1. The Study Database Robert R. Kelley, Ph.D.

2. Clinical and Translational Research Support Center Outline The Study Database Overview Designing the Database Building the Database

3. Clinical and Translational Research Support Center Over The Study Database The Study Database: – Tool(s) used to store data electronically for queries and data analysis

4. Clinical and Translational Research Support Center Components of the Study Database The Study Database

5. Clinical and Translational Research Support Center Designing the Study Database The Study Database

6. Clinical and Translational Research Support Center The Case Report Form The Study Database Good database design starts with a good Case Report Form Should be driven by the study protocol Should support the study statistical plan Should be divided into logical sections or multiple forms

7. Clinical and Translational Research Support Center Carefully consider variable names The Study Database case id Case ID Procedure Type Physician Comments Temperature Diastolic BP Systolic BP Use only lower case procedure type physician procedure_type Abbreviate when possible dbp temp Use underscore to separate words case_id Consider prefixing exam_temp Use the shortest variable name you can!!! Be consistent!!!

8. Clinical and Translational Research Support Center Coding levels The Study Database Case ID Sex Congestive Heart Failure Comments Diabetes Antibiotic Diagnosis For binary data always code with 1/0 1 = Male, 0=Female 1=Yes, 0,No For multiple choice data, code 1...N 1, Beta-lactam monotherapy only 2, Beta-lactam + macrolide combination only 3, Beta-lactam + quinolone combination only 4, Quinolone monotherapy only For Yes/No, always code with 1/0 Don’t forget to code for NA/UNKNOWN 1 = Yes, 0=No -1 UK Use alpha numeric codes when they make sense blmono, Beta-lactam monotherapy only blmac, Beta-lactam + macrolide combination only blq, Beta-lactam + quinolone combination only quin, Quinolone monotherapy only

9. Clinical and Translational Research Support Center The Data Dictionary The Study Database Variable name Can be a simple spreadsheet with... Data type Coding levels Coding restrictions Description Units

10. Clinical and Translational Research Support Center An example... The Study Database Variable NameDescriptionData TypeCoding LevelsRestrictionsUnits case_idCase IdentifierInteger>0NA ageAgeIntegerContinuous>18Years sexSexInteger1,Yes 0,NoNA doaDate of ArrivalDateShort Date>Study StartNA dodDate of DischargeDateShort Date>Study Start and >doaNA icuAdmitted to ICUInteger1,Yes 0,NoNA rulRight Upper LobeInteger1,Yes 0,NoNA rmlRight Middle LobeInteger1,Yes 0,NoNA rllRight Lower LobeInteger1,Yes 0,NoNA lulLeft Upper LobeInteger1,Yes 0,NoNA lllLeft Lower LobeInteger1,Yes 0,NoNA pePleural EffusionInteger1,Yes 0,NoNA resp_rateRespiratory RateIntegerContinuous>60Breaths/Minute tempTemperatureIntegerContinuous>35 and <40.5Celsius psi Pnuemonia Severity IndexIntegerContinuous0-350NA Defined according to rules Can be as detailed as necessary This will often be database dependent Very important for consistency Derived from protocol and study definitions Very important – especially for lab values

11. Clinical and Translational Research Support Center Building the Study Database The Study Database

12. Clinical and Translational Research Support Center Types of Studies from a Data Perspective The Study Database Large Studies Small Studies > 100 cases <20 Variables <20 Variables <100 cases > 20 Variables

13. Clinical and Translational Research Support Center Tools for Smaller Studies The Study Database Spreadsheet Applications Personal Database Applications MS Excel OpenOffice-Calc Apple - Numbers MS Access OpenOffice-Base Filemaker Pro

14. Clinical and Translational Research Support Center Excel The Study Database Many people in science and medicine are already familiar with Excel Supports descriptive statistics and calculations Provides rudimentary data visualization Easy to back up and have multiple copies for safekeeping. MS Excel Limitations Strengths No capability for metadata Need to encrypt manually Does not provide authentication, authorization, audit trail Inadvertent data corruption Depending on verison, may be limited to 256 columns (variables)

15. Clinical and Translational Research Support Center Access The Study Database Provides a front-end for easy form creation Supports descriptive statistics and calculations Provides rudimentary data visualization Easy to back up and have multiple copies for safekeeping. MS Access Limitations Strengths Must understand the basics of database design to be able build effective databases Need to encrypt manually Does not provide authentication, authorization, audit trail Programming help may be required for complicated features

16. Clinical and Translational Research Support Center Tools for Larger Studies The Study Database Database / Applications OpenClinica LabKey REDCap Medidata Rave Custom Software

17. Clinical and Translational Research Support Center The Study Database Unlike Excel and Access these tools require infrastructure and specialized skills to maintain.

18. Clinical and Translational Research Support Center Tools for Larger Studies The Study Database Infrastructure Licenses for software (much more expensive than Excel/Access) Technical Skills to install and maintain system Place to “host” your database Recommendation Hire a dedicated person to administer this system or contract it out.

19. Clinical and Translational Research Support Center OpenClinica The Study Database Specifications Windows Server 2008 or Linux Variant Java Java Application Server (Apache) Database: PostgreSQL 8.4 or Oracle 10.2g Specifications Windows Server 2008 or Linux Variant Java Java Application Server (Apache) Database: PostgreSQL 8.4 or Oracle 10.2g Designed for capturing data for clinical trials Has paid and free versions Can be hosted locally or by Akaza Research LLC Supports exporting data to: – HTML – Tab-Delimited – SPSS Syntax and Data – CDISC ODM xml 1.3 and 1.2 – CDISC OpenClinica Exentsion 1.3 and 1.2 https://www.openclinica.com

20. Clinical and Translational Research Support Center LabKey The Study Database Specifications Windows Server 2008 or Linux Variant Java Java Application Server (Apache) Database: PostgreSQL 8.4 or Microsoft SQL Server Specifications Windows Server 2008 or Linux Variant Java Java Application Server (Apache) Database: PostgreSQL 8.4 or Microsoft SQL Server Designed for storing lab data such as: – Specimen data – Gene Sequences – Flow Cytometry Data – Proteomics Data – Any Assay Data It also supports storing other clinical data Has paid and free versions Can be hosted locally or by Akaza Research LLC Supports exporting data to: – Excel – Text – Javascript – R – SAS https://www.labkey.org/

21. Clinical and Translational Research Support Center Medidata Rave The Study Database A comprehensive commercial clinical data management system Very flexible Expensive and requires significant technical support Supports exporting data to: – SAS – CSV – XML Specifications Windows Server 2008 or Linux Variant Java Java Application Server (Apache) Database: PostgreSQL 8.4 or Microsoft SQL Server Specifications Windows Server 2008 or Linux Variant Java Java Application Server (Apache) Database: PostgreSQL 8.4 or Microsoft SQL Server http://www.mdsol.com/products/rave_overview.htm

22. Clinical and Translational Research Support Center REDCap The Study Database http://project-redcap.org/ Specifications Windows Server 2008 or Linux Variant PHP Database: MySQL Server SMTP email server Specifications Windows Server 2008 or Linux Variant PHP Database: MySQL Server SMTP email server A comprehensive open source clinical data management system Supports creating: – Surveys – Data Entry Forms (eCRFs) – Longitudinal Studies Free, but requires significant technical support Supports exporting data to: – Excel – SPSS – SAS – R – STATA

23. Clinical and Translational Research Support Center Custom Software The Study Database If your requirements are extremely particular you may want to build your own system Can be time consuming and resource intensive NOT RECOMMENDED

24. Clinical and Translational Research Support Center Questions?

25. Clinical and Translational Research Support Center References Beyond CRES: Excel - Informatics tools for managing your clinical research data, Anderson N. www.iths.org/bmiwww.iths.org/bmi Why not use Excel for data management?, Carlin L., Bondy J, Wolfe P. http://connect.ucdenver.edu/excel/ http://connect.ucdenver.edu/excel/