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EPI 218Database Management for Clinical
Research
Michael A. Kohn, MD, MPP
January 10, 2010
Clinical Research*• Choose the study design, and define the study population,
predictor variables, and outcome variables;• measure these variables and anticipate problems with
measurement;• analyze the results
In this course, we discuss the “nitty gritty” of collecting, storing, updating, and monitoring the study measurements.
*Private companies that make data management systems for clinical research understand “clinical research” to include only RCTs preparatory to FDA drug or device approval, not observational studies.
Assumptions about Students
• Actively involved in a clinical research study
• Some experience with entering and maintaining data in single-table spreadsheet or statistical software
Outline
• Housekeeping
• Data Tables– Rows = Records; Columns = Fields
• Normalization of Data Tables
• Queries
• Front End or Interface/On Screen Forms
Housekeeping
Epi 218
• Course website: http://www.epibiostat.ucsf.edu/courses/schedule/data_management.html
• Labs will be in China Basin Landing 6704 with overflow into 6702, 8:45 – 10:15
• http://apps.epi-ucsf.org (For log-on: [email protected])
Citrix Metaframe Presentation Server MS Office Desktop
• “Learn MS Access 2000” videohttp://mkanders.com/learn_access_video.htmUsername: ucsfdbclassPassword: access2000(We can also loan you the video on CD.)
Course ObjectivesLearn how to develop a multi-table, relational
database for a research study. We will be using Microsoft Access*, but we are familiar with other database software.
Learn how to query a database for monitoring and analyzing data in a research study.
Example: Infant Jaundice Study
*SQL-based, widely available, desktop DBMS
Requirements
• Turn in all 4 assignments on time
• Fill out course evaluation.
Assignment 4/Final ProjectDue 2/16/2010
Send in a copy of your research study database* with a data management plan.
We prefer a database that you are currently using or will use for a research study.
However, a demonstration or pilot database is acceptable.
*If you are unable to package your database in a file to email, you can send us a link or work out another way to review your database.
Assignment 4/Final ProjectDue 2/16/2010
If you are doing secondary analysis of data collected by someone else,
• obtain the data collection forms* used in the original data collection,
• set up a new database that you would use for a follow-up study.
*Often easily obtained by doing a Google search or emailing the author of the original study.
Assignment 4/Final ProjectDue 2/16/2010
Start thinking about this now.
Build up your own study database as you work through the labs.
Use extra time in lab to work on your study database.
Set up appointments with course faculty early.
TICR Professional Conduct StatementClarifications for this class
• I will maintain the highest standards of academic honesty• I will neither give nor receive aid in examinations or
assignments unless such cooperation is expressly permitted by the instructor
• I will conduct research in an unbiased manner, reports results truthfully, and credit ideas developed and work done by others
• I will not use answer keys from prior years• I will write answers in my own words, and, when
collaboration is permitted, acknowledge collaborators when answers are jointly formulated
For Epi 218 – Just don’t turn in somebody else’s work as your own.
Rows = Records = Entities
Columns = Fields = Attributes
Data Tables
DCR Chapter 16 Exercise 2
The PHTSE (Pre-Hospital Treatment of Status Epilepticus) Study was a randomized blinded trial of lorazepam, diazepam, or placebo in the treatment of pre-hospital status epilepticus. The primary endpoint was termination of convulsions by hospital arrival. To enroll patients, paramedics contacted base hospital physicians by radio. The following are base-hospital physician data collection forms for 2 enrolled patients:
Lowenstein DH, Alldredge BK, Allen F, Neuhaus J, Corry M, Gottwald M, et al. The prehospital treatment of status epilepticus (PHTSE) study: design and methodology. Control Clin Trials 2001;22(3):290-309.
Alldredge BK, Gelb AM, Isaacs SM, Corry MD, Allen F, Ulrich S, et al. A comparison of lorazepam, diazepam, and placebo for the treatment of out-of-hospital status epilepticus. N Engl J Med 2001;345(9):631-7.
Display the data from these 2 data collection forms in a 2-row data table.
SubjectID
KitNumber
AdminDate
AdminTime
SzStopPreHosp
SzStopPreHospTime
HospArrTime
HospArrSzAct
HospArrGCSV
189 A322 3/12/1994 17:39 FALSE 17:48 TRUE
410 B536 12/1/1998 01:35 TRUE 01:39 01:53 FALSE 4
Create a 9-field data dictionary for the data table
Field NameData Type Description Validation Rule
SubjectID Integer Unique Subject Identifier
KitNumber Text(5) 5-character Investigational Pharmacy Code
AdminDate Date Date Study Drug Administered
AdminTime Time Time Study Drug Administered
SzStopPreHosp Yes/No Did seizure stop during pre-hospital course?
SzStopPreHospTime
Time Time seizures stopped during pre-hosp course (blank if seizure did not stop)
HospArrTime Time Hospital Arrival Time
HospArrSzAct Yes/No Was there continued Seizure Activity on Hospital Arrival?
Check against SzStopPreHosp
HospArrGCSV Integer Verbal GCS on Hospital Arrival (blank if seizure continued)
Between 1 and 5
Methods:
Design-Nested double cohort study.Setting-KaiserSubjects-Infants with neonatal jaundice and randomly selected non-jaundiced infantsPredictor Variable-Presence or absence of jaundiceOutcome Variable- Neuropsychological score (ranging from 55 to 145) at age 5Analysis- ?
JIFeeJaundice and Infant Feeding Study
Newman, T. B., P. Liljestrand, et al. (2006). "Outcomes among newborns with total serum bilirubin levels of 25 mg per deciliter or more." N Engl J Med 354(18): 1889-900.
Infant Jaundice Study Data
1. Approximately 400 children2. 5 examiners (doctors)3. Approximately 700 neuropsychological examinations,
measuring weight, height, and “NPScore” (IQ)4. Some children to be examined more than once5. No examiner to see the same child twice6. If child died before age 5, store age and circumstances of
death
Infant Jaundice Study Table of Subjects
Row = Individual Infant
Columns = ID#, Name, DOB, Sex, Jaundice.
If one set of measurements per subject, put measurements in subject table.
This is a single-table database.
Table of Study Subjects
Demonstration: Creating a Data Table
Label columns and enter rows of data in datasheet view
Where is predictor on data collection form?
Demonstration: Data Dictionary
Table design view:•field (=column) names, •data types, •definitions, •validation rules
(More on data types, free-text vs. coded responses, later)
Acceptable table showing one set of exam results per participant.(BabyExamForFigure3)
Demonstration
Disallowed values
Duplicate primary keys
This automatic error checking and data validation IS why you need to enter your data into a computer; it is NOT why you need a relational DBMS. Many single-table products (Filemaker Pro, SAS FSP, even Excel) can do error checking and data validation.
Demonstration: Same Table in Excel, Stata
• Excel
• Stata
• Etc
Rows = Records = Entities
Columns = Fields = AttributesAccess and Stata have a special row at the top for column headings (=field names); Excel just uses the first row.
Normalization
Table of Study Subjects
Row = Individual Infant
Columns = ID#, Name, DOB, Sex, Jaundice
If some infants have more than one exam, what do you do?
Table of Study Subjects
Undesirable table showing multiple exam results per study participant.(BabyExamForFigure4)
Demo
• Find highest IQ Score
• Find all exams done in April
Common Error
• If you find yourself creating multiple columns for the same measurement, e.g., Date1, Score1, Date2, Score2, Date3, Score3, …
• Or if your table is more than about 30 columns wide,
– It is time to restructure your table.
Undesirable table with participant-specific data duplicated for each exam. (Note problem with Helen’s DOB.)(ExamBabyForFigure5)
Demo
• Find highest IQ Score
• Find all exams in a particular month
• What is Helen’s birth date?
• What happened to Alejandro, Ryan, Zachary, and Jackson?
If some infants have multiple exams,
“normalize” the records into two tables, one for subjects and one for examinations.
Normalization
Data normalized into two tables: one (“Baby”) with rows comprising subject-specific information; the other (“Exam”) with rows comprising exam-specific information. Note that Helen can only have one birth date. Subjects with no exams, e.g. Alejandro, still appear in the database. “SubjectID” functions as the primary key in the “Baby” table and as the foreign key in the “Exam” table.
Figure 7. Relationships diagram showing the one-to-many relationship between the table of subjects (“Baby”) and the table of measurements (“Exam”).
Demonstration
Inability to create integrity violations with normalized tables.
This IS why you need a multi-table relational DBMS.
Lab Results
Occasionally, the subjects had blood tests.
Robert had a CBC on 1/30/2010.
Helen had a CBC on 1/30/2010, LFTs on 2/28/2010, and a CD-4 count on 3/31/2010.
LabResultQry
Undesirability of Storing Calculated Values
Store raw data, not calculated fields, e.g., store dates and times; calculate intervals.
Storing a patient’s birth date allows calculation of his or her exact age on the date of a particular measurement.
Figure 15. Storing calculated fields such as “AgeInMonths” is undesirable. What if the birth date for SubjectID 2322 (Helen) is corrected in the “Baby” table?
Queries
Select Queries
Select queries (aka “Views”) organize, sort, filter, and display data.
Queries use Standard Query Language (SQL), but you don’t have to learn it, because of graphical query design tools.
A query can join data from two or more tables, display only selected fields, and filter for records that meet certain criteria.
Demonstration
Age in months and BMI at exam of subjects who were examined in January and February of 2010.
QueryDemo
Select Queries Produce “Table-Like” Results
Note that the result of a select query that joins two tables, displays only certain fields, selects rows based on special criteria, and calculates age and BMI still looks like a table in datasheet view.
But, remember that it is a dynamic “view” of data from the underlying tables.
“Action Queries” Change Data
1) Update Query -- changes the values of specific fields in existing records
2) Append Query -- adds new records (rows) to a table
3) Delete Query -- deletes records from a table
Front End or Interface
On-screen forms
Advantages of On-Screen Forms
• Data keyed directly into the computer data tables without a transcription step
• Include validation checks and provide immediate feedback when a response is out of range
• Incorporate skip logic
Standard Data Entry Conventions
•Several conventions for data entry and display have developed over time.
•Most users of screen forms have come to expect them subconsciously.
•mutually exclusive, collectively exhaustive choices are displayed as an “option group” consisting of several different “radio buttons”.
•choices which are not mutually exclusive are displayed as check boxes.
N.B. An “option group” of mutually exclusive choices is a single column or field. A group of N check boxes represents N yes/no fields.
Use check boxes when options are not mutually exclusive. (5 fields)
Use radio buttons when options are mutually exclusive. (1 field)
Computer chart abstraction form showing two common data entry conventions.
Demonstration
Option group for examiner’s medical specialty
MasterRaceAsFieldList, MasterRaceAsOptionGroup, MasterRaceAsAllThatApply
On-screen vs. paper formsMinimize the extent to which study measurements are recorded on paper
forms. Enter data directly into the computer database or move data from paper
forms into the computer database as close to the data collection time as possible.
When you define a variable in a computer database, you specify both its format and its domain or range of allowed values. Using these format and domain specifications, computer data entry forms give immediate feedback about improper formats and values that are out of range. The best time to receive this feedback is when the study subject is still on site.
Can only monitor data for outliers, systematic differences between data collectors or study sites, and study progress (I.e., query the data) once the data are in the computer.
You can always print out a paper copy of the screen form or a report of the exam/interview results once the data are collected.
Outline
• Housekeeping
• Data Tables– Rows = Records; Columns = Fields
• Normalization of Data Tables
• Queries
• Front End or Interface/On Screen Forms
Don’t Forget
Lab 1 next Tuesday 1/12/2010
View the Learn MS Access 2000 Video
http://mkanders.com/learn_access_video.htm
Username: ucsfdbclass
Password: access2000
(We can also loan you the video on CD.)
Start thinking about your study database and Assignment 4/Final Project.
