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caTissue Core In Action: An Introduction for Users A Tool Demonstration from caBIG™

caTissue Core In Action: An Introduction for Users A Tool Demonstration from caBIG™. Mark A. Watson, MD, PhD Washington Univ. School of Medicine Siteman Cancer Center February, 2008. Agenda and Goal. Overview and Introduction to caTissue Core caTissue Core Functionality

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caTissue Core In Action: An Introduction for Users A Tool Demonstration from caBIG™

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  1. caTissue Core In Action: An Introduction for UsersA Tool Demonstration from caBIG™ Mark A. Watson, MD, PhD Washington Univ. School of Medicine Siteman Cancer Center February, 2008

  2. Agenda and Goal • Overview and Introduction to caTissue Core • caTissue Core Functionality • Resources and Next Steps The goal of this demo is to introduce you to the capabilities and benefits of a tool that is available for adoption from caBIG™. You can also adapt your existing tool to become caBIG™ compatible, or set up your tool to interface with this one.

  3. caBIG™ Overview caBIG™ is an information network enabling all constituencies in the cancer community – researchers, clinicians, patients – to share data and knowledge to accelerate the discovery of new diagnostics and therapeutics, and improve patient outcomes. caBIG™ Vision • Connect the cancer research community through a shareable, interoperable infrastructure • Deploy and extend standard rules and a common language to more easily share information • Build or adapt tools for collecting, analyzing, integrating and disseminating information associated with cancer research and care

  4. Introduction to caTissue Core

  5. How caTissue Core fits into the Research Continuum Description: A tool for tracking the receipt, processing, storage, quality review, and distribution of biospecimens. Imaging Clinical Research Pathology Molecular Biology

  6. More on How caTissue Core Benefits Your Research • Data capture and biospecimen annotation by multiple users and multiple sites involved in biospecimen management and utilization.. Process Store Collect Ship Distribute Specimen Bank Collection Site Investigator Lab Accession Specimen Create Specimen Distribute Register Participant Search caTissue Core Biospecimen Inventory Add Protocol Add User Add Site Coordinating Center Trials Database

  7. Using caTissue Core: Who and Why? • Target Users: • Biospecimen resource staff who want to track and store data about their biospecimen collection, inventory, and distribution. • Scientists who want to search for biospecimens and associated data for their translational research projects. • Core Functions / Modules • Administration: Create and edit users, protocols, and storage systems associated with a biospecimen inventory. • Biospecimen: Create and edit data concerning participants and their corresponding biospecimens. • Query: Identify biospecimens and their data based upon one or more selection criteria.

  8. Demonstration of caTissue Core

  9. Some adopters of caTissue Core: A Quick Preview: Key Functions and Benefits of caTissue Core • Query. Allows scientists and biospecimen resource staff alike to search for biospecimens based on a combination of attributes. • Simple searches • Complex queries • Role-based access • Biospecimen Tracking. Allows biospecimen resource staff to record events related to biospecimen processing and quality assurance. • Biospecimen Inventory Management. Allows biospecimen resource staff to record data about biospecimen collection, storage, and distribution.

  10. caTissue Core Workflow – Simple Search (Query) Main Menu Bar Select the object that is the subject of the search Simple or Advanced Search Options Select the object attribute Select the condition and value of the attribute Boolean logic “Find all pre-RX serum samples from patients registered to protocols whose title contains the word ‘prostate’”

  11. caTissue Core Workflow – Advanced Query Add specifications about an object Object specifications and their relationships in the query

  12. caTissue Core Workflow – Biospecimen Data Add / Edit Biospecimen Objects - Participants - Protocol registrations - Specimen collection groups - Specimens - Aliquots - Derived specimens - Specimen arrays - Distributions Collection Protocol View / Workflow (Default)

  13. caTissue Core Workflow – Administration Add / Edit Administrative Objects - Users - Sites - Storage Containers (Freezers) - Collection Protocols

  14. A Quick Review: Key Functions and Benefits of caTissue Core • Query. Allows biospecimen resource staff and scientists alike to search for biospecimens based on a combination of attributes. • Biospecimen Tracking. Allows biospecimen resource staff to record events related to biospecimen processing and quality assurance. • Biospecimen Inventory Management. Allows biospecimen resource staff to record data about biospecimen collection, storage, and distribution. • Clarifying Tool Boundaries. No tool meets all user expectations. Here are some functions that are outside the scope of caTissue Core: • Clinical, pathology, and experimental annotation of biospecimens. • Protocol consent tracking

  15. Getting Started: A Glance at the Technology • Tool Platform: Designed to be a centralized database and web page server (generally a single database per institution or biospecimen resource) that is accessible to end users through most standard web browsers. • Key Prerequisites: Installation requires a back-end database application (Oracle, MySQL), application server, and moderate IT support for installation and maintenance. • End User Readiness: End users interact through a simple web user interface, but will need to gain familiarity with the data terminology and workflow functionality.

  16. Resources and Next Steps

  17. Interested organizations are not required to adopt this caBIG™ application to connect with caBIG™ There are other ways to share data and use common data elements and controlled vocabularies by adapting current or non-caBIG™ applications Two Pathways: Adopt or Adapt

  18. Release Information caTissue Core v1.2.1 (LSD)- February 2008. caGrid enabled Development Schedule Next Release: caTissue Suite (April 2008) Enhanced biospecimen annotation, consent tracking, advanced query creation, facilitated (automated) workflows for high-throughput data entry. Currently a semi-annual iterative release cycle with on-going support and improvements based on end-user feedback. Future development iterations will include integration with other caBIG tools and additional functionality based on end-user feedback. Support Available http://catissuecore.wustl.edu Adopting caTissue Core: Release Timeline and Future Plans

  19. The Next Step: Accessing Online Resources for caTissue Core

  20. Thanks for Attending! • We’d like to know what you think! • Did you get useful information from this presentation? • What additional information or future presentation topics would you like to see? • Send your feedback to caBIGconnect@cancer.gov

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