# Presentation: 157111

## caBIG Compatibility:  Cross-Cutting Workspaces

***Vocabularies and Common Data Elements (VCDE) and Architecture Workspaces ***
***Brian Davis and Michael Keller***

**February 5, 2007**

## Table of Contents

- Crosscutting Workspace Roles and Responsibilities
- Syntactic and Semantic Interoperability
- caBIGTM Compatibility Guidelines
- Enabling Technology used to satisfy caBIGTM Compatibility Requirements
- Defining the 4 caBIGTM Compatibility Criteria
- Messaging Interface
- Information Models
- Terminologies
- Metadata
- Crosscutting Workspace Mentoring Process
- Process used to satisfy caBIGTM Silver Compatibility Requirements

## Architecture Workspace

- The Architecture workspace is charged with building the caBIGTM Grid and ensuring syntactic interoperability
- Develop caBIGTM compatibility guidelines in the area of interface integration
- Provide mentors to caBIGTM funded development projects in the area of interface integration
- Create caGrid, the “G” in caBIG
- Perform silver compatibility reviews of caBIGTM funded development projects to ensure compliance with compatibility guidelines for interface integration

**Vocabularies and Common Data Elements (VCDE) Workspace**

- The VCDE workspace is charged with ensuring semantic interoperability
- Develop caBIGTM compatibility guidelines in the areas of information modeling, metadata and vocabularies
- Provide mentors to caBIGTM funded development projects in the area of information modeling, metadata and vocabularies
- Facilitate development of caBIGTM data standards, both vocabularies and CDEs
- Perform silver compatibility reviews of caBIGTM funded development projects to ensure compliance with compatibility guidelines for semantics

- Crosscutting Workspace Roles and Responsibilities

## ability of a system to access and use the parts or equipment of another system

- Semanticinteroperability

- Syntacticinteroperability

*Courtesy: Charlie Mead*

- Interoperability Defined

**From Charlie Mead**

**Notes:**

Interoperability is a relatively new concept, centered on the idea that one system can use parts of another.  

If you focus on computer interoperability, the IEEE definition includes two concepts.

Functional interoperability – the ability to exchange information – and semantic interoperability – the ability to use the information that has been exchanged.

As an aside, standards are frequently thought of as focusing primarily on functional interoperability, whereas the critical sine qua non for health care is semantic interoperability -  if you don’t know exactly what the information you received means, having received it is useless, or worse, maybe even dangerous!

## caBIGTM Compatibility Guidelines

- The caBIGTM **compatibility guidelines** are designed to insure that systems designed in a **federated **environment are still interoperable on the caBIGTM Grid, both **syntactically** and **semantically**
- Since achieving interoperability is a process, caBIGTM recognizes **four levels of compatibility**, starting from
**Legacy (not interoperable) **through
**Bronze, **
**Silver and **
**Gold (fully interoperable)**
- caBIGTM compatibility is all about **interfaces** rather than the scientific content of the system

## caBIGTM Compatibility Guidelines

**Semantic**

**Semantic & **
**Syntactic**

## caBIGTM Compatibility Enabling Technology

- The NCI provides freely available enabling technology for caBIGTM compatibility
- These technologies are distributed under a ‘non-viral’ open source license
- Cancer Common Ontologic Representation Environment (caCORE) _[http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview](http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview)_
- Enterprise Vocabulary Services (EVS)
- Cancer Data Standards Repository (caDSR)
- caCORE Software Development Kit (caCORE SDK) _[http://ncicb.nci.nih.gov/NCICB/infrastructure/cacoresdk](http://ncicb.nci.nih.gov/NCICB/infrastructure/cacoresdk)_
- When complete process is followed, the outcome is a caBIG ‘Silver’ compliant data system.
- Includes Semantic Integration Workbench (SIW), UML Loader, and Code Generator

## Syntactic Interoperability

- The solution for syntactic interoperability    in caBIG at the silver level of compatibility is for all systems to provide an **Object Oriented Application Programmer Interface (API)**.
- Object Oriented Interfaces can be implemented in many programming languages.
- This interface can be connected to the caGrid so that the local data repository is globally accessible in a language independent way.
- The interface is described by an **information model**, which acts as the junction between the syntactic components and the semantic components.

## Semantic Interoperability

- The Solution for **semantic interoperability** lies in **object oriented UML design** of the service, an **unambiguous description** of elements within the system and storage of the description in a publicly accessible repository (**metadata**).
**UML model**
**Use of publicly accessible terminologies/ vocabularies/ontologies (EVS-NCI Thesaurus)**
**Use of publicly accessible metadata repository (caDSR)**

## Domain Information Modeling

- A Domain Information Model is a representation of our understanding of an area of knowledge.
- Domain Information Models consist of ‘Classes’ that represent ‘things’ in the real world
- Classes contain ‘attributes’ that are characteristics of different instances of things in the real world.
- Relationships between the classes are described by ‘associations’ and indicated by lines with directionality and cardinality
- Each class plus attribute creates one Common Data Element (CDE)

##  Enterprise Vocabulary Services

- Controlled vocabulary resources for caCORE and the cancer research community
- Vocabulary Products and Services
- NCI Thesaurus
- NCI Metathesaurus
- External Vocabularies
- NCI Thesaurus - controlled vocabulary source for metadata
- Has excellent coverage of cancer terminology
- Expands based on needs for additional terminology
- Based on concepts rather than terms
- Each concept has a unique identifier or CUI with definitions and synonym
- LexBIG
- a caBIG-funded vocabulary server to enable a Federated Vocabulary environment.

**Publicly Accessible Terminologies**

## Preferred Name

- Synonyms

- Definition

- Relationships

- Concept Code

**Publicly Accessible Terminologies:  ****NCI Thesaurus**

##  Enterprise Vocabulary Services

**Storage of Metadata**
**caDSR = ****ca****ncer ****D****ata ****S****tandards ****R****epository**
- Common Data Elements = CDEs
- Enable end-users to access information about data and services without having to access human developers
- = Fusion of UML models + Concepts/Definitions

**Metadata stored in caDSR**

## Cross-Cutting WS Mentoring Process

## The caCORE SDK workflow can help achieve Silver level compliance

**Notes:**
Finally, as I remarked earlier, NCI and caBIG have created tools and workflow to help this process, as shown here.

## The caCORE SDK workflow can help achieve Silver level compliance

**The caCORE SDK workflow can help achieve Silver level compliance**

- Info Model

- Messaging
- Interfaces/
- API

- Common
- Data
- Elements

- Vocabularies

**Notes:**
Very briefly, the UML model of class objects is built and the descriptions are described by terms in EVS, the vocabulary repository (SIW).
When the ANNOTATED UML model is ready the UML Loader Soiftware can convert those objects into CDEs and find CDEs in the caDSR that can be re-used.  There is also a piece of software that can generate the public API. Using these tools and processes, helps to build a silver level compliant system, tho these tools are not nessasary to build one.

I’ll now turn it over to my Colleague, Patrick McCOnnell from Duke.

## Acknowledgments

- VCDE Workspace Participating Organizations
- Albert Einstein Cancer Center
- Cancer Research Center of Hawaii
- City of Hope National Medical Center and Beckman Research Institute
- Duke Comprehensive Cancer Center
- Fred Hutchinson Cancer Research Center
- Jackson Laboratory
- Lombardi Comprehensive Cancer Center at Georgetown University
- Mayo Clinic Comprehensive Cancer Center
- Siteman Cancer Center - Washington University School of Medicine
- UC Davis Cancer Center- University of California, Davis
- University of Pittsburgh Medical Center
- University of Utah-Huntsman Cancer Center
- V/CDE WS Leadership
- George Komatsoulis
- Brian Davis
- Michael Keller
- NCICB caCORE and caCORE SDK Teams

- Arch Workspace Participating Organizations
- Cold Spring Harbor Laboratory
- Duke Comprehensive Cancer Center
- Fox Chase Cancer Center
- Fred Hutchinson Cancer Research Center
- Lombardi Comprehensive Cancer Center at Georgetown University
- Mayo Clinic Comprehensive Cancer Center
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University
- Ohio State University Research Foundation
- Semantic Bits
- Siteman Cancer Center - Washington University School of Medicine
- University of Chicago Cancer Research Center
- University of Pittsburgh Medical Center
- Arch WS Leadership
- Avinash Shanbhag
- Arumani Manisundaram
- Michael Keller
- caBIGTM Program Team

## caBIG Resources

- caBIGTM Website: http://cabig.cancer.gov/index.asp
- caBIGTM Compatibility Guidelines:  https://cabig.nci.nih.gov/compatibility_guidelines_documentation/
- Cancer Common Ontologic Representation Environment (caCORE): _[http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview](http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview)__ _
- Enterprise Vocabulary Services (EVS):  _[http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/vocabulary](http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/vocabulary)_
- Cancer Data Standards Repository (caDSR):  http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr
- caCORE Software Developer’s Kit (caCORE SDK):  http://ncicb.nci.nih.gov/NCICB/infrastructure/cacoresdk
- caCORE Training:  http://ncicb.nci.nih.gov/NCICB/training/cadsr_training
- Model Driven Architecture: http://www.omg.org/mda/
- UML Modeling:  http://www.sparxsystems.com.au/UML_Tutorial.htm