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Peter A. Covitz, Ph.D. Chief Operating Officer National Cancer Institute PowerPoint PPT Presentation


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TM. 0. caBIG and caGrid: Interoperable Computing Infrastructure for the Nation’s [and World’s] Cancer Research Enterprise. Peter A. Covitz, Ph.D. Chief Operating Officer National Cancer Institute Center for Bioinformatics.

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Peter A. Covitz, Ph.D. Chief Operating Officer National Cancer Institute

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Peter a covitz ph d chief operating officer national cancer institute

TM

0

caBIG and caGrid: Interoperable Computing Infrastructure for the Nation’s [and World’s] Cancer Research Enterprise

Peter A. Covitz, Ph.D.

Chief Operating Officer

National Cancer Institute

Center for Bioinformatics


Peter a covitz ph d chief operating officer national cancer institute

  • The Center for Bioinformatics is the NCI’s strategic and tactical arm for research information management

  • We collaborate with both intramural and extramural groups

  • Mission to integrate and harmonize disparate biomedical research data

  • Production, service-oriented organization. Evaluated based upon customer and partner satisfaction.


The problem

The Problem

1,372,910 new cancer cases and 570,280 deaths due to cancer expected in the U.S. in 2005

Jemal et al.,CA Cancer J Clin 2005; 55:10-30


A national response

A National Response

  • Enable investigators and research teams nationwide to combine and leverage their findings and expertise.

  • Create scalable, actively managed organization that will connect members of the NCI-supported cancer enterprise by building a biomedical informatics network

The Cancer Biomedical Informatics Grid™ (caBIG™)


Scenario from cabig strategic plan

Scenario from caBIG Strategic Plan

A researcher involved in a phase II clinical trial of a new 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 inother clinical trials involving agents known to affect these specific pathways, and identify any studies inmodel organisms involving tissues with similar pathway activity.


Interoperability

Interoperability

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

Syntacticinteroperability

Semanticinteroperability


Peter a covitz ph d chief operating officer national cancer institute

SEMANTIC

SEMANTIC

SEMANTIC

SYNTACTIC

caBIG Compatibility Guidelines


Model driven architecture computable semantics platform for syntactic and semantic interoperability

Model Driven Architecture + Computable Semantics =

Platform for Syntactic and Semantic Interoperability

caCORE


Cacore

S

E

C

U

R

I

T

Y

Bioinformatics Objects

Common Data Elements

Enterprise Vocabulary

caCORE


Peter a covitz ph d chief operating officer national cancer institute

Bioinformatics Objects


Common data elements

Common Data Elements

  • What do all those UML data Classes and Attributes actually mean, anyway?

  • UML model components are mapped to semantic concepts drawn from Enterprise Vocabulary sources, then registered in the Cancer Data Standards Repository (caDSR).

  • caDSR is a metadata registry, implements ISO/IEC 11179 standard for Common Data Elements (CDEs).


Peter a covitz ph d chief operating officer national cancer institute

Description Logic

Enterprise Vocabulary

Concept Code

Relationships

Preferred Name

Definition

Synonyms


Cacore software development kit

caCORE Software Development Kit


Cacore sdk components

caCORE SDK Components

  • UML Modeling Tool (any with XMI export)

  • Semantic Connector (concept binding utility)

  • UML Loader (model registration in caDSR)

  • Codegen (middleware code generator)

  • Security Adaptor (Common Security Module)

caCORE SDK Generates a

caBIG Silver-Compliant System


Cacore architecture

caCORE Architecture

Clients

Middleware

Data

HTTP Clients

A

P

I

Web Application Server

Biomedical

Data

Interfaces

Java

SOAP

XML

A

P

I

SOAP

Clients

Common

Data

Elements

Domain

Objects

[Gene, Disease, etc.]

Domain

Objects

[Gene, Disease, Agent,

etc.]

Data

Access

Objects

A

P

I

Perl

Clients

Enterprise

Vocabulary

Data Access

Objects

A

P

I

Java Applications

Authorization


From silver to gold cagrid

From Silver to Gold:caGrid


Use cases not satisfied by cacore alone

Use cases not satisfied by caCORE alone

  • Advertisement

    • Service Provider composes service metadata describing the service and publishes it to grid.

  • Discovery

    • Researcher (or application developer) specifies search criteria describing a service of interest

    • The research submits the discovery request to a discovery service, which identifies a list of services matching the criteria, and returns the list.

  • Invocation

    • Researcher (or application developer) instantiates the grid service and access its resources


Peter a covitz ph d chief operating officer national cancer institute

Silver

Silver

Silver

Silver

Gold

Silver

Silver

Silver

OTHER

TOOLKITS

NCI

OTHER caBIG

SERVICE

PROVIDERS

Cancer Center

Cancer Center

Cancer Center

Cancer

Center

Cancer Center


Peter a covitz ph d chief operating officer national cancer institute

caGrid 1.0 Architecture

Functions

Quality of Service

Semanticservice

ID Resolution

Workflow

Business Process

Portal

caDSR

DORIAN

Security

Resource Management

Service Registry

Grid ID

Service

FQE

Introduce

GSI

GME

caDSR

Service Description

Index

Grid Communication Protocol

GLOBUS Toolkit

GTS

GT4

EVS

GT4

Transport


Data object semantics metadata and schemas

Data Object Semantics, Metadata, and Schemas

  • Object oriented, APIs, well-defined data types

  • Classes defined in UML and converted into ISO/IEC 11179, registered in the caDSR

  • Definitions drawn from Enterprise Vocabulary Services (EVS), relationships semantically described

  • XML serialization of objects adhere to XML schemas registered in the Global Model Exchange (GME)


Service data elements

Service Data Elements

  • Two types of top-level grid services defined

    • Data Services

    • Analytical Services

  • Service Data Elements (SDEs) describe services so clients can discover what they do


Integrating with other grids

Integrating with other Grids

  • caGrid intentionally focused on federated data and analytic service interoperability, not computing power

  • Adoption of standard grid tooling intended to facilitate integration other grids with compute power focus

  • Seeking partnership with established compute grids to install caGrid Analytical Service nodes that would be transparently available to caGrid users


Acknowledgements

caGrid

Avinash Shanbhag, NCI

Joel Saltz and colleagues, Ohio State U.

Ian Foster and colleagues, U. Chicago/Argonne

Booz Allen Hamilton

SAIC

SemanticBits

Acknowledgements

  • caCORE

    • Denise Warzel

    • George Komatsoulis

    • Avinash Shanbhag

    • Frank Hartel

    • Dianne Reeves

    • Sherri De Coronado

    • Gilberto Fragoso

    • SAIC

    • Terrapin Systems

    • Oracle

    • Ekagra

    • ScenPro

    • Apelon

    • MSD


Links

Links

  • caBIG:

    • https://cabig.nci.nih.gov

  • caGrid

    • https://cabig.nci.nih.gov/News_Folder/caGrid_1.0_Beta_Release

  • caCORE

    • http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview


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