Title: caTissue Core In Action: An Introduction for Users A Tool Demonstration from caBIG
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
2Agenda 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.
3caBIG 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
4Introduction to caTissue Core
5How 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
6More 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
7Using 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.
8Demonstration of caTissue Core
9A 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.
10caTissue 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
11caTissue Core Workflow Advanced Query
Add specifications about an object
Object specifications and their relationships in
the query
12caTissue 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)
13caTissue Core Workflow Administration
Add / Edit Administrative Objects - Users -
Sites - Storage Containers (Freezers) -
Collection Protocols
14A 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
15Getting 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.
16Resources and Next Steps
17Two 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
18Adopting 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
19The Next Step Accessing Online Resources for
caTissue Core
20Thanks 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