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

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.

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. The point here is that we have separated terminology development from data element development. caDSR is a customer of EVS.

* Training * Goals of the Registry Goals tools development: Simplify development and creation of ISO/IEC 11179 compliant metadata by Data Element Curators and UML Modelers Simplify consumption of Data Elements and standard vocabularies by end users and application developers through APIs and web services Enhance reuse of Data Elements across domains Enable semantic consistency across research domains Support metadata life-cycle and governance processes Created, maintained by NCI Contractors and Open Development model Available as an open-source download By ISO/IEC compliant, we mean that our implementation of the standard, while it includes NCICB specific extensions, still maps to the mandatory and optional metadata items prescribed by ISO/IEC 11179, Part 3. There are various levels of conformance, because of these business needs related extensions, caDSR is considered “conforming” as opposed to “strictly conforming”. * Training *

* Training * By ISO/IEC compliant, we mean that our implementation of the standard, while it includes NCICB specific extensions, still maps to the mandatory and optional metadata items prescribed by ISO/IEC 11179, Part 3. There are various levels of conformance, because of these business needs related extensions, caDSR is considered “conforming” as opposed to “strictly conforming”.

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) Guest Form Builder Create form from existing content and download it Form Builder Only User (Adopter) Revising Browser Classification Schemes to support Forms Ways to track usage of data elements (you didn’t create) Designating - “Used by” Ascribe additional attributes Alternate Names Reference Document Easier to track or search DEs that you are using Classifying - “Classification Schemes” Using on a Form - “Used on a Forms” Access, Develop, Manage, Consume

Curation Tool To Create, Edit or Version: ISO 11179 Wizard Data Element Concepts Value Domains Data Elements ISO 11179 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

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 emails a report of changes matching “Alert” criteria

CDE Browser “CONTEXT Browsing” Basic Search View, Search, Download Shopping cart feature FormBuilder 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 Basic Search

CDE Browser Advanced Search Advanced Search Leverages ISO 11179 and Concept semantic attributes Find all with “18254-3” permissible value Find all with “Gene*” Find all with “Released” workflow status Find all with “Standard” Registration status Etc. Advanced Search

Form Builder Create and Manage Forms “Printer Friendly” version 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

Form Builder Create and Manage Forms “Printer Friendly” version 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

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

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

Administration Tool System Administration Create “Framework”: 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” IVA: Searching Individual DEs VA:Curating Individual DEs IID: Overview of existing tools

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

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

Create For Standard Codes

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

caDSR URLs caDSR Home Page http://ncicb.nci.nih.gov/core/caDSR Browser and Form Builder: http://cdebrowser.nci.nih.gov/ Admin Tool: http://cadsradmin.nci.nih.gov/ Curation Tool: http://cdecurate.nci.nih.gov/ Sentinel Tool: http://cadsrsentinel.nci.nih.gov/ Freestyle search: http://freestyle.nci.nih.gov/ Semantic Integration Workbech: http://cadsrsiw.nci.nih.gov/ caDSR Users, Developers ListServ http://list.nih.gov to subscribe to caDSR_Users@list.nih.gov http://list.nih.gov to subscribe to caDSR_Software_Developers@list.nih.gov caDSR Training Home Page http://ncicb.nci.nih.gov/NCICB/core/caDSR/Training caDSR Training ListServe http://list.nih.gov to subscribe to caDSR_Training-L@list.nih.gov

caCORE Reading Materials caCORE Homepage: http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview caCORE User Application Manual: ftp://ftp1.nci.nih.gov/pub/cacore/NCICBapplications/NCICBAppManual.pdf NCICB GFORGE http://gforge.nci.nih.gov caGRID Browser http://cagrid-browser.nci.nih.gov/cagrid-browser/ caCORE Technical Guide: ftp://ftp1.nci.nih.gov/pub/cacore/caCORE3.1_Tech_Guide.pdf – caCORE APIs caCORE Training http://ncicb.nci.nih.gov/NCICB/training caDSR Business Rules http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr/business_rules caDSR_Users List serv subscribe: http://list.nih.gov Send Request for caDSR Account to: ncicb@pop.nci.nih.gov caBIG home page: documentation about the Grid http://cabig.nci.nih.gov

Questions?