Cancer MetaData Standards                                     

Peter A. Covitz, Ph.D.

HL7 RCRIMOctober 1, 2002

NCI Center for Bioinformatics

Established in early 2001 by Kenneth BuetowFolded in several existing programs, launched new onesMission to bridge basic and clinical research via bio- medical- informatics

caCORE

Core Infrastructure for biomedical application development NCI Enterprise Vocabulary Services

Thesauri and Ontologies Bioinformatics Infrastructure

Objects UML-modeled middleware and APIs Cancer Data Standards Repository

Metadata

NCICB-supported initiatives

Cancer Genome Anatomy Project ESTs, SAGE, SNPs, Pathways

Molecular Signatures of Cancer Microarray-based tumor classification

Mouse Models of Human Cancer Consortium Pathology, microarray

Clinical Trials Protocols, agents, targets, patient cases

Cancer Data Standards Repository

Metadata management system for NCI Common Data Elements

                                                                                                                                                                                                                                                 

Cancer Data Standards Repository (caDSR)

Registry for Common Data ElementsImplemented in Oracle DBMSLogically separate ContextscaDSR Tools: CDE Form Compliance Review CDE Browse/Query/Export CDE Curation

caDSR Programming Interfaces: PL/SQL XML

ISO/IEC 11179 Model

Contexts

Value Domain

Conceptual Domains

Data ElementConcept

AdministeredComponent Statuses

AdministeredComponents

ClassificationSchemes

ClassificationScheme Items

Data Element

PermissibleValues

Contexts

Conceptual Domains

Data Element Concept

Value Domain Permissible Values

Data Element

Administered Component Status

Administered Component

Classification Schemes

Classification Schemes Items

Example CDEs

Context: NCI-CTEPNCI-CTEP

Data Element Concept:Person AgePerson Age

Data Elements:Patient Age - Number (3,1)Patient Age - Number (3,1)Patient Birthday – DatePatient Birthday – Date

Conceptual Domain:AGEAGE

Value Domains:YearsYearsMonthsMonthsDatesDates

Permissible Values0 – 1300 – 1301-1201-12001/01/1850-01/01/215001/01/1850-01/01/2150

Common Data Element Contexts

Different Curators for each Context

CDEs in Production

Therapeutic Phase III Cancer trials Extramural trials overseen by NCI-CTEP

must transmit data to the using CDEs

Prevention Trials NCI-Division of Cancer Prevention

NCI Intramural Trials NCI Center for Cancer Research

Spiral CT trial NCI Biomedical Imaging Program and

partners

caDSR Next Steps

Tool and Interface CompletionAdditional CDE Domains Pediatrics Phase I/II Trials Genomics

Harmonization of CDEs... Across Contexts, if it makes sense to do

so With Public Standards (HL7, LOINC, etc.)

HL7

Seeking for suggestions on how to harmonize with HL7CDEs as part of HL7 messages?What are the “metadata” adoption mechanisms for HL7?

Acknowledgements

Kenneth

Buetow Denise Warzel Beverly

Meadows Jeff Abrams

Christo Andonyadis Jasur

Ishmukhamedov Ram Chilukuri Prerna Aggarwal

Bill McCurry

Claudine Valmonte Pam West Mary Supley

Info and mailing lists

caDSR web sitehttp://ncicb.nci.nih.gov/core/caDSR caDSR users listhttp://list.nih.gov/archives/

sbr_users.html