# Presentation: 534306

## caBIG Tissue Bank and Pathology Tool 

- July 10, 2004

**caBIG Tissue Bank and Pathology Tool **
**Workspace (TBPTW) Efforts**

## Agenda

- Tissue Bank and Pathology Tools Workspace (TBPTW) Overview
- caBIG Principles and Compatibility Requirements
- Overview of Cancer Center and Prostate Cancer SPORE TBPTW Requirements Survey Results

## caBIG Tissue Bank and Pathology Tool 

- July 10, 2004

**caBIG Tissue Bank and Pathology Tool **
**Workspace (TBPTW) Overview**

## caBIG Cancer Center Needs 

**Clinical Trial Management Systems**

**Tissue ****Banks ****& Pathology**

**Integrative Cancer Research**

**Notes:**
Three areas of critical need were identified based on this information and these facilitated the groupings of pilot project activities into three Workspaces:
(1)	Clinical Trial Management Systems
(2)	Integrative Cancer Research
(3)	Tissue Banks and Pathology Tools

## caBIG Workspaces

- There are two types of Workspaces – Domain and Cross Cutting
- Tissue Banks and Pathology Tools is a Domain Workspace

## Workspace Roles

**Cross Cutting **
**WORKSPACE**

**Architecture**

**Vocabularies & Common Data Elements**

**Cross Cutting ****WORKSPACE**

**Developer**

**Developer**

**Adopter**

**Developer**

**Developer**

**Adopter**

**Developer**

**Developer**

**Developer**

**Developer**

**Developer**

**Workspace**
**Working Group**

**Workspace**
**Working Group**

**Workspace**
**Working Group**

**Domain **
**WORKSPACE**

**Clinical Trial Mgmt System**

**Integrative Cancer Research**

**Tissue Banks & Pathology Tools**

**Workspace**
**Working Group**

**Workspace**
**Working Group**

**Adopter**

**Developer**

**Developer**

**Adopter**

**Developer**

**Developer**

**Adopter**

**Domain **
**WORKSPACE**

**Domain **
**WORKSPACE**

## TBPTW Goals

- Provide for the implementation and integration of tissue bank and pathology tools and infrastructure components that will facilitate information sharing.  This involves:
- The integration and implementation of tools for the collection and maintenance of tissue and pathology data
- The development of specifications and interface techniques facilitating the creation and federation of repositories that can be leveraged by geographically and temporally dispersed clients
- The identification of tissue banking and pathology systems already developed by the Centers, and the integration and federation of those resources
- The provision of specifications and guidance for the development of future tissue and pathology software compatible with the caBIG
- Tissue banks and pathology tools will ultimately:
- Provide More effective mechanism for researcher to locate and analyze tissue specimens for use in cancer trials based on tissue, clinical, and genomic characteristics
- Provide a platform for rapidly surveying available tissue and pathology resources across cancer centers
- Establish standards and interoperable tools for working with tissue and pathology data and resources

## TBPTW Participants

## TBPTW Center Needs

- Support for tissue databases
- Access to tissue banks for research samples
- Sample tracking systems - including bar coding
- More effective community-wide integration of tools for tissue banking database and collaboration
- Tissue pathology bioinformatics

*** Identified during the August 2003                          Cancer Center Cooperative Development Meetings:**

## TBPTW Priority Requirements

| Functional Area | High-Level Functional Requirement |
| --- | --- |
| Policy/Program Requirements
 | IRB Privacy Board Guidance
Support/Training/Documentation |
| General System Requirements | Common Data Elements (CDEs) 
Common Terminology
Modularized Web Accessible Tools
Software Development Toolkits (SDKs) and APIs
Interface Specifications
Data Mapping Tools
De-identification Services
Transaction Auditing
Security
System Backup/Recovery |
| Tissue Resource System | Specimen Tracking
Tissue Processing
Biological Annotations
Clinical Annotations
Inter-Site Communication |
| Quality Control | Sample Quality
Quality Indicators |

*** Identified during the February 2004 caBIG Kickoff Meeting:**

## TBPTW Future Requirements

| Functional Area | High-Level Functional Requirement |
| --- | --- |
| Policy/Program Requirements | Access and Material Transfer Policies |
| Tissue Resource System
 | Multi-Dimensional Specimen Annotations
Billing Annotations
Tissue Imaging |
| Pathology Tools | UMLS Coding of Free Text
Image Analysis/Whole Slide Imaging
Pathway Histological Analysis |
| Quality Control | Data Validation
User Survey |
| Patient/Clinical/Population Information | Clinical Data Capture
HL7 Interface Modules 
Cancer Registry Information
Laboratory Data Interfaces
Epidemiology Exposure Data |
| Sample Array Tools | Tissue Arrays
Sample Microarrays
Protein Arrays |
| Micro-Dissection Tools | Micro-Dissection Modules
Micro-Dissection Protocols and Images |

*** Identified during the February 2004 caBIG Kickoff Meeting:**

## TBPTW Project Planning

**TBPTW Project Planning**

- Phase 1:
- Developer Phase 1 (a): Support for centers _without_ existing systems or inventory/tracking modules
- CDEs and terminology
- Basic specimen/inventory tracking module (caTISSUE Lite)
- Developer Phase 1 (b): Support for centers _with_ existing systems or databases
- XML schema, Object Models, APIs, Web Services, SDKs, Data Mapping Tools
- Adopter Phase 1: Support for requirements analysis and validation
- Work with developers during requirements analysis and CDE development
- Validate developer artifacts
- Phase 2:
- Developer Phase 2: Support for additional annotations (genomic, procedures, clinical demographics)
- Adopter Phase 2: Workspace requirements analysis and validation
- Phase 3:
- Developer Phase 3:  Additional components (clinical trials interfaces, etc.)
- Adopter Phase 3: Workspace requirements analysis and validation

*** Identified during the February 2004 caBIG Kickoff Meeting:**

## TBPTW Requirements Analysis

- A TBPTW survey was submitted to all participating TBPTW cancer centers to capture center requirements and use cases
- The survey addressed :
- Scope of Specimen Bank
- Inter-Bank Relationships
- Current Database Systems and Tools
- System Access
- IRB and Patient Confidentiality
- Distribution, Sharing, Material Transfer, and Intellectual Property (IP)
- Data System Objects
- System Data Elements
- Use Cases
- Virtual Specimen Repository
- Other (Free Text)
- TBPTW survey results are currently being analyzed

## Data Entry
Includes use cases for submitting the following types of data:
Study/Site Data
Participant Data
Admission Data
Specimen Data
Segment Data
Sample Data
Array Data
Distribution Data
Data Update
Includes use cases for updating all submitted data
Data Querying
Includes use cases for querying for specimens/samples by each type of submitted data
Other
Will be determined and prioritized based on feedback from TBPTW surveys

- Includes use cases for submitting the following types of data:
- Study/Site Data
- Participant Data
- Admission Data
- Specimen Data
- Segment Data
- Sample Data
- Array Data
- Distribution Data
- Data Update
- Includes use cases for updating all submitted data
- Data Querying
- Includes use cases for querying for specimens/samples by each type of submitted data
- Other
- Will be determined and prioritized based on feedback from TBPTW surveys

**TBPTW Use Cases**

## TBPTW Current Status

- Working with the caBIG program to solidify contracts
- Drafting TBPTW project plans
- Gathering results of the caBIG TBPTW survey for use in requirements analysis
- Assessing required and existing CDEs (e.g. EDRN)
- Working with the caBIG cross-cutting workspaces to ensure caBIG compatibility
- Participating in ongoing workspace telecons (bi-weekly)

## caBIG Compatibility Guidelines

- Prostate Cancer SPORE Task Force for National Biospecimen Network (NBN) Implementation Informatics Meeting
- July 10, 2004

## What are the caBIG Compatibility Guidelines?

- Provide guidelines on caBIG compatibility for:
- caBIG participants
- Interested stakeholders on caBIG compatibility
- Set of definitions that caBIG participants can use to measure the maturity level of potential caBIG applications
- A “living” document that will be driven by input and participation of the caBIG community

## caBIG Compatibility Matrix

| Maturity Model | LEGACY | BRONZE | SILVER | GOLD |
| --- | --- | --- | --- | --- |
| Interface Integration | No Programming interfaces to the system are available. Only local data files in a custom format can be read
 Some ad hoc data transfer mechanism such as FTP  | - Provide baseline* programmatic access to data. Data can be read from remote electronic sources or from commonly used file formats Data can be pushed  out to from applications to other external data sources.  | - Well-described API’s that provide access to data objects.
- System architecture separated into tiers and interoperable components
- Data read in from standards-based electronic sources that support standard or commonly used interchange formats
- Documented component description of the underlying data structures that are accessible
- Standard messaging systems where appropriate  | - All features of Silver, plus:
- Interoperable with data grid architecture to be defined by caBIG
- Fully componentized provide access to individual resources in the form of grid services  |
| Vocabularies / Terminologies & Ontologies |  Free text used throughout for data collection  | - Use of publicly accessible standardized controlled vocabularies as well as local terminologies  | - Messages need to be based on a common messaging model (such as HL7)  | - All features of Silver, plus:
- Fully compliant with caBIG recommended standards for vocabulary terminology services and content sources
- Common Data Elements should be built using controlled terminology  |
| Data Elements | - No Structured metadata is recorded  | - Some type of metadata describing the information in the system is used for data collection and external reporting. Metadata is retrieved from external repository shared by multiple applications.  | - Use common standard electronic representation for CDE’s such as ISO 11179 or comparable standard
 - CDEs are harmonized and re-used from across the Domain Workspace  | - All features of Silver, plus:
- Programmatic access to all metadata, including data class descriptions, site and source information, and any other caBIG-defined metadata requirements and use information models
- Use the caBIG standard or electronic representation of metadata and Common Data Elements  |
| Information Models | - No particular information model is used to represent data  | - Some type of diagrammatic model describing the data relationship is available in electronic format  | - Information models defined in a standard modeling language such as UML  | - All features of Silver, plus:
- Information models are harmonized with other s across the caBIG Domain Workspace  |

## “Legacy” Level of Maturity

## “Bronze” Level of Maturity

## “Silver” Level of Maturity

## caBIG Compatibility Guidelines Next Steps

- Defining the “Gold” Standard
- The caBIG cross-cutting workspaces are defining the “**Gold**” standard
- Revisions/Updates to the guidelines are occurring based on caBIG participant feedback
- Updates are posted to the caBIG web site (_[http://cabig.nci.nih.gov](http://cabig.nci.nih.gov/)_) on an ongoing basis
- A standards body supporting the caBIG community is under development

## Overview of Cancer Center and Prostate Cancer SPORE TBPTW        Requirements Survey Results

- July 10, 2004

**Overview of Cancer Center and Prostate Cancer SPORE TBPTW        Requirements Survey Results**

## TBPTW Prostate Cancer SPORE Survey Participants

- TBPTW surveys were submitted by the following Prostate Cancer SPORE sites:
- UCSF
- Mayo Clinic
- NW (Seattle)
- Memorial Sloan-Kettering
- University of Michigan

## Survey Results - Scope of Specimen Bank

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – Inter-Bank Relationships

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – Current Database System and Tools

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – System Access

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – IRB and Patient Confidentiality

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – Distribution, Sharing, and IP

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – Data System Objects

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – System Data Elements

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – Use Cases

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – Virtual Specimen Repository

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |

## Survey Results – Other (Free Text)

| Site | Survey Results |
| --- | --- |
| UCSF |  |
| Mayo Clinic
 |  |
| NW (Seattle) |  |
| Memorial Sloan-Kettering |  |
| University of Michigan |  |