University of Southern California Dissertations and Theses

CAFÉ (Common Application Framework Extensible) - a framework to support data capture for clinical trials

(USC Thesis Other)

CAFÉ (Common Application Framework Extensible) - a framework to support data capture for clinical trials

PDF

Download a page range

Download transcript

Copy asset link

Request this asset

Transcript (if available)

Content

CAFÉ (Common Application Framework Extensible)
A framework to support data capture for clinical trials

by

Charanya Ram Kumar

A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
MASTER OF SCIENCE
(APPLIED BIOSTATISTICS AND EPIDEMIOLOGY)

DECEMBER 2012

Copyright 2012 Charanya Ram Kumar
ii
DEDICATION
I dedicate this thesis to the various people who have influenced my life. To my parents for
constantly believing in me and motivating me to reach higher. To my husband, Ram for just
being there for me. To my two wonderful kids, Adrishya and Vivash without whom my life
would be incomplete.

iii
ACKNOWLEDGMENTS
I thank my committee chair Dr. Stanley Azen for his pervasive guidance and support throughout
my graduate study. Thanks to Dr. Wendy Cozen for her contribution to and review of my
dissertation. I specially want to thank Dr. John Casagrande for his patient and repeated reviews
of my thesis and for the valuable feedback. I also thank my supervisor Aarti Vaishnav for
providing the idea and the basis for this thesis.
iv
TABLE OF CONTENTS
Dedication ii
Acknowledgments iii
List of Figures v
Abstract vi
Introduction 1

Materials and Methods 2
Architecture 2
UI Interface 4
Features of CAFÉ 6

Results 8

Discussion 10

Conclusions 13

References 14

Appendices
Appendix A: Dashboards 15
Appendix B: Forms 16
Appendix C: Reports 18
Appendix D: Websites within CAFE 20

v

LIST OF FIGURES

Figure 1: CAFÉ UI Interface 5

Figure 2: CAFÉ Report 7

Figure 3: CAFÉ Applications by study 8

Figure 4: Current number of CAFÉ Applications 9

Figure 5: Process in setting up an application in CAFÉ 11
vi
ABSTRACT
CAFÉ (Common Application Framework Extensible) is a secure windows based application
developed at the University of Southern California’s (USC) Norris Comprehensive Cancer
Center to support data collection for various types of investigations. CAFÉ is an object-oriented
development environment that combines common objects with study-specific data entry form(s)
libraries with common and study specific metadata. This article provides: (1) a brief introduction
to CAFÉ; (2) an overview of the architecture of CAFÉ; (3) some unique features of CAFÉ; and
(4) future development and enhancement plans. CAFÉ is currently supporting over 100
applications at the University of Southern California’s Norris Comprehensive Cancer Center and
elsewhere.
1
INTRODUCTION
Investigators need help managing data for small and medium sized research
projects but do not always have funds to acquire off the shelf products or buy expensive
commercial systems. Research investigators have diverse computing needs that range
from specimen/lab data management to study translational research type activities. These
needs have been addressed in the past using a variety of tools but every solution available
has its own costs and challenges and there is no single solution that works for all
situations. It is a challenge to be able to “quickly” develop and support the data collection
needs for the various types of investigations undertaken in a comprehensive cancer
center. This need is met by CAFÉ which is a framework developed to support the data
collection activities at the University of Southern California’s Norris Comprehensive
Cancer Center (USCNCCC).

CAFÉ was initially developed for protocol management, patient enrollment and
electronic data capture to manage clinical and translational research trials at the
USCNCCC. It has now been generalized and has been used for a variety of situations
including, tissue microarray data capture, epidemiologic studies, prevention trials,
laboratory data management, tissue repositories and administrative systems at USC and
elsewhere.

2
MATERIALS AND METHODS
CAFÉ utilizes the .NET platform with Microsoft SQL Server as the back end
database. It uses Windows Forms along with VB.Net for the front end. SQL Reporting
Services is used for creating reports; a web-browser control is incorporated inside CAFÉ;
third party controls are also used to enhance the windows user interface.
2.1. Architecture
Initially CAFÉ was developed for use in the USC environment supported by the Cancer
Center’s Informatics Core (CRIC) [1]. As the number and scope of CAFÉ supported
applications grew and to accommodate portability of the Framework outside of the USC
environment, several enhancements were needed. This included the use of “interfaces” or
abstract classes that defined the contracts for environment specific-implementations. In
addition, several odata services [3] were added upon start-up to return the status of CAFÉ
for the environment. These abstract classes also allow for local implementations for user
authentication that could be based on LDAP (Lightweight Directory Access Protocol) or
Shibboleth authentication, if desired. Some of these changes also made it possible to
utilize CAFÉ for the development of “disconnected” applications that use laptop-based
SQL (Structured Query Language) Server instances for the back-end metadata and data
storage. Most of the “workspace” (local implementation) specific settings were moved to
a database table and those that are “sensitive” were encrypted to prevent clear text
information to be visible in SQL Management Studio by even the development/server
manager staff.

3
In addition, several additions/plug-ins were added to Visual Studio 2010 which is used to
maintain Café and build applications. The first allows easier deployment of an
application from the development to production environments. The second automates the
creation of an initial application using templates. These were instrumental in making the
creation of applications quicker and easier for the development staff. Finally, a new
installation package was created that allows for simpler deployment and initial
installation from a URL (Uniform resource locator) using reflection [4].

A CAFÉ framework application consists of ten VB (Visual Basic) projects – nine of these
are “common” for all applications developed in CAFÉ and one is application specific,
and it is referred to as the forms library project, since it contains the application specific
data collection forms and ”business logic”. The nine common projects are: (1)
AppExplorer which contains the Login form and the CAF-Elite form, which is the main
UI container for all applications. (2) BaseFormsLibrary - This project contains several
base forms and user controls that are used to develop every application. (3) BaseObjects
contains classes used in the CAFÉ framework that are used for developing an application.
(4) CafeDataService is a web service that does the authentication for a specific
workspace implementation of Cafe (5) CafeDevLauncher which is the startup project
for the framework (6) CRICWebWorkSpace uniquely defines the settings for a specific
implementation of the CAFÉ framework; i.e. “workspace”. (7) DataAccess contains all
the data layer code to connect to a SQL Server database, retrieve data from the database,
and store data to the database. (8) NCCGUIControls contains many graphical user
interface (GUI) controls that are used by a CAFÉ application. (9) SharedCode houses
4
many common items for the CAFÉ framework that do not logically belong in other
projects. It has a module called Utilities which contains common utility functions used by
the CAFÉ framework and by CAFÉ applications.

2.2 UI (User Interface)
CAFÉ’s user interface as shown in Figure 1, it consists of 3 windows. The main menu
window displays all the forms and reports in the application. On the right pane, there is
the display area for forms, reports, web pages or dashboards (To do lists). On the bottom
left pane, is the context menu which shows the current patient/subject for whom the
forms are being displayed. The users have to work on one patient/subject at a time. The
users can move from working on forms to reports to dashboards at the same time. They
can also have multiple forms or reports open at the same time. The menu or the context
windows can also be excluded from the application and they can be customized to suit
the needs of the intended application. The Framework also has the ability to set a
property that identifies a data item as “required” as shown by the fields in red in Figure 1.

5

Figure 1: CAFÉ UI Interface

6
2.3. Features of CAFE
CAFÉ can be used to manage various kinds of studies but at the same time offers several
features that are common among many different types of biomedical studies. Some of
these include: (1) Audit trace –To capture each data element insertion or change in the
database and the details of the entry such as who made it (user id), when it was made
(date and time), which information was changed (PatientId, Table name, column name),
the old value, the new value and many more possible variables. (2) Access tracking -
Track all successful as well as unsuccessful login attempts. For each user session, all
forms that were viewed are also tracked. (3) Rolebased security – form-level and control
level access to users based on their roles. Different roles are assigned to users based on
their nature of work. The roles can be "Read Only", "Read and Write" and "Write Only"
(4) Document Management - Many research investigations need to manage documents
like informed consents and authorization forms. CAFÉ also has the ability to upload these
documents for storage in SQL Server. (5) Automated message system - applications
require an automated email to be sent to the administrator or billing office; there also is a
need to send messages to developer when users encounter unexpected errors; both these
features are integrated with the CAFÉ framework. (6) Fully customizable data acquisition
screens - All CAFÉ Screens and Reports can be customized to meet the needs of the
individual research/user group. (7) Record locking - this feature helps with Quality
Control and data change control. Once the users have completed data entry, they can lock
the record, which notifies a reviewer/supervisor that the form is ready for higher level
review. The reviewer can login and review the form and either approve or makes
comments and alert the user of the errors/ issues which need fixing, this iterative cycle
7
can continue until all data is validated. (8) Remote login – Terminal server access is
maintained which users can remotely log in from anywhere to access their CAFÉ
applications. (9) Multi-user application - Multiple users can access CAFÉ applications
concurrently. (10) Dashboard/To do lists- a fully customizable form that allows users to
get an overview of requests that need their attention for study management. CAFÉ also
has the ability to maintain multiple dashboards in an application. (11) Reports - Reports
can have static data with predefined templates or they can have customized templates
based on the requirements for the application. Reports can be exported to various formats
like Word, Excel, pdf. An example of a report is shown in Figure 2.

Figure 2: CAFÉ report
8
RESULTS
CAFÉ was first used in 2004 for USCNCCC’s clinical trials database but has
since been expanded to capture data in a variety of studies. Figure 3 shows the
number of studies in each category.

Figure 3: CAFÉ Applications by study

9
Clinic-based cohorts have been a major resource for USC’s Cancer center members. The
cohort databases in bladder, prostate, renal and testis and breast have all been migrated
from Microsoft Access to the CAFÉ platform and include many of the same advanced
features like the clinical trials applications. In addition to the Disease Specific cohorts, a
number of CAFÉ applications have been developed for population-based epidemiological
studies. The number of studies captured in CAFÉ has also steadily grown from 2004.
Figure 4 highlights this. More than 100 projects are now supported in CAFÉ-based
applications.

Figure 4: Current number of CAFÉ Applications

10
DISCUSSION
Once a researcher decides that they want to capture data electronically, they set up
a meeting with CRIC (Cancer Research Informatics Core group) in the USC Norris
Cancer Center. In a series of detailed meetings, all the requirements are captured and a
short demonstration is done of existing similar CAFÉ applications. After this, a prototype
is developed and is discussed with the researchers. After getting a sign-off on the
prototype, the actual system is developed, tested and deployed. The time that it takes
from the initial meeting to the actual setup of the CAFÉ system can be as short as four
weeks thereby making CAFÉ a very viable option to researchers who want their systems
to be developed as quickly as possible. In our experience, most investigators do not have
the requisite skills to create their own data collection systems using off the shelf systems
such as Microsoft Access or REDCAP [5] to successfully implement their own solution.
Figure 5 shows the process that is followed to develop a CAFÉ system.

11

Figure 5: Process in setting up an application in CAFE

One of the several advantages of CAFÉ is that it offers reusability of forms between
similar applications. We have been able to reuse the same forms across different studies,
making it less expensive and quicker to setup these studies. This also helps our new
investigators to learn and implement proven methodologies for their studies. In CAFÉ,
we also offer the ability to contain and manage documents so all consents, questionnaires
and supporting documents can be managed efficiently. Lookups are maintained to display
the drop down values and the use of lookups has enabled us to maintain consistent
12
metadata across an enterprise. The browser control that is embedded in CAFÉ also
facilitates the incorporation of not only web based applications but also pdfs, Excel,
Word files and even images( tif or png) within the network.
CAFÉ currently uses a Windows forms front-end for its presentation layer and a thin stub
application has to be initially installed on each client machine. This stub then uses
reflection to download and install the framework’s dlls from a URL. Some institutions
have restrictions on the installation of software directly on client desktops and so this
poses a limitation of the use of CAFÉ applications. To overcome this issue, a web front-
end for Café Framework has been proposed to facilitate easy data access into CAFÉ from
any location with internet connectivity. Also, a print feature is being planned on being
added to the forms make it more user-friendly so that the forms can be printed.

13
CONCLUSIONS
Investigators have long faced the problem of managing their research data. CAFÉ
is very suitable to use in situations where expensive alternatives are not an option for
researchers. When they quickly need to come up with a system to capture data
electronically, CAFÉ is a very suitable option.

14
REFERENCES
[1] Ochs, MF, Casagrande JT, Davuluri R (2010): Biomedical Informatics for Cancer
Research (12): 227-239
[2] Ochs, MF, Casagrande JT (2008): Information Systems for Cancer Research. Cancer
Invest. 26 (10):1060-7
[3] Open Data Protocol Specification (2012): Retrieved from http://www.odata.org/
[4] Bill Evjen, Rockford Lhotka et all (2006): Professional VB 2005 (18): 687-689
[5] Paul A. Harris et al. (2009): Research electronic data capture (REDCap) – A
metadata-driven methodology and workflow process for providing translational research
informatics support". Journal of Biomedical Informatics 42 (2): 377–381

15

APPENDIX A: DASHBOARDS

16

APPENDIX B: FORMS

17

18
APPENDIX C: REPORTS

19

20
APPENDIX D: WEBSITES WITHIN CAFÉ

21

Abstract (if available)

Abstract CAFÉ (Common Application Framework Extensible) is a secure windows based application developed at the University of Southern California’s (USC) Norris Comprehensive Cancer Center to support data collection for various types of investigations. CAFÉ is an object-oriented development environment that combines common objects with study-specific data entry form(s) libraries with common and study specific metadata. This article provides: (1) a brief introduction to CAFÉ

Linked assets

University of Southern California Dissertations and Theses

Conceptually similar

PDF

Exploring the association of number of cigarettes smoked and confidence to quit smoking in Korean American emerging adults: a multilevel modeling approach

PDF

Carboplatin and vincristine chemotherapy for progressive low grade gliomas in pediatric patients with or without neurofibromatosis type 1 (NF1)

PDF

Evaluating the use of friend or family controls in epidemiologic case-control studies

PDF

Association of oophorectomy with progression of carotid atherosclerosis

PDF

Development and validation of survey instrument designed for cervical cancer screening in Malawi, and other low resource settings

PDF

A randomized controlled trial of hormone therapy on postmenopausal women’s quality of life

PDF

Obesity paradox in acute heart failure decompensation

PDF

Methodological approaches to assessing diurnal cortisol rythms in epidemiological studies: how many salivary samples are necessary?

PDF

A cohort study of air-pollution and childhood obesity incidence

PDF

Relationship of blood pressure and antihypertensive medications to cognitive change in the BVAIT, WISH, and ELITE clinical trials

PDF

The study of germ cell tumors and related conditions: an analysis of self-reported data with characterization and comparison of Family History Questionnaires respondents and non-respondents

PDF

Fish consumption and risk of colorectal cancer

PDF

Association between informed decision-making and mental health-related quality of life in long term prostate cancer survivors

PDF

Expansion of emergency medical service regional routing for stroke patient care in the United States from 2000-2010

PDF

Analysis of SNP differential expression and allele-specific expression in gestational trophoblastic disease using RNA-seq data

PDF

Extent, prevalence and progression of coronary calcium in four ethnic groups

PDF

Contemporary outcomes for adult congenital heart surgery in an adult tertiary care hospital

PDF

Street connectivity and childhood obesity: a longitudinal, multilevel analysis

PDF

Associations between isoflavone soy protein (ISP) supplementation and breast cancer in postmenopausal women in the Women’s Isoflavone Soy Health (WISH) clinical trial

PDF

Effect of α₁-adrenergic antagonist use on clinical outcomes in patients with heart failure

Asset Metadata

Creator Ram Kumar, Charanya (author)

Core Title CAFÉ (Common Application Framework Extensible) - a framework to support data capture for clinical trials

School Keck School of Medicine

Degree Master of Science

Degree Program Applied Biostatistics and Epidemiology

Publication Date 11/01/2012

Defense Date 11/01/2012

Publisher University of Southern California (original), University of Southern California. Libraries (digital)

Tag Cafe,clinical trials,framework,OAI-PMH Harvest

Language English

Contributor Electronically uploaded by the author (provenance)

Advisor Azen, Stanley P. (committee chair), Casagrande, John (committee member), Cozen, Wendy (committee member)

Creator Email cramakri@usc.edu

Permanent Link (DOI) https://doi.org/10.25549/usctheses-c3-105677

Unique identifier UC11289272

Identifier usctheses-c3-105677 (legacy record id)

Legacy Identifier etd-RamKumarCh-1263.pdf

Dmrecord 105677

Document Type Thesis

Rights Ram Kumar, Charanya

Type texts

Source University of Southern California (contributing entity), University of Southern California Dissertations and Theses (collection)

Access Conditions The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the a...

Repository Name University of Southern California Digital Library

Repository Location USC Digital Library, University of Southern California, University Park Campus MC 2810, 3434 South Grand Avenue, 2nd Floor, Los Angeles, California 90089-2810, USA