caDSR Briefing for Small Scale Harmonication Project

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caDSR Briefing for Small Scale Harmonication
Project

• Denise Warzel
• Associate Director, Core Infrastructure
• caCORE Product Line Manager
• July 25, 2007

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NCI Center for Biomedical Informatics and
Information Technology (CBIIT)

• The CBIIT is the NCIs 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.

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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.

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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

Training
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Training
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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
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Curation Tool

• To Create, Edit or Version
• 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

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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

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CDE Browser
CONTEXT Browsing

• 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
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CDE Browser

• 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
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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

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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

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CDE Side-by-Side Compare

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

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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

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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

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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

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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

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

• caDSR Home Page http//ncicb.nci.nih.gov/core/caDS
  R
• Browser and Form Builder http//cdebrowser.nci.ni
  h.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_at_list.nih.gov
• http//list.nih.gov to subscribe to
  caDSR_Software_Developers_at_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_at_list.nih.gov

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caCORE Reading Materials

• caCORE Homepage
• http//ncicb.nci.nih.gov/NCICB/infrastructure/caco
  re_overview
• caCORE User Application Manual
• ftp//ftp1.nci.nih.gov/pub/cacore/NCICBapplication
  s/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_G
  uide.pdf caCORE APIs
• caCORE Training
• http//ncicb.nci.nih.gov/NCICB/training
• caDSR Business Rules
• http//ncicb.nci.nih.gov/NCICB/infrastructure/caco
  re_overview/cadsr/business_rules
• caDSR_Users List serv subscribe
• http//list.nih.gov
• Send Request for caDSR Account to
  ncicb_at_pop.nci.nih.gov
• caBIG home page documentation about the Grid
• http//cabig.nci.nih.gov

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Questions?