caBIG Pilot Project Selection Process

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TM
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caBIG and caGrid Interoperable Computing
Infrastructure for the Nations and Worlds
Cancer Research Enterprise
Peter A. Covitz, Ph.D. Chief Operating
Officer National Cancer Institute Center for
Bioinformatics
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• The Center for Bioinformatics is the NCIs
  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.

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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 5510-30

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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)
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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 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.

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Interoperability

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

Semanticinteroperability
Syntacticinteroperability
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SYNTACTIC
caBIG Compatibility Guidelines
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caCORE

• Model Driven Architecture Computable Semantics
  
• Platform for Syntactic and Semantic
  Interoperability

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(No Transcript)
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caCORE
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Bioinformatics Objects
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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).
  

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Description Logic
Enterprise Vocabulary
Concept Code
Relationships
Preferred Name
Definition
Synonyms
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caCORE Software Development Kit
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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
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caCORE Architecture
Clients
Data
Middleware
Web Application Server
HTTP Clients
A P I
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
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From Silver to GoldcaGrid
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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

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OTHER TOOLKITS
NCI
OTHER caBIG SERVICE PROVIDERS
Cancer Center
Cancer Center
Cancer Center
Cancer Center
Cancer Center
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caGrid 1.0 Architecture
Functions
Quality of Service
Business Process
Semantic service
ID Resolution
Workflow
Portal
Security
Resource Management
DORIAN
caDSR
Service Registry
Grid ID
Service
Introduce
FQE
GSI
GME
Service Description
caDSR
Index
Grid Communication Protocol
GLOBUS Toolkit
GT4
GTS
Transport
EVS
GT4
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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)

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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

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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

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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

• caGrid
• Avinash Shanbhag, NCI
• Joel Saltz and colleagues, Ohio State U.
• Ian Foster and colleagues, U. Chicago/Argonne
• Booz Allen Hamilton
• SAIC
• SemanticBits

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Links

• caBIG
• https//cabig.nci.nih.gov
• caGrid
• https//cabig.nci.nih.gov/News_Folder/caGrid_1.0_B
  eta_Release
• caCORE
• http//ncicb.nci.nih.gov/NCICB/infrastructure/caco
  re_overview