduct preliminary analysis, and prepare an abstract for submission to a clinical or informatics forum/conference.

Method of instruction is in person and composed of a) 2 hour lecturesincluding interactive group discussion, exercises, and applying critical thinking towards development of case studies or their individualized projects;b) one hour laboratory providing hands on supervision by the instructor or clinical informatics coordinators in developing their computable phenotypes and analytic datasets using SQL and REDCap. Depending on enrollment, students may be paired in teams of two or three.

Prerequisites:

PVRM 800 – Principles of Epidemiology or BIOS 714 Fundamentals of Biostatistics

Online completion of KUMC Human Subjects Training (provided through CITI) and KUMC Computer Security Training modules

Course Goals / Objectives:

Identify secondary data sources available for observational and prospective clinical research and have a basic understanding the underlying workflows of that generate those data.
Demonstrate competent use of informatics methods for hypotheses generation, computable phenotyping, data management, and analytic dataset preparation
Analyze the strengths and weaknesses of various source systems and their secondary data for clinical research
Design an observational study or cohort for a prospective trial, create an analytic ready dataset, and complete preliminary analysis

Textbooks, Materials & Assignments:

Text & Readings:

Supplemental materials will be provided by the instructor based largely upon articles in pubmed, websites, and online training materials for informatics methods used in the course (HERON, i2b2, REDCap, SQL and SQLite).

Optionally, students may wish to purchase books on Structured Query Language such as “SQL Queries for Mere Mortals(R): A Hands-On Guide to Data Manipulation in SQL” by Michael J. Hernandez and John L. Viescas.

Assignments

Weekly participation

In addition to in person class participation, students are required to document their progress in developing their research topic, from study design, computable phenotype creation, study database creation, and preliminary analysis and presentation. They will document progress weekly on weekly on the informatics TRAC ( wiki and issue/project tracking system used by our PCORI Greater Plains Collaborative

Their postings will document their methodologic choices and include uploading their software with documentation of their design decisions following very basic best practices for software development.

Research Project: Cohort Definition, Analysis, and Presentation

Students are required to prepare a research proposal which is developed into a computable phenotype, analytic files, conduct preliminary analysis, and prepare an abstract targeted towards a clinical, health services, or informatics conference. Documentation of the proposal and progress will be created using the wiki. A presentation based upon the abstract will be provided to the class.

The topic must be approved by the instructor.

Cohort and SQL exams

Two exams will be conducted as take home exercises where students will need to a) develop cohort queries using i2b2 and b) write and execute SQL statements that result in the correct number of patients and patient characteristics. Answers will also include justification of the approach taken by the student.

The results will be discussed after submission in a class setting.

Grading Scale:

A = 90% - 100%

B = 80% - 89.9%

C = 70% - 79.9%

D = 60% - 69.9%

F = 59.9% and below

Assignments/Evaluation:

In Class Participation:15%

Weekly Project Documentation via wiki: 20%

Cohort Exam: 20%

SQL Exam: 20%

Final Presentation:25%

Course Outline:(Tuesday classes one hour; Thursday classes two hours)

10/14-17 Fall Break

11/22-26 Thanksgiving

Last day of class 12/7;

Final exams 12/11-15

Session

Date

Title / Topic / Readings Activities

1 8/22;8/24

Introduction: Medical Informatics and Integrated Data Repositories

2 8/29;8/31

Clinical, Administrative, Research Information Systems as Sources

3 9/5;9/7

Potential Research Topics Discussion

9/12;9/14

Hypotheses Generation and Computable Phenotyping using i2b2

9/19;9/21

Variable Selection and Data Management (SQL introduction)

9/26;9/28

Cohort Exam Due & Discussion; Data Request Oversight

10/3;10/5

Relational Databases, SQL exercises, and introduction to REDCap

10/10;10/12

SQL data preparation, scoping/refining cohort, REDCap Analysis

10/19

SQL Manipulation and TEMP Tables

10/24;10/26

SQL Exam Due & Discussion; Finalizing projects

10/31;11/2

Finalizing Cohort Computable Phenotypes

11/7;11/9

Analytic Dataset preparation

11/14;11/16

Finalizing Analytic Dataset preparation; Draft abstract review

11/21

Reviewing Analytic Files and Preliminary Analysis Methods

11/28;11/30

Abstracts and Preliminary Results Review

12/5;12/7

Final Abstract Presentations and Evaluations

Confidentiality

Students should not expect that all work they produce in an MS-CR course is confidential. The MS-CR program may review course deliverables such as papers, projects, on-line discussion postings and the like with persons other than fellow students in the course and the course instructor. Students’ work may be shown to faculty and staff, or accrediting bodies. Examples of students’ work and performance may be used to market the MS-CR program and KU School of Medicine, and during efforts to secure grant funding to support the MS-CR program and related faculty research and service projects. Therefore students should not include in their course assignments any sensitive personal information that they wish to keep confidential. Students wishing to discuss a confidential issue with a classmate or the instructor should use telephone calls or personal e-mails for this purpose.

Students with Special Needs

Students who believe they may need accommodations in the class are encouraged to contact Cyn Ukoko in the Academic Accommodations Services Office at or 913-945-7035 as soon as possible. To schedule an appointment online, go to online information about academic accommodations, please go to

Additional Notes

This syllabus is subject to change by the instructor. Any changes will be announced.

Sponsor students: done. Note: need to check with Carlee Oakley on the preferred email to use (MSCR one or the affiliate account).

Sponsor reuse of Jasmin’s class project as a teaching exercise: done

Background logistics:

-Sponsor students – done (check on Carlee Oakley exact account to use)

Tell students to login to HERON and sign system access agreement

-Sponsor data reuse for Jasmin’s class project - done

-CITI training for human subjects

Be sure to you sign in via “log in through my institution”

-KUMC Information Security training

link off your my.kumc.edu account

-Shared drive for files. – Maren to work with team to create a new folder on the S: drive. Either mimic PRVM_806_MI_Research but ideally place on the Medical Informatics portion. PVRM_868_2017

Curriculum content mods:

Consider relevant chapters from Shortliffe et al.

Information security, data privacy, de-identification

-Partially mentioned in slides for HERON

-Consider a manuscript for review

Note that JAMIA article devoted to the topic

Shortliffe Chapters: 2,6,12

HIMSS primers on info systems

Source systems and documentation

-Medication delivery

-Charting

-Physician visits notes

-Hospitalization and ADT

-Lab order and results

-Cancer Registries and other registries

-Billing

-Nutrition diet

Informatics and terminology resources

-UMLS

-ICD9/10 and CPT

If people want, they can do last year’s cohort and SQL exams as homework.

Have students find their topic or a topic; then visit the unit and shadow personnel.

-Then write this up for their topic and to share on the wiki for future students and HERON users. For example PT flowsheet documentation

-CF, ALS, BC

Topic identification from last class

-Move up as much as possible but if they don’t have a topic, help them quickly arrive at one that’s going to make sure they develop their skills and could be the basis for a paper

HERON and computable phenotyping

-Review prior outline

-All the tools SFE, sequence of events, venn diagrams

-Multiple source systems means different answers.

-Note all the training videos for HERON

MI and IDRs:

-Paper on how biased the sample may be and which kinds of data are likely required.

-What can you answer? What is hard (healthy people’s golf scores)

-Notes: de-id on the cohort.

-Pathology and radiology notes

-Claims ala GROUSE – for the future but intro the concept.

Observational study design :

-informatics epi intersection?

-Have someone try out some exposure analytics ala OHDSI?

-Survival analysis?

SQL and data prep. How much hands on SQL versus the expectation they have it covered from online tutorials.

-Note the online materials for SQL prepared by Maren.

-Spend the class time grounding this is HERON data. Working on their projects or with one student as an example was good.

old outline