# Presentation: 241514

## caBIGTM Industry Partners’ MeetingCancer Center Perspective

- J. Robert Beck, M.D.
- Fox Chase Cancer Center
- Strategic Level Strategic Planning Working Group of the Cancer Biomedical Informatics GridTM

## The Knowledge Explosion: Challenges to Research

- Small group research -> Lab notebooks
- Clinical trials individual investigators or cooperative groups
- Ad hoc collection of biomedical samples
- All of these are changing!

## What is the caBIGTM  Community?

- A Community of Communities
- Sharing Common Interests
- Data Standards
- Sharable and Interoperable Architectures
- Informatics Tools
- Cancer Research
- To the Ultimate Benefit of Patients

## caBIG’s Five Year Mission

- Develop Standards, Tools, and Prototypes
- Bias Toward Action and Interaction
- Easy Methods of Dissemination
- Open Source
- Open Access
- Open Development
- Federation

## A Focus on Interaction

## Scenario, 2008

- 	A researcher involved in a phase II clinical trial of a new molecularly targeted therapeutic for brain tumors observes that cancers derived from one specific tissue progenitor appear to be strongly affected.  The trial has been generating proteomic and microarray data.  The researcher would like to identify potential biochemical and signaling pathways that might be different between this cell type and other potential progenitors in cancer, deduce whether anything similar has been observed in other clinical trials involving agents known to affect these specific pathways, and identify any studies in model organisms involving tissues with similar pathway activity.

- Small Molecules

- Cell Type

- Pathways

- Clinical Trials

- Therapeutics

- Animal Models

- Homologous Proteins

## Today vs 2008?

- 	In 2005 such a study would involve immense manual work getting information locally and from other sites, precluding the possibility of identifying the required data and thus being unable to deduce the likely significance of the trial observation.

- However, with caBIGTM compliant components now under development, the researcher would be able to perform the analysis routinely, with data flowing through systems and analysis being automatic.  This analysis will yield biomarkers and potential drug targets gathered from multiple workspaces and make it possible to develop treatment modalities faster, less expensively, and more effective for patients.

## CTMS Workspace

- Discovery utilizing caBIGTM
- Integrated Cancer Research Tools

## Overall Goals for caBIGTMThree-year (mid-2008)

- Develop sufficient research tools and standards to have a positive impact on the cancer research community, as measured by adoption of relevant caBIGTM  principles in project proposals.
- Ensure widespread adoption of developer standards so that funded developer projects are operating under the Gold standard of compatibility.
- Adopt and use caBIGTM  interoperable tools and data sets within the caBIGTM  community.
- Develop mechanisms for engaging and promoting caBIGTM  compliant technologies and established datasets within the oncology research community.

## Overall Goals for caBIGTMFive-year (mid-2010)

- Ensure widespread adoption, dissemination, and use of caBIGTM  interoperable tools, standards, and data sets within the larger cancer community, to include the biopharmaceutical industry, non-NCI cancer centers, and the national cancer research enterprise.
- Begin to see results of caBIGTM -compliant interdisciplinary and inter-institutional research affecting clinical oncology care.

## What does caBIGTM  mean to the Cancer Centers?

- Product—in CTMS, ICR, Tissue Banking
- Support for large scale collaborative research
- No need to “go it alone” with bioinformatics or other quantitative support tools

## The Workspaces Meet Centers’ Needs

**ICR –data sharing**

**caTIES – info extract**

**caTissue – tissue bank**

** ****Clinical trials tools are Cancer Centers’ & caBIG’s TOP Priority**

**All Development activities**

## Clinical Trials Management

- Inventory of Tools
- Available now:  C3D – Cancer Central Clinical Database
- Available 4th Qtr 2005:  Data Mapping Foundation
- Available 1st Qtr 2006: Adverse Events Reporting, Protocol Submission Tools and Data Export tools for commercial systems
- Pathway for Cancer Centers to implement tools at their sites
- Adopters and Working Group roles
- Funded and Volunteer roles and pathway to get there
- Developer roles for future projects

## Clinical Trials Management:  Three Levels of Interaction Based on Institutional Readiness

**New caBIG modules**

**Existing System:**
**Change Imminent**

**exchange data**

**caBIG Open Source**
**Core Functionality**

**Interoperable**
**caBIG Community**

**No Existing System**

**C3D Adoption**

**Additional**
**Functionality**

**Existing System:**
**No Change**

**caBIG compatibility**
**efforts with vendor**

**Additional**
**Functionality**

## What does caBIGTM  offer the Cancer Center for Clinical Trials Management?

**Cancer Center Clinical Database or C3D – available today**
**Data Mapping Foundation or caDMF – caBIGTM   compliant data sharing between centers – available 4****th**** Qtr 2005**
**Adverse Event Reporting or caAERS – available 1****st**** Qtr 2006**
**Clinical Trial Structured Protocol Authoring or caSPR – available 1****st**** Qtr 2006**
**Key is to understand the workflows to support clinical trials and choose a starting point for use of caBIGTM  tools**

## Tools for Translational Research

- caBIGTM  Compatibility Guidelines
- 3 year plan:  all tool development at Gold level
- Successful Developer-adopter relationships
- Extension to other research areas
- Imaging
- Population Science

## ICR Software Maturity Table

|  | Maturity Level | Description |
| --- | --- | --- |
| 1 | Basic research/Design | The key concepts for the system have been defined, algorithms outlined, use cases documented, requirements and specification document(s) prepared.  |
| 2 | Prototype/Proof of Principle | A semi-functional system has been implemented for the purpose of getting feedback from potential end-users on the execution of the design. |
| 3 | First working implementation (“beta”) | System has gone through at least one round of testing by end users and some feedback has been incorporated.  System is in trial use by a limited number of users.  Only intended for limited distribution by users in close contact with the development team. |
| 4 | Deployed and in use | System has gone though a thorough beta test and is deployed and in use at at least one site.  Additional sites may deploy the software with possible assistance from the development team. Initial user and developer guides are available.  Known defects are documented.   |
| 5 | Post deployment and maintenance | System is readily deployed by any interested party with no assistance from the development team.  Known defects are documented.  Mature user and developer guides are available as well as training materials.   |

## Slide 18

| Project Name | Maturity Level at the end of caBIGTM  Year 1 Project Development | caBIGTM  Compatibility Level at the end of caBIGTM  Year 1 Project Developement |
| --- | --- | --- |
| Cancer Molecular Pages | GUI:  4
API:  3 | Silver Level |
| FunctionExpress | 5 | Designed to be Silver Level |
| GoMiner | 4 | Silver Level |
| PIR | 3 | Silver Level |
| SEED | Analysis: 3/4
Readout: 2/3 | Silver Level
Silver Level |
| TrAPSS | 4 | Silver Level |
| Magellan | 4 |  |
| Distance-Weighted Discrimination | 3/4 | Silver Level |
| GenePattern | Year 1 caBIG mods:  3/4 | Silver Level |
| VISDA | 4 | Silver Level |
| caWorkbench | 3/4 | Silver Level |
| Pathways Tools | 4 overall | Silver Level |
| QPACA | 3/4 | Silver Level |
| caArray | 4 (current release) | “pre-Silver” (current release) |
| RProteomics | 2/3 | Gold |
| Proteomics LIMS | 3 | Silver |
|  |  |  |

## Data Sharing and Intellectual Capital

## Training Working Group

## Cancer Center Roles in caBIGTM 

**Developer (20% of centers)**
**Key is to create an environment for sharing tools with other centers**
**One of the most important issues is not to ignore the need for common data elements and vocabulary services**
**Adopter (20% of centers)**
**Key is to understand the needs at local center (and be vocal)**
**Don’t abandon other development efforts; think modular**
**When adopting tools make sure they “talk” to legacy systems**
**Working Group & Strategic Planning (60% of centers)**
**These are not “soft” roles**
**Critical to the success of the program**
**White paper development will guide caBIGTM successes**
**Make sure to communicate internally to all parts of the Cancer Center**

## caBIGTM  Compatibility

- What does caBIGTM  “compatibility” mean to CC
**caBIGTM  is all about Interoperability**
**Key is to create tools for sharing info with other centers**
**Not an easy task due to “silo” mentality**
**CDEs and EVS enable common language and data values**
**Software design principles ensure cross compatibility of developed software**
**Extensible infrastructure**
**Expandable and modular software to plug in to existing systems so current development efforts are not wasted**
**Scalable so that efficiency is gained by software engineering**
**Ensures partnerships**
**Built on commercial software development principles**
**Encourages relationships between academia, government and industry**
**Scalable so that commercial partners can utilize “open source”**

## Industry Partners with Cancer Centers

- Plug and Play with caBIGTM  architecture:  requirement for new tool or system adoption
- Take caBIGTM  developed tools at Silver or Gold level of compliance, create commercially supportable versions thereof and take to market
- Evaluate intellectual property in grid context