caBIG: the cancer Biomedical

Informatics GridKen Buetow

NCICB/NCI/NIH/DHHS

NCI biomedical informatics! Goal: A virtual web of

interconnected data, individuals, and organizations redefines how research is conducted, care is provided, and patients/participants interact with the biomedical research enterprise

•Trials•Animal Models

states

context•pathways•ontologies

agents•therapeutics•probes

components•genes•genotypes•geneexpression•proteins•proteinexpression

etiology,treatment,prevention

MolecularPathology

ClinicalTrials

caCORE

accessportals

participatinggroup nodes

CancerGenomicsMouse

Models

building common architecture, common tools, and common standards

Interoperability

SemanticSemanticinteroperabilityinteroperability

SyntacticSyntacticinteroperabilityinteroperability

Courtesy: Charlie Mead

! in·ter·op·er·a·bil·i·ty- ability of a system...to use the parts or equipment of another systemSource: Merriam-Webster web site

! interoperability- ability of two or more systems or components to exchange information and to use the information that has been exchanged.Source: IEEE Standard Computer Dictionary: A Compilation of IEEE Standard Computer Glossaries, IEEE, 1990]

! Information integration

! Cross-discipline reasoning

caCORE – common ontologicrepresentation environment

biomedical objects

common data elements

controlled vocabulary

Enterprise Vocabulary! NCI Meta-Thesaurus

(Cross-map standard vocabularies/ontologies,e.g. SNOMED, MEDRA, ICD)

- Semantic integration, inter-vocabulary mapping

- UMLS Metathesaurus extended with cancer-oriented vocabularies

• 800,000 Concepts, 2,000,000 terms and phrases

• Mappings among over 50 vocabularies

! NCI Thesaurus- Description logic-based- 18,000 “Concepts”

• Concept is the semantic unit• One or more terms describe a Concept

– synonymy• Semantic relationships between

Concepts

biomedical objects

common data elements

controlled vocabulary

Common Data Elements

! Structured data reporting elements(e.g. LOINC)

! ISO11179 compliant

biomedical objects

common data elements

controlled vocabulary

Biomedical Information Objects

! Computer model of a biomedical object –“Plato’s Forms”- capture properties of object- can be joined together to make

complex systems- isolate data from data source- isolate applications from data

! Examples:- HL7-RIM- MAGE-OM

biomedical objects

common data elements

controlled vocabulary

Standards Supporting Infrastructure

! Enterprise Vocabulary Services (EVS)! cancer Data Standards Repository

(caDSR)! cancer Bioinformatics Infrastructure

Objects (caBIO)

Data AccessObjects

Object Managers

DomainObjects

RMI

Web Server

TomcatServlets

JSPsSOAP

UI BeanXML

XSL/XSLT

HTML/XML Clients

(Browsers)

SOAP Clients

Java Applications

DataObjectPresentationClient

NCI

Files

Other Data Others [caBIG]

UCSC

architecture

Prototype GRID Core architecture extension

caBIO server

caBIO client

OGSA-DAI +Globus

Globus

OGSA-DAI caGRID extension(metadata)

caGRID extension (caBIO adapter)

caGRID extension(query)

Client

Grid

Data Source

caGRID extension (Concept Discovery)

caGRID extension (Federated Query)

caGRID Extension (Integration of Discovery and Query Services)

NCICB applications:• clincial trials support - C3DS• molecular pathology - caArray• cancer images - caImage• pre-clinical models - caModelsDb• laboratory support - caLIMS

• Data System for the conduct of clinical trials in CCR that is generalizable to academic environments.

• Components:– C3D (Cancer Central Clinical Database)

• Primary data capture by protocol – C3PR (Cancer Central Clinical Participant Registry)

• Central registration of participants across protocols – C3PA (Cancer Central Clinical Protocol Administration)

• Scientific management system for clinical protocols – C3TR (Cancer Central Clinical Tissue Repository)

• Tissue repository – C3DW (Cancer Central Clinical Data Warehouse)

• De-identified patient information accessed via caBIO

C3DS Data Flow

C3D(Clinical DataManagement)

C3D(Clinical DataManagement)

C3PA(ProtocolAdmin)

C3PA(ProtocolAdmin)

C3TR(Tissue

Repository)

C3TR(Tissue

Repository)

C3DW(Clinical DataWarehouse)

C3DW(Clinical DataWarehouse)

Adverse EventReporting

System

Adverse EventReporting

System

Legacy DBs

AEDetails

ProtocolReporting

Requirements

ProtocolAccruals/Approvals

Active ProtocolData

PatientSpecimens

Non-AccruingProtocol Data

PeriodicUpdates

Source DBs

Batch LoadClinical (Lab) Data

PeriodicDownloads

EnrollPatients

FDA

PatientDetails

AEReports

PeriodicUpdates

Patient Demographics

C3PR(ParticipantRegistry)

C3PR(ParticipantRegistry)

PatientSpecimens

De-Identified Patient Details

SponsorsSponsors

electronic data capture for clinical research• WWW

accessible• Reusable

eCRFlibrary built using NCI CDEs

• Electronic Regulatory reporting

Image Portal• The NCICB has

developed an image portal to allow researchers to search for mouse and human images and annotations– Human and

mouse images and annotations were provided by the MMHCC

Pathway Database • Enhance value of imperfect, but

available, pathway knowledge• Make biological assumptions

explicit• Combine sources of data (e.g.

KEGG, BioCarta, ...)• Merge data from separate

pathways• Build a causal framework to

support (future) quantitative simulation/analysis

Cancer Biomedical Informatics Grid (caBIG)

! Common, widely distributed infrastructure permits cancer research community to focus on innovation

! Shared vocabulary, data elements, data models facilitate information exchange

! Collection of interoperable applications developed to common standard

! Raw published cancer research data is available for mining and integration

caBIG will facilitate sharing of infrastructure, applications, and data

caBIG action plan! Establish pilot network of Cancer Centers

- Groups agreeing to caBIG principles- Mixture of capabilities- Mixture of contributions

! Expanding collection of participants! Establish consortium development process

- Collecting and sharing expertise- Identifying and prioritizing community needs- Expanding development efforts

! Moving at the speed of the internet…

Three Domain Workspaces and two Cross Cutting Workspaces have been launched during the Pilot phase

DOMAIN WORKSPACE 3Tissue Banks & Pathology Tools

provides for the integration, development, and implementation of tissue and pathology tools.

DOMAIN WORKSPACE 2Integrative Cancer Research

provides tools and systems to enable integration and sharing of information.

DOMAIN WORKSPACE 1Clinical Trial Management Systems

addresses the need for consistent, open and comprehensive tools for clinical trials management.

CROSS CUTTING WORKSPACE 2Architecture

developing architectural standards and architecture necessary for other workspaces.

CROSS CUTTING WORKSPACE 1Vocabularies & Common

Data Elements

responsible for evaluating, developing, and integrating systems for vocabulary and ontology content, standards, and software systems for content delivery

caBIG deliverables! Componentized, standards-based Clinical Trials

Management System- e-IND filing/regulatory reporting with FDA- Electronic management of trials- Integration of diverse trials

! Tissue Management System- Systematic description and characterization of tissue

resources- Ability to link tissue resources to clinical and

molecular correlative descriptions! “Plug and Play” analytic tool set! Diverse library of raw, structured data

Cancer Molecular Analysis Project (CMAP)- a prototypic biomedical data integration effort

biomedical objects

common data elements

controlled vocabulary

Profiles, Targets, Agents, Clinical Trials

CGAPNCBIUCSC

(via DAS)

BioCartaKEGGGene

Ontologies

CTEP clinical trialsCGAP gene expression

NCI drug screening

NCI drug screening

caBIG community contributions! Infrastructure

- Ontologies- Databases

! Applications- Clinical trials

support- Analytic tools- Data mining

! Data- Trials- Experimental

outcomes• Genomic• Microarray• Proteomic

acknowledgements! NCICB

- Peter Covitz- Sue Dubman- Carl Schaefer- Mervi Heiskanen- Denise Hise- Kotien Wu- Fei Xu- Ulli Wagner- Frank Hartel- Sheri De Coronado- Gilberto Fragoso

! LPG/CCR- Michael Edmundson- Bob Clifford- Cu Nguyen

http://ncicb.nci.nih.govhttp://cmap.nci.nih.govhttp://caBIG.nci.nih.gov