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Technologies at CHS

The diversity of research interests at Group Health Center for Health Studies (CHS) allows IT staff to work and experiment with a variety of technologies. These include:

• Microsimulation Models—C# 
• Internet Technologies—Windows 2000, IIS, Macromedia Dreamweaver MX, Microsoft FrontPage, C#, SQL, Visual Studio.NET, ASP.NET, VB.NET Smart Client, .NET XML Web Services
• Data Warehousing—SAS, SQL, and Sybase Databases
• Automated Chart Review Systems and Tracking Databases—Microsoft Access, SQL Server, Visual Basic, C# and .NET

Microsimulation Models

The Cancer Intervention and Surveillance Modeling Network’s (CISNET) microsimulation model of the natural history of colorectal cancer is implemented using the C# programming language. The model’s programming implementation is based on the well documented state design pattern. This design pattern decentralizes computing amongst the separately implemented microsimulation model processes. Each model process is responsible for transitioning the programming model to the next proper model process. For example, the microsimulation process that models preclinical invasive cancers is solely responsible for transitioning an individual either to a condition in which they die from a cause not related to colorectal cancer or to a condition in which they have preclinical invasive cancer that is subsequently clinically detected. The microsimulation model program executes in two separate modes. An estimation mode outputs the data required to infer the Bayesian posterior distribution of the model’s input parameters. A ‘run’ mode persists the simulated outcomes of the natural life histories of individuals given that the model parameters are specified from their posterior distribution.

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Internet Technologies and Web Programming

CHS has an intranet and an external web site. Both are stored on Windows 2000 Servers and are managed using Microsoft Internet Information Server 5.0. For the intranet, our primary web editor is Dreamweaver MX and web applications are developed in ASP and ASP.NET. For the external web site, we have continued to use FrontPage 2000 with plans to switch to Dreamweaver MX in the future. Our external server hosts project-based listserv mailing lists using Lyris List Manager software. 

To further our research, CHS makes use of Internet technology and Web programming in projects such as

• Case Management Systems
  Web applications that facilitate depression care management have been deployed on multiple studies. Case managers gather information on both the patient's current clinical status and their use of antidepressant medications. Assessment based reports alert both case managers and their supervisors to possible critical patient conditions. A summary report is printed and mailed to the patient’s provider. Selected web applications contain a recruitment component that facilitates recruitment into the case management program. Each web application is written in the C# programming language. Object oriented constructs such as web page inheritance and component construction are used to dynamically generate web pages. Patient assessments are dynamically generated using web components and data stored in an SQL Server database.
  
  
• Data Exploration Tools
  Designed with faculty and managers in mind, the CHS intranet hosts a number of different data exploration tools including
  • Data Counters
    Created with ASP.NET/ VB.NET or ASP/VBScript  front ends and SQL Server back ends, these tools allow staff to obtain utilization summary data counts for writing grants, determining feasibility of studies and checking which codes are used in practice— without asking a programmer for help. CHS staff may point and click their way to counts of Group Health SEER cancer data, diagnosis data, pharmacy data, and procedure data.
  • Data Plotter
    The data plotter allows staff to easily access frequency trend plots of diagnosis or procedure codes in a graphical format. Monthly frequencies are generated in SAS and stored in SQL Server. An ASP.NET front end allows users to search for and select codes and clinics of interest. The resulting plots are displayed in an ActiveX control produced and distributed by SAS.
  • Web SAS Data
    View the contents of a dataset, produce one-way frequencies of variables, generate two-way crosstabs, calculate univariate statistics of numeric variables, and join two tables on a common variable and make inter-table crosstabs. Web SAS Data enables staff to perform simple analyses on their project SAS data without ever having to write a single line of code. SAS runs in the background and users access the data via an interface that was created using ASP.NET/VB.NET.

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Data Warehousing

We have two data warehouses: the CHS Data Warehouse and the Breast Cancer Consortium Statistical Coordination Center (SCC) Data Warehouse.

The CHS data warehouse is a LAN repository of SAS data sets. Development of this warehouse began in 1996, and it was in use by 1997. It is comprised of subsets of the most commonly used clinical and administrative Group Health data sets. Enrollment information is available from 1980, and clinical data date back to the inception of various Group Health automated systems, many originating in the 1980s. Before data are copied to the CHS data warehouse, they are reformatted to standardize variables. The data sets are password-protected, and consumer identifiers are encrypted. At present, the CHS data warehouse stores 737 million records, taking up approximately 230GB of space. This system provides more efficient access to data than MVS or UNIX, and it ensures that historical data are retained.

CHS is also home to the Breast Cancer Surveillance Consortium SCC data warehouse. Using SQL Server, this data warehouse stores breast cancer information from seven sites across the United States. Each site sends eight different text files that cover a whole sequence of events from mammography to cancer, if diagnosed. The text files are run through an "error check" stored procedure written in SQL to check for invalid values. A "longitudinal" SAS data set is created that links information across some of the files. This data set is used in most analytical work. Using an Internet browser as a front-end, secure access is provided to consortium members to run programs against the data. To date, the consortium has collected data for more than 1.8 million women and more than 5.6 million mammography exams that are associated with more than 38,000 breast cancers.

Future Plans: Continue to convert SAS data warehouse data to SQL Server, providing access to summarized data for non-SAS users.

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Automated Chart Review Systems and Tracking Databases

Many of the research projects at CHS require chart reviews and tracking databases to capture patient data. For most studies, we design these databases in Microsoft Access or SQL.

• Chest X-ray Abstraction System Using SQL and .NET
  A project undertaken by the Center's Immunization and Infectious Disease Group seeks to test for a change in the incidence of pneumonia coincident with the introduction of a new children's vaccine. The task involves reviewing roughly 65,000 radiology reports for chest x-rays taken over a period of seven years in order to confirm positive cases of pneumonia. A SQL Server database holds the radiology reports and the data collected in the abstraction process. A system of Windows forms, developed with the C# language in the .NET environment, serves as the interface for the abstractors. As many as six abstractors use the system simultaneously. A parallel system allows project staff to review completed abstractions, revise collected data as needed, and complete abstractions of records flagged as unclear by the abstractors. Records are presented to the abstractors in a predetermined random order so that episodes (clusters of radiology reports) do not appear in chronological order, yet subsequent reports within a given episode may be skipped once the earliest positive report is found. Tasks such as random selection and assignment of records for re-review, as well as weekly and monthly progress and consistency reports, are automated using stored procedures and scheduled jobs.
  
  
• CHCRTracker 
  CHCRTracker is a multithreaded client-server application for tracking study recruitment of Group Health members for a study of smoking cessation. The application is capable of tracking recruits' contact information, staff/recruit contacts, recruit statuses, and generating recruitment letters.
  
  The user interface was built in VB.NET, using the WinForms engine. The data reside on a central SQL Server, and are manipulated through the use of a combination of stored procedures, table triggers, scripts and raw SQL. Reports are generated through Microsoft Access.
  
  
• Automated Chart Abstraction Using VB and Access
  One innovative use of an Access database and Visual Basic programming was designed for the DAHRT study. This study of the relationship between post-menopausal hormone replacement therapy and heart disease in women with diabetes required over 3,000 medical chart reviews at one hour plus per review. An Access database was designed with forms similar to the paper forms used for chart data collection. This enabled chart reviewers to do direct entry of the chart information into the database via the automated forms. Direct data entry saved 5–15 minutes per record, and eliminated the need for re-pulls due to missing values.

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