Health Analytics Database Project
Kpatel
how_to_-_practical_database_management_system_for_clinical_research.pdf
How I do it: A Practical Database Management System to Assist Clinical Research Teams with Data Collecting, Organization, and Reporting
Howard Lee, B.S.1, Julius Chapiro, M.D.1, Rüdiger Schernthaner, M.D.1, Rafael Duran, M.D. 1, Zhijun Wang, M.D., Ph.D1, Boris Gorodetski, B.S.1, Jean-François Geschwind, M.D.1, and MingDe Lin, Ph.D2
Howard Lee: [email protected]; Julius Chapiro: [email protected]; Rüdiger Schernthaner: [email protected]; Rafael Duran: [email protected]; Zhijun Wang: [email protected]; Boris Gorodetski: [email protected]; Jean-François Geschwind: [email protected]; MingDe Lin: [email protected] 1Russell H. Morgan Department of Radiology and Radiological Science, Division of Vascular and Interventional Radiology, The Johns Hopkins Hospital, Sheikh Zayed Tower, Ste 7203, 1800 Orleans St, Baltimore, MD, USA 21287
2U/S Imaging and Interventions (UII), Philips Research North America, 345 Scarborough Road, Briarcliff Manor, New York 10510
Introduction
With the growing amount of clinical research studies in the field of interventional oncology,
selective patient data is becoming more difficult to store and organize effectively. Existing
hospital EMR (electronic medical record) systems store patient data in the form of reports
and data tables. Our institution’s EMR system placed our researchers in a position where
time consuming methods are needed to search for suitable patients for clinical studies.
Researchers had to manually read through the reports and data tables to filter patients and
gather data. For most studies, spreadsheet programs such as Microsoft Excel® (Microsoft,
Washington, USA) are often used as a data repository similar to a database to record and
organize patient data for research. Once the spreadsheet is populated, it is manually filtered
by set study parameters and then pushed to statistical analysis software for further analysis.
For statistical analysis, columns containing text are translated into binary values (1 or 0) to
be in a format acceptable by statistical analysis software. For example, each tumor entity is
assigned a new column. Patient histological reports are read manually to assign a 1 or 0 to
each tumor entity column, 1 for positive, 0 for negative. Under a tumor entity column,
researchers would write a 1 for all patients with the tumor and a 0 for all patients without the
tumor.
© 2014 AUR. All rights reserved.
Correspondence to: Jean-François Geschwind, [email protected].
Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
HHS Public Access Author manuscript Acad Radiol. Author manuscript; available in PMC 2016 April 01.
Published in final edited form as: Acad Radiol. 2015 April ; 22(4): 527–533. doi:10.1016/j.acra.2014.12.002.
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This method of data storage has limitations in the organization and the quality of the data.
Data input and analysis without a database run a higher risk of incorrect data entry, patient
exclusion, and a higher risk of introducing duplicates. Furthermore, data selection and
calculation is time consuming. An alternative could be the clinical research database that
Meineke et. al. proposed (1). However, it is too unspecific for interventional oncology
research and would need additional optimization, for example, the capability to
automatically calculate various variables such as tumor staging systems and to record
information about multiple treatment sessions.
The purpose of this study was to provide an improved workflow efficient tool through the
use of a clinical research database management system (DBMS) optimized for interventional
oncology clinical research.
Materials and Methods
This was a single-institution prospective study. The study was compliant with the Health
Insurance Portability and Accountability Act (HIPAA) and was waived by the Institutional
Review Board.
Database and Query Interface Design
The presented database management system has two distinct parts, the database server and
client interface, illustrated in Figure 1. The database is run by software (MySQL, Oracle
Corporation, California, USA and phpMyAdmin, The phpMyAdmin Project, California,
USA) on a central computer server within the department (2, 3). Authorized users were
granted access to this password protected and encrypted secured server (HIPAA compliant).
Multiple users concurrently add, edit, and query data remotely through a customized
graphical user interface (GUI) utilizing Microsoft Access® (Microsoft, Washington, USA).
Any data changes are immediately logged for others to see. The database performed
automatic calculations using queries, user-defined search criteria. Queries were saved, rerun,
and exported to spreadsheets. Queries aid in data analysis and increase study productivity
(4). They are powerful tools for filtering and sorting datasets. Figure 2 illustrates the query
interface and an example of request from the database.
Graphical User Interface Design and Utility
In our research environment, the database GUI was created to facilitate patient data input.
This was done by using custom user-friendly interface forms that contain textboxes and
labels including demographic data, treatment information (e.g. conventional transarterial
chemoembolization (TACE)), tumors types, dates and types of radiological exams, etc. The
GUI is used to view patient data and allows users to add/edit data (Figure 3). The database
interface is not limited to one form. It can have multiple forms, shown as tabs, to assist
grouping various medical data. Figure 4 shows an example of multiple tabs for groups of
related data.
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Automatic Calculations
Automatic calculations may be run between values, such as dates. For example, the database
may calculate the time between baseline imaging, follow-up imaging, treatment dates, pre-
and post-treatment dates, date of diagnosis, and patient’s date of death in relation to a
particular treatment or event (e.g. randomization), essential for survival studies. Using these
queries, the database can also calculate the median overall survival automatically. The
database does also automatically calculate clinical scores such as Child-Pugh score and
Barcelona Clinic Liver Cancer (BCLC) stage as shown in Figure 5 (5). For our purposes, the
Child Pugh score and BCLC were calculated using baseline data before a patient’s first
embolization as is typically done for staging. The illustrated calculators can be revised as
needed. Once patient blood data is available, queries are run to produce a list of all patients
with Child-Pugh scores. Researchers can then quickly retrieve them.
Statistical Output
Another powerful feature of the database is its ability to provide a first tier of statistical
information. Using this GUI, the user defines the search criteria and runs queries to obtain
immediate statistical information about a particular set of parameters. With this feature, the
database can quickly output an accurate summary of patient data such as, for example, how
many patients have colorectal carcinoma and undergo conventional TACE.
Questionnaire Assessment
A questionnaire (15 questions) was designed and distributed to 21 board-certified
interventional radiologists who conduct clinical research at our academic hospital that
include Phase I, II, and III clinical trials, and retrospective studies. The questionnaire
determined how data is controlled in retrospective studies and the likelihood to use the
database. The questionnaire is shown in Table 1. The purpose of the questionnaire was to 1)
illustrate the general scope of where researchers were having problems within Excel and
data organization, such as wasted effort working with duplicate patients and unintentional
failure to include available patients, and 2) to gauge how receptive they would be to a
database system. Using this information, the database system was constructed. There were
weekly progress updates with the clinical research team to ensure that the original goals set
out to address the deficiencies of Excel were being resolved.
Results
Questionnaire Results
All 21 interventional radiologists completed the questionnaire. Self evaluation results are
shown in Figure 6. In data collection and analysis, over 50% (11/21) spent most of the time
searching, filtering, and/or categorizing data. However, about 50% (10/21) spent little to no
time calculating the data. 67% of respondents (14/21) realized at some point that there were
erroneously included patients who should have been excluded and there were patients who
were erroneously not included. Over 85% (18/21) were very receptive to using software that
produces group summaries such as totals of each tumor type with minimal effort, calculates
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clinical staging and score systems automatically, and also allows remote access for multiple
users to add/edit data in a central server with data modification logs.
Query Interface Output
In Figure 7, the query of male patients, over 40 years old, with HCC is run. Figure 8 shows a
query result of patients with TACE and Child-Pugh score A calculated by the database.
Figure 9 illustrates an interval of time between two events as a query that can be calculated
automatically (e.g. time elapsed between two embolization procedures). The output of the
queries as described above is shown in a structured and concise list, which can be exported
for further research study specific analysis.
Discussion
The main finding of this study is that there is a need for a much more time efficient and
accurate way to store, retrieve, and analyze patient data for clinical research studies. The
database management system presented here fulfills these needs. This was achieved through
the use of automatic calculations, interface forms, queries, etc. With a personalized
interface, data access, entry, organization, queries, calculations, and export processes are
seamlessly performed to assist clinical research with data and statistical analysis.
Furthermore, the database is a unified repository of clinical research information and a
shared resource among the clinical research team. This allows for a multi-user level
experience where there can be simultaneous access to the data and where the efforts of each
individual in adding/appending new information can be used by the entire team.
With the presented database put into use, the effort for clinical studies can truly focus on
conducting various statistical analysis and data interpretation rather than preparing data for
analysis (6). All retrospective data can be merged into this database, enabling a centrally
maintained and shared resource. Our clinical research team now has access to a customized
database of patients with a large number of clinical parameters, allowing a vast combination
of queries to form or support study hypotheses. The user defined GUI-connected interface is
invaluable for anyone collecting data as it facilitates data entry and minimizes data entry
errors.
In previous data collection and analysis, converting spreadsheet data to binary/numeric
format was time consuming and impractical. The database presented in this study relieves
the inconvenience of manually searching, organizing, and calculating data. Processing
calculations, especially more complex calculations such as clinical staging scores, can now
be done automatically. Prior to implementing the presented database system, a typical Excel
spreadsheet for the clinical studies at our institution would have over 100 columns. These
columns included patient demographics, repeat treatment dates and types (new columns per
TACE session), and repeated pre-/post-imaging dates and types (new columns per multi-
modular scan). Tracking medical data is frequently difficult due to the large amount of
columns in the spreadsheet. Compared to a typical Excel spreadsheet with many columns,
browsing and adding prospective data through the database interface presented here is more
organized and practical with ten defined tabs for data groups, ranging from a patient’s basic
information to treatments to survival status. In addition, the database interface lists all
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repeating treatments and imaging per patient as rows instead of columns, facilitating
comparisons between multiple treatments of a patient. Combining the database’s ability to
calculate statistical analysis with automatic calculation queries, reports can be generated
with virtually any parameter. This is not only helpful in radiology, but also beneficial for
other studies and hospital information systems.
The database management system in this study has some limitations. A database system may
not be suitable for all kinds of research teams. There are several factors that may illustrate
the need of a database. In a previous report on data collection, applicable examples and
guidelines were addressed to determine whether or not implementing a database is feasible
in the current environment (7). Depending on the environment and context, a database may
not be implemented right away as it needs additional testing. Furthermore, the database will
need a dedicated server to host the database along with the data. In order to use the database
interface, training is required. Someone who specializes in databases, such as a database
administrator, needs to teach researchers and other potential users how to use the database
interface and query interface for filtering patients and obtaining statistics. This is especially
needed in more advanced queries and in developing additional GUIs. It should be noted that
Microsoft Access is being used in this work as a “front-end” interface that communicates
with the SQL database to query (filter) data, and for input/appending to existing data. Other
software such as FileMaker Pro (FileMaker, Santa Clara, CA) and REDCap would serve a
similar function (8). The need for the SQL database is so that multiple users can access the
stored data at the same time, increased level of security, stability, and performance, and
serving as a unified repository of clinical research information that can be shared by the
research team (9, 10). Also, the database administrator has to not only construct a database
on a server with input from clinicians and other end users, but in addition would need to
maintain the database (11, 12). Typical maintenance includes routine backups, altering
database structure and interface for new data types, and updating database and client
software. A server can be hosted on a PC or online, both of which all parties involved can
access in the same network locally or remotely. Furthermore, databases can be enabled to
communicate with other databases. While the initial setup and learning curve is high, the
database allows for fluid data entry in an organized fashion, querying results including
calculations, and storing data while supporting simultaneous user access. With the variety of
research teams and departments, ideally each suitable team should have their own database.
This is not necessarily only for interventional oncology but also for any specific area of
research, for example, studies with patients undergoing ablation, percutaneous abscess
drainage (PAD), etc. These databases can be connected for interdisciplinary research to
provide a broader scope of data and facilitate data search (13).
Conclusion
The current database implementation and interface allows a much faster and more detailed
retrospective analysis of patient cohorts. In addition, it facilitates data management and a
standardized information output for ongoing prospective clinical trials. The database
management system with an interface is a work efficient and robust tool that provides a
significant edge over manual retrieval of patient records by filtering data and assisting
statistical analysis in a study-relevant fashion.
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Acknowledgments
Funding and support has been provided by NIH/NCI R01 CA160771, P30 CA006973, and Philips Research North America, Briarcliff Manor, NY, USA.
References
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7. Schmier JK, Kane DW, Halpern MT. Practical applications of usability theory to electronic data collection for clinical trials. Contemporary clinical trials. 2005; 26(3):376–85. [PubMed: 15911471]
8. Harris PA, Taylor R, Thielke R, Payne J, Gonzalez N, Conde JG. Research electronic data capture (REDCap)—A metadata-driven methodology and workflow process for providing translational research informatics support. Journal of Biomedical Informatics. 42(2):377–81. [PubMed: 18929686]
9. MySQL Database Provides Full Transactional Support. Worldwide Databases. 2002; 14(11) 0-N/A.
10. Oracle Improves Database Performance with Latest Development Milestone Release for MySQL 5.7; New Release of the World’s Most Popular Open Source Database is 2x Faster than MySQL 5.6 and Over 3x Faster than MySQL 5.5 in Benchmark Tests. Book Oracle Improves Database Performance with Latest Development Milestone Release for MySQL 5.7; New Release of the World’s Most Popular Open Source Database is 2x Faster than MySQL 5.6 and Over 3x Faster than MySQL 5.5 in Benchmark Tests. City2014.
11. Xie SX, Baek Y, Grossman M, et al. Building an integrated neurodegenerative disease database at an academic health center. Alzheimer’s & dementia : the journal of the Alzheimer’s Association. 2011; 7(4):e84–93.
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Figure 1. The Dataflow Chart This chart shows a general layout of the database server and its clients. It illustrates how the
database management system performs queries (orange circle) such as statistical analysis.
Multiple computers are granted access to the database. The blue rectangles represent the
database management system software. Researchers can utilize the database client graphical
user interface (GUI) to import data without needing to format. Researchers also control data
through the GUI. Queries are usually run through the GUI to provide wanted results. Once
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the results are obtained, researchers export the query to a spreadsheet, illustrated by the
green rectangle.
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Figure 2. This figure illustrates the query interface. In this example query, a list of male patients over
the age of 40 with hepatocellular carcinoma (HCC) is wanted. The user inputs search criteria
for age, gender, and tumor type, “>40”, “m”, and “HCC” respectively. MRN: medical record
number.
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Figure 3. This form illustrates how users input data to the database. The form is divided into three
parts:
(a) Patient Form – Data consists of basic patient information. Patient Identification (PID) is
a unique number generated by the database to uniquely identify patients. LAST MODIFIED
is a timestamp of when the data was most recently updated or added. MODIFIED BY is a
text box that records who updated/added data. (a1) shows the total amount of patients in the
database.
(b) Tumor – Data consists of a patient’s primary and secondary tumors in the liver. The
dropdown allows users to select a tumor or add new tumor types (e.g. metastatic disease).
(b1) shows how many tumors types the patient has in the liver.
(c) Embolization Procedures – Data consists of intra-arterial therapies (IATs) sessions. (c1)
shows how many IATs sessions a patient has went through.
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Figure 4. This figure illustrates the tabular form where each group of related data is shown as
individual tabs to assist user navigation. The display of patient identification information
and comments are maintained while the user navigates to different tabs to preserve the scope
and field of view for each patient.
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Figure 5. This form shows a patient’s Child-Pugh score and Barcelona Clinic Liver Cancer (BCLC)
stage. They are automatically calculated when provided with pertinent patient data. The
“Calculate” buttons are used to refresh the form should any patient data value change.
PT/INR: Prothrombin Time/International Normalized Ratio; PS: Performance Status.
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Figure 6. The self evaluation results are from Table 1.
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Figure 7. This figure illustrates the output of a query for male patients with hepatocellular carcinoma
(HCC). The interface outputs a list of all patients matching the search criteria.
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Figure 8. This is the output of a query for patients who had undergone TACE in 2006
(P_PROC_DATE column) with Child Pugh Class A, here labeled as “Classification”. The
automatically calculated Child-Pugh Class can be used also for querying.
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Figure 9. The database automatically calculates the days between TACE sessions for each patient as a
query (red circle). The current treatment “EMBODate,” is subtracted from the next
treatment, “Next_EMBO.” Empty fields indicate that the patient has undergone only one
treatment or the session is the latest treatment. Because the query is saved, double clicking
the query indicated by the red circle refreshes the calculation for the entire database of
patients.
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Table 1
Questionnaire Assessment
Response: Yes No
Question: I searched and filtered data manually Example: Sorting and copying relevant data
Question: I inputted formulas and Excel functions to calculate scores, response rates, or statistics in my Excel spreadsheet
Question: I summarized my Excel data in a report Example: Total number of Child Pugh A patients
Question: I converted non-binary data (volume measurements, numeric values, occurrence rates of symptoms) into binary data (0/1) by defining a cut-off point to differentiate Example: Between responder and non-responder to a given therapy for statistical analysis
Question: I have done statistical analysis myself
Question: I unknowingly produced duplicate data that I later found out was already collected by another colleague
Response: 0–20% 21–40% 41–60% 61–80% 81–100%
Question: From the beginning of data collection to finishing analysis, about what percentage of the total time spent for a single retrospective study did you spend on:
Question: Querying/filtering/categorizing data? Example: Defining subsets of patients with certain criteria such as patients treated only with cTACE or only with DEB-TACE
Question: Calculating data? Example: Min, Max, Mean, Sum, Clinical Scores such as Child-Pugh
Response: Very Unlikely Unlikely Neutral Likely Very Likely
Question: If given the opportunity, how likely will you use software that:
Question: Produces group summaries with minimal effort? Example: Total number of Child Pugh A patients
Question: Calculates clinical staging and score systems automatically?
Question: Allows multiple users to add and edit data into the same database so that redundant collection of the same patients by different colleagues can be avoided?
Question: Allows users to track data modifications?
Question: Stores data in a centralized location with remote access?
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