caTissue Suite: An open-access, feature-rich tool for biospecimen annotation and data sharing.
Honorable Mention - BioinformaticsMark Watson ; Washington University School of Medicine;
Content:
Advances in molecular technologies and clinical trial design have increased the importance of biospecimen resources and the requirements associated with the collection and storage of human biospecimens. caTissue Suite is a caBIGTM application designed to manage the associated complexities of biospecimen annotation data.
Technology:
JBOSS 4.0.0 (Red Hat Middleware, LLC); Java Development Kit 1.5 (Sun Microsystems, Inc); Apache Ant 1.6 (The Apache Software Foundation); and either of MySQL 4.1.19 (MySQL Inc.) or Oracle 9i (Oracle Corporation).
Design:
caTissue Suite is an n-tiered application. A web browser submits requests to the application server, which in turn persists or acquires data in a relational database. A Java-based Application Programming Interface permits more advanced, automated, and customized access to all of the applications features. The application supports administrative functions (protocol and storage system definition), biospecimen accessioning (including provisions for consent tracking and iterative biospecimen derivation and aliquoting), and investigator queries (advanced query creation and specimen requisition system). A caTIES-like interface allows for import and concept coding of textual based pathology data, and discrete pathology and clinical data entry is supported through customized form creation.
Results:
caTissue Suite is scalable, configurable, and flexible enough for broad deployment across repositories of varying size and function. To date, at least eight institutions have adopted the application and are using it in the daily operation of their biospecimen resource. A grid-based biospecimen data sharing initiative is underway. Continuous end-user feedback provides new requirements for each iteration of the application release. Planned enhancements in caTissue Suite v1.1 (December 2008) include the ability to use a single instance to independently manage multiple biospecimen repositories, support for temporal queries (e.g. find all biospecimens that were frozen within 30 minutes of collection), and functionality to create and use complex data forms dynamically from a new Unified Modeling Language-based object model.
Conclusion:
caTissue Suite is an open-access / open-architecture application that has been developed, formally tested, and successfully deployed by a number of NCI-designated cancer centers and other biospecimen resources. Use of caTissue Suite by these institutions is providing a rapid and facilitated path toward standardizing biospecimen informatics both nationally and globally.
