National Cancer Institute caDSR Briefing for Small Scale Harmonication Project Denise Warzel Associate Director, Core Infrastructure caCORE Product Line Manager July 25, 2007

National Cancer Institute NCI Center for Biomedical Informatics and Information Technology (CBIIT) The CBIIT 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 research data Production, service-oriented organization. Evaluated based upon customer and partner satisfaction.

National Cancer Institute caDSR and EVS Distinctions caDSR is a metadata repository –maintains metadata to permit a user to locate the correct data element defining the characteristics of a piece of datum, an instance of a specific concept, in sufficient detail to be collected and stored on a computer EVS is a terminology server –provides services for synonymy, mapping between vocabularies, hierarchical structures, Subconcepts, Superconcepts, Roles, Semantic type, etc.

National Cancer Institute Goals of the Registry Goals tools development: development and creation –Simplify development and creation of ISO/IEC compliant metadata by Data Element Curators and UML Modelers consumption –Simplify consumption of Data Elements and standard vocabularies by end users and application developers through APIs and web services reuseacross domains –Enhance reuse of Data Elements across domains semantic consistency –Enable semantic consistency across research domains metadata life-cycle –Support metadata life-cycle and governance processes Created, maintained by NCI Contractors and Open Development model Available as an open-source download * Training *

National Cancer Institute * Training *

National Cancer Institute Introduction to caDSR Tools –CDE Browser to Search for, View and Download –Form Builder to Create user specified collections of CDEs Skip patterns, repeating groups, default values –Side-by-Side Compare –UML Model Browser to View and manage UML Model metadata –CDE Curation Tool to Create Data Elements –Admin Tool to Administer caDSR and curate content - “Power Users” –Sentinel Tool to Generate end user ‘Alerts’ triggered by metadata changes –Semantic Integration Workbench – Semantic Integration/Annotation Tools, annotate, transform and register metadata –Batch Load to import Administered Items Excel Loader (MS Excel) Semantic Integration Workbench UML Model Loader (XMI) Case Report Form Loader (MS Excel) Access, Develop, Manage, Consume

National Cancer Institute To Create, Edit or Version: Data Element Concepts Value Domains Data Elements ISO Wizard –Construct ISO compliant Data Elements by building up the pieces Builds Names and Definitions from underlying components. “Get Associated” –Leverage ISO to retrieve related CDEs “Block Edit” “shopping cart” Assign classification schemes Versioning Curation Tool

National Cancer Institute Sentinel Tool Create “Alerts” –User defined triggers based on data element metadata attributes –“notify me of any change to the Value Domain for any CDE on the Adverse Event Form Generates and s a report of changes matching “Alert” criteria

National Cancer Institute View, Search, Download –Shopping cart feature FormBuilderFormBuilder to Build / Download Forms and Data Elements “Context Browsing” Tree –By Classification Schemes –By Forms CDE Basic Search Criteria –Google-like search –Sortable search results by clicking on column headings CDE Browser “CONTEXT Browsing” “CONTEXT Browsing” Basic Search

National Cancer Institute Advanced Search –Leverages ISO and Concept semantic attributes Find all with “ ” permissible value Find all with “Gene*” Find all with “Released” workflow status Find all with “Standard” Registration status Etc. CDE Browser Advanced Search

National Cancer Institute Form Builder Create and Manage Forms –Organize CDEs into modules within a Form –Create skip patterns, default values, repeating groups –Attach pdf or word format –Classify Forms into groupings for specific end user communities –“Publish” “Un-Publish” for Browser Catalog visibility “Printer Friendly” version Download CDEs

National Cancer Institute Form Builder Create and Manage Forms –Organize CDEs into modules within a Form –Create skip patterns, default values, repeating groups –Attach pdf or word format –Classify Forms into groupings for specific end user communities –“Publish” “Un-Publish” for Browser Catalog visibility “Printer Friendly” version Download CDEs

National Cancer Institute CDE Side-by-Side Compare –Build shopping cart, compare CDE metadata side by side –Download to excel spreadsheet

National Cancer Institute UML Model Browser View CDEs as part of a UML Domain Model Classes Attributes Associations View Contact information, like to UML source file, documentation, etc

National Cancer Institute Administration Tool System Administration User Accounts and Security Lists of Values (LOVs) used in content creation Create “Framework”: Conceptual Domains Classification Schemes (basis for organizing CDEs in Browser) Define high level “Protocol”

National Cancer Institute Batch Loading Semantic Integration Workbench and UML Loader –XMI representation of a UML Class Diagram Class  Object Class Attribute  Property Enumeration  Value Domain Mapped EVS Concepts Data Element Concept, Value Domain and Data Element harmonized with existing content and created from the above Excel Loaders –Formatted MS Worksheet –Administered Items

National Cancer Institute ISO/IEC Administered Item Administration Record and Common Attributes Unique Identifier Registration Authority (RA) Data Identifier (within RA) Version Administrative Status Registration Status Creation Date Administrative Note(s) Effective Date Change Date(s) Change Description(s) Origin Until Date Created By Modified By Name(s) Definition(s) Stewardship Information Submitter Information Reference Document(s) Classifications Additional Value Domain Attributes Datatype (ISO 11179) Name, Description, Scheme Reference, Annotation (ISO 11179) Codegen compatible, Comment Format (ISO 11179) Maximum Characters (ISO 11179) Unit of Measure (ISO 11179) Minimum Characters High Value Low Value Character Set If Enumerated: Permissible Values (ISO 11179) Value, Value Meaning, Begin Date, End Date (ISO 11179) High Value, Low Value If Non-enumerated: Reference Document pointing to External ‘Top Node’ Concept

National Cancer Institute Create For Standard Codes

National Cancer Institute Create For Standard Code Sets - Use this if you want everyone store the code the same way Create For Standard Code Sets - Use this if you want everyone store the code the same way

National Cancer Institute caDSR URLs caDSR Home Page –Browser and Form Builder: –Admin Tool: –Curation Tool: –Sentinel Tool: –Freestyle search: –Semantic Integration Workbech: caDSR Users, Developers ListServ – to subscribe to – to subscribe to caDSR Training Home Page – caDSR Training ListServe – to subscribe to

National Cancer Institute caCORE Reading Materials caCORE Homepage: – caCORE User Application Manual: –ftp://ftp1.nci.nih.gov/pub/cacore/NCICBapplications/NCICBAppManual.pdfftp://ftp1.nci.nih.gov/pub/cacore/NCICBapplications/NCICBAppManual.pdf NCICB GFORGE caGRID Browser – caCORE Technical Guide: –ftp://ftp1.nci.nih.gov/pub/cacore/caCORE3.1_Tech_Guide.pdf – caCORE APIs caCORE Training – caDSR Business Rules – caDSR_Users List serv subscribe: – –Send Request for caDSR Account to: caBIG home page: documentation about the Grid –

National Cancer Institute Questions?