Clinical Data Management - Global Health Trials

musicincurableData Management

Jan 31, 2013 (4 years and 4 months ago)

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Introducing OpenClinica


Investigator

Monitor

Involved

Laboratories

Data Manager

Statistician

Clinician

Regulatory

Authority

Subject

Diary

CRF

DCF

CRF

DCF

Sample

Lab

Results

Clinical

Data

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 Open
Clinica

Free, 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 Open
Clinica

Item_name

Label

Units

Col_No

Page no

Resp_Type

Resp_Lab
el

Resp_opti
ons

Resp_Valu
es

Date type

Validation

Required

childini


Child Initials

1

1

text

ST


regexp
: /[A
-
Z]{3}/


1

pidnu

PAD No.

2

1

text

ST

regexp
: /[0
-
9,
A
-
Z]{7}/


1

WHZsco
re


Wght
/
hght

Z
score


1

2

text

REAL


func
:
gte
(
-
3.0)


1

A part of CRF Excel Template:
“Some tricks”.

Data Base Creating in Open
Clinica

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.





Creating Databases in Open
Clinica


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 Open
Clinica


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 Open
Clinica

Done in excel using a blank CRF template
provided by Openclinica


Designing CRFs

The excel sheet is then uploaded onto Open
Clinica




Uploading CRFs

Event Definition

Data Entry

Data Extraction

System End of Open
Clinica


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

NAS1

Database

Database
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 Open
Clinica


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 Open
Clinica


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