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O'Reilly Open Source Convention
Sheraton San Diego Hotel, San Diego, CA
July 23-27, 2001

News Coverage


Applications of Perl in Medical Informatics

Rex Jakobovits

Track: Perl Conference 5
Date: Friday, July 27
Time:†2:30pm - 3:15pm
Location: Grande Ballroom B

In this talk, Rex Jakobovits describes how WIRM is used in several ongoing medical informatics projects: the Digital Anatomist Repository, a service enabling medical schools to build image archives; Fathom, a repository for a natural language processor of patient records; MyPACS, a telediagnosis system for radiologists, and Brain Mapper, an experiment management system for neuroscientists. For each of these projects, he describes the requirements, how WIRM was used to build the solution, show examples of the API at work, and explain which CPAN modules or Perl features were particularly helpful in solving the problem.

With the advent of new technologies for generating medical research data, there is a growing need for innovative tools that enable clinicians, researchers, and educators to manage multimedia information. Open source technologies are beginning to have an impact in the medical informatics arena, making it possible for medical professionals to develop systems that effectively manage the acquisition, organization, and dissemination of their data and knowledge. By enabling domain experts to build their own individually-tailored interfaces for managing biomedical data, Perl is helping to speed the process of scientific discovery, reduce the cost of research, and facilitate the sharing of knowledge.

The web provides a framework for exporting interfaces to share data, but there is currently a lack of high-level web application development tools suitable for use by scientists and health professionals who are not skilled programmers. A biomedical information system often needs to provide individually-tailored interfaces for different classes of end-user, handle the modeling of complex data types, offer customizable forms for acquisition and editing of data, interface with databases and other software applications, and provide support for a wide range of multimedia documents. While CPAN does provide the building blocks for meeting these requirements, the level of expertise needed to tie them together often exceeds the capabilities of the personnel involved in the project (there just arenít enough gurus out there). Hence, laboratories and hospitals tend to buy into proprietary systems, and find themselves at the mercy of a vendor.

We are developing an open source application server, the Web Interfacing Repository Manager (WIRM), which makes the power of CPAN more accessible to medical professionals. WIRM is a layer over CGI.pm, DBI, Perl Magick, and other modules, providing a high-level API for building persistent web objects. Like the popular application server Zope, WIRM provides a simple framework for building web applications. But WIRM-based applications enjoy the added benefit of seamless access to CPAN modules, and of course, the pattern-matching capabilities of Perl.

WIRM includes a browser-based console that allows scientists and clinicians to describe the structure of their domain knowledge. Using this information, WIRM automatically generates a web application that enables end-users to import, organize, query, and visualize domain data. By following a simple methodology, the system developer may then customize the application for different classes of end user.

STATUS: The five applications described in this article are all running and accessible over the web (see http://mypacs.net, http://digitalanatomist.com, http://radbay.com, and http://wirm.org/brain). WIRM 1.0 was released last year. It is currently undergoing a major rewrite, and it will be released "real soon now" as an object-oriented module, with an improved interface and a more scalable way of reusing web objects. See http://wirm.org.


  • Introduction
    • Summary of requirements of medical informatics applications
    • Need for open source solutions in medical informatics
  • WIRM overview
    • System Architecture
    • Application development Methodology
      • Persistent Objects
      • Query by Context
    • Features
      • Schema definition and evolution
      • User sessions and groupware features
      • Document management
      • Image manipulation
      • Context sensitive interfaces
    • Applications
      • Fathom
      • MyPACS
      • Digital Anatomist Repository
      • Brain Mapper

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