TMAJ: OPEN SOURCE SOFTWARE TO MANAGE A TISSUE MICROARRAY DATABASE
Angelo M. De Marzo
Johns Hopkins University
Baltimore, MD USA
James D. Morgan1
Christi Iacobuzio-Donahue2
Brian Razzaque1
Dennis Faith2
Angelo M. De Marzo2
1 Vision Multimedia Technologies
2 Johns Hopkins University, Baltimore, MD USA
Background: TMAJ is a database and set of software tools to manage Tissue MicroArray (TMA) information. TMAJ is presently implemented at The Johns Hopkins TMA Laboratory, and is being made available as free, open-source software for academic use (http://www.tmaj.com).
Technology: TMAJ is written in Java, which allows the client to be run on most commonly used platforms. Java Web Start, a free component from Sun Microsystems, handles application distribution, and ensures the client is running the latest version of the software. Apache Tomcat handles requests to the Sybase Adaptive Server Anywhere Database Engine. Images are served across the Internet using Apache HTTP Server.
Design: The DataEntry client application facilitates automated and manual entry of data related to patients, specimens, tissue blocks, and tissue sub-blocks (individual pathological diagnoses). ArrayBuilder allows users to design their own TMA's using data that was input either from DataEntry or from its own limited data entry tools. TMAJImage allows digital images of TMA spots to be viewed and diagnosed online. It also facilitates entry of immunohistochemical or in situ hybridization scoring data. Digital images from a TMA slide are imported into the database using TMAJImageImport. A microscope slide-scanning device, such as the Bacus Labs Inc. Slide Scanner (BLISS), is used to generate images of tissue cores. The TMAJAdministrator controls access to the database. Security is enforced through permissions protected by passwords assigned to users. TMAJ allows users to either share or separate their data based on study and sample permissions. These permissions can, in turn, be used to securely limit access to specific specimens, blocks, array-blocks and sessions.
TMAJ allows the storage of a wide variety of information related to TMA samples, including: patient clinical data, specimens, donor blocks, core, and recipient block information. TMAJ supports multiple discrete organ systems and different TMA scoring strategies, and the data structure is compatible with the Tissue Microarray Data Exchange Specification.
Once completed, a user may decide to publish a session, which makes the session’s images, diagnoses and scoring data publicly available.
HIPAA regulations are addressed in the software. Information about the specimen that is considered identifying health information (such as Surgical Pathology Numbers) is available only to users with specific permission. For increased protection, personal patient information is sent to the database through a separate import program and is encrypted using the Blowfish encryption algorithm.
Results: TMAJ contains data from over 13,500 specimens, 7,000 blocks, and 235 TMA's containing greater than 35,000 tissue cores. There are currently 42 users from 8 different institutions. TMAJ has been adapted to house information from several organ systems including the prostate, ovaries, bladder, lymph nodes, colon and pancreas.
Conclusion: Pathologists or other researchers who analyze data from Tissue Microarrays may wish to implement this free software package.