Introducing OpenClinica
It’s all about data
Subject
Diary
CRF
DCF
Investigator
Monitor
Sample
CRF
DCF
Clinical
Data
Lab
Results
Involved
Laboratories
Statistician
Data Manager
Clinician
NDA
Regulatory
Authority
What is CDMS?
• A clinical data management system or CDMS
is used in clinical research to manage the data
of a clinical trial
• It is set up to help with processing data from
source through validation checks, analysis,
reporting and storage;
• Also useful for Coding (particularly for AEs and
Medications)
– MEDRA (Medical Dictionary for Regulatory Activities)
– WHOART (WHO Adverse Reactions Terminology)
Institutional Approach
• Setting up a specific CDMS requires institutional
decision making at policy level
• Whatever the choice, it comes with a cost
• Requires infrastructure and equipment set up
• Requires minimum core competencies
• Dedicated time for learning and development
• Opportunities to try out
Preferred Software characteristics
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Standards based
Well known  many skilled practitioners available
Readily mastered and modified
Should run on any platform
Should be affordable for small groups in resource
constrained countries
Why an open source approach?
• Potential advantages of Open Source solution
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Cheaper
More amenable to change
No vendor lock in
More able to be integrated with other systems
Likely to be well documented
Designed to be multilingual
Open source software works eg R, Apache, MySQL
Used by major IT players eg Google, HP & IBM
Has been argued provides better software
• saved the Human Genome Project according to Lincoln Stein
Introducing OpenClinica
Free, open source, web-based software for EDC built by
Akaza Research
Features:
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Management of diverse clinical studies through a unified interface
Clinical data entry and validation
Data extraction
Study oversight, auditing, and reporting
Creating Data Bases in OpenClinica
Designing a database in OC; requirement and flow of data.
Submit data Module; Webbased Data entry and validation
Clinical Case Report Forms (CRF)
OC - DataBase
Define CRFs in Excel Temp.
CRF Design, validation and
import
Data Base Creating in OpenClinica
Page no
Resp_Type
Validation
Required
1
1
text
ST
regexp: /[AZ]{3}/
1
pidnu
PAD No.
2
1
text
ST
regexp: /[0-9,
A-Z]{7}/
1
1
2
text
REAL
func: gte(-3.0)
1
WHZsco Wght/hght Z
re
score
ons
Resp_Valu
es
Date type
Col_No
Child Initials
Resp_Lab
el
Resp_opti
Label
childini
Units
Item_name
A part of CRF Excel Template: “Some tricks”.
Creating Databases in OpenClinica
Defining CRF on Excel Template
ITEM_NAME - This is the unique label or variable name for this data element.
DESCRIPTION_LABEL - give an explanation of the data element and the value(s) it captures.
UNITS - the units that the value of this data element should be captured in.
GROUP_LABEL - grouped items will display as a row within a table.
COLUMN_NUMBER - allow adjacent items or items with the same parent to be aligned
together.
RESPONSE_OPTIONS_TEXT - list of the text values of the responses for this response set as
a comma-delimited string.
RESPONSE_VALUES_OR_CALCULATIONS - comma-delimited list of the encoded values.
DATA_TYPE - data type; ST, INT, REAL, DATE.
VALIDATION - validation expression to run an edit check on this item
VALIDATION Expression - Expression Type:
1) regexp - Supports Java-style regular expressions. regexp: /regular expression/ e.g
regexp: /[A-Z]{3}/, requires a three-letter string (all uppercase)
2) func - Supports built-in library of basic integer functions. func: func(args) e.g func:
range(1, 10), func: eq(1), func: gte(10.5) etc.
The Back End of OpenClinica
• Developed using Java J2EE framework
• Application Server- Tomcat 5.x
• Uses JDBC with JSP based front-end.
• Database PostgreSQL 8.x or Oracle 10g
– custom ports to DB2, SQL Server, or MySQL also
possible
– Has 74 related tables
Important Features of OpenClinica
• Organization of clinical research by study protocol and site.
• Dynamic generation of web-based CRFs in portable Excel templates.
• Management of longitudinal data for recurring patient visits
• Data import/export tools for migration of clinical datasets.
• Interfaces for data query and retrieval across subjects, time, and clinical
parameters
• Compliance with regulatory guidelines e.g. 21 CFR Part 11
• Built on robust and scalable technology infrastructure interoperable with
relational databases
Designing CRFs
Done in excel using a blank CRF template
provided by Openclinica
Uploading CRFs
The excel sheet is then uploaded onto OpenClinica
Event Definition
Data Entry
Data Extraction
System End of OpenClinica
The Back Up Setting
Database
server
Database
NAS1
PgDump utility Creates a backup file
on the secondary HDD on the main
server. File automatically copied to
NAS1
• Backups implemented via a scheduled
command running as a batch file that writes out
the data and metadata for each of the studies
databases adding Timestamp information to the
filename.
Restore Process
• Installing Application Stack I.E. Postgresql, Apache
Jarkata Tomcat,J2SE runtime environment and
Deploying OpenClinica
• Using a suitable Postgres database GUI(e.g.
pgadmin III) create a new blank database on the
database server
• Run the pg_restore command on the server and
select the backup file to restore
Deploying O/C for Multiple Sites
• OC is deployed a as Openclinica.war file “Web Application
archive“. It is a JAR(JAVA ARCHIVE) file used to distribute a collection of Java
Server Pages, servlets, Java classes, XML files, tag libraries and static Web pages
(HTML and related files) that together constitute a Web application.
• Standard Installation Process is well documented inside
an instructions file that ships with the application.
• To deploy separate instances, rename the
Openclinica.war to [studyname].war
• Deploy as a normal OC application using the standard
procedure and effect changes in database credentials
inside the datainfo.properties of the deployed web
Application.
Working with OpenClinica
• Policy determination needed
• Required human and material resources allocated
• When know-how is established, utilization requires
only 5 main steps:
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Designing
Creating CRF’s
Event definitions
Data Entry
Data Extraction
GCP Regulations and OpenClinica
• O/C by design, is compliant to the most stringent
regulatory requirements
• O/C is designed to be compliant to FDA 21 CFR Part 11Electronic Records; Electronic Signatures
• These are guidelines that govern the use of electronic
records and signatures ; and can be summarized in two
broad categories:
– Technology best practice
– Policy and procedures best practice
Technology Best Practices
• Audit trail must be independently generated
• Ensure that system maintains a “irrefutable link” between documents,
metadata and the electronic signature.
• Establish clear electronic signature manifestations for all electronic
records.
• Validate the system.
• Establish role-based access and control.
• Establish password and identification controls.
• Series of signings.
• Avoid hybrid systems, where practical.
• Do not over customize technology solutions.
Policy & Procedures Best Practices
• Establish corporate internal policies and guidelines for:
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Validation and procedures
Disaster recovery
Revision and change control procedures
System access and security procedures
Training procedures
Document control procedures
• Develop a clear, comprehensive migration strategy.
• Understand the impact of “open” or “closed” system
definitions.
• Establish retention policies based on current predicate rule
requirements.