Download - Intro to OpenClinica
Introducing OpenClinica
Investigator Monitor
Involved Laboratories
Data Manager
Statistician
Clinician
RegulatoryAuthority
Subject
Diary
CRF
DCF
CRF DCFSample
LabResults
ClinicalData
NDA
It’s all about data
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
• 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– 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 OpenClinicaFree, open source, web-based software for EDC built by Akaza Research
Features:– Management of diverse clinical studies through a unified interface– Clinical data entry and validation– Data extraction– Study oversight, auditing, and reporting
Designing a database in OC; requirement and flow of data.
Define CRFs in Excel Temp.
CRF Design, validation and import
Submit data Module; Web-based Data entry and validation
OC - DataBase
Clinical Case Report Forms (CRF)
Creating Data Bases in OpenClinica
A part of CRF Excel Template: “Some tricks”.
Data Base Creating 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 itemVALIDATION 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.
Creating Databases in 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
The Back End 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
Important Features of OpenClinica
Done in excel using a blank CRF template provided by Openclinica
Designing CRFs
The excel sheet is then uploaded onto OpenClinica
Uploading CRFs
Event Definition
Data Entry
Data Extraction
System End of OpenClinica
• 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.
PgDump utility Creates a backup file on the secondary HDD on the main server. File automatically copied to NAS1
NAS1DatabaseDatabase
server
The Back Up Setting
• 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
Restore Process
• 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.
Deploying O/C for Multiple Sites
• Policy determination needed• Required human and material resources allocated• When know-how is established, utilization requires
only 5 main steps:– Designing – Creating CRF’s– Event definitions– Data Entry– Data Extraction
Working with 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 11-Electronic 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
GCP Regulations and OpenClinica
• 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.
Technology Best Practices
• Establish corporate internal policies and guidelines for:– 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.
Policy & Procedures Best Practices