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Cancer MetaData Standards

Cancer MetaData Standards. Peter A. Covitz, Ph.D. HL7 RCRIM October 1, 2002. NCI Center for Bioinformatics. Established in early 2001 by Kenneth Buetow Folded in several existing programs, launched new ones Mission to bridge basic and clinical research via bio- medical- informatics. caCORE.

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Cancer MetaData Standards

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  1. Cancer MetaData Standards Peter A. Covitz, Ph.D. HL7 RCRIM October 1, 2002

  2. NCI Center for Bioinformatics • Established in early 2001 by Kenneth Buetow • Folded in several existing programs, launched new ones • Mission to bridge basic and clinical research via bio- medical- informatics

  3. 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

  4. 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

  5. Cancer Data Standards Repository Metadata management system for NCI Common Data Elements

  6. Cancer Data Standards Repository (caDSR) • Registry for Common Data Elements • Implemented in Oracle DBMS • Logically separate Contexts • caDSR Tools: • CDE Form Compliance Review • CDE Browse/Query/Export • CDE Curation • caDSR Programming Interfaces: • PL/SQL • XML

  7. ISO/IEC 11179 Model Administered Component Status Contexts Administered Component Conceptual Domains Classification Schemes Items Classification Schemes Data Element Concept Value Domain Permissible Values Data Element

  8. Example CDEs Context: NCI-CTEP Conceptual Domain: AGE Permissible Values 0 – 130 1-120 01/01/1850-01/01/2150 Data Element Concept: Person Age Value Domains: Years Months Dates Data Elements: Patient Age - Number (3,1) Patient Birthday – Date

  9. Common Data Element Contexts Different Curators for each Context

  10. 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

  11. caDSR Next Steps • Tool and Interface Completion • Additional 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.)

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

  13. Kenneth Buetow Denise Warzel Beverly Meadows Jeff Abrams Christo Andonyadis Jasur Ishmukhamedov Ram Chilukuri Prerna Aggarwal Bill McCurry Claudine Valmonte Pam West Mary Supley Acknowledgements

  14. Info and mailing lists • caDSR web site http://ncicb.nci.nih.gov/core/caDSR • caDSR users list http://list.nih.gov/archives/sbr_users.html

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