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

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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

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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.
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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

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Introduction to caTissue Core
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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
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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
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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.

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Demonstration of caTissue Core
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A Quick Preview Key Functions and Benefits of
caTissue Core

• Some adopters 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.

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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
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caTissue Core Workflow Advanced Query
Add specifications about an object
Object specifications and their relationships in
the query
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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)
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caTissue Core Workflow Administration
Add / Edit Administrative Objects - Users -
Sites - Storage Containers (Freezers) -
Collection Protocols
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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

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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.

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Resources and Next Steps
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Two Pathways Adopt or Adapt

• 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

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Adopting caTissue Core Release Timeline and
Future Plans

• 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

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The Next Step Accessing Online Resources for
caTissue Core
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Thanks for Attending!

• Wed 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_at_cancer.gov