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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 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.

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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 creationdevelopment and creation of ISO/IEC 11179 compliant metadata by Data Element Curators and UML Modelers

– Simplify consumptionconsumption of Data Elements and standard vocabularies by end users and application developers through APIs and web services

– Enhance reusereuse of Data Elements across domainsacross domains

– Enable semantic consistencysemantic consistency across research domains

– Support metadata life-cyclemetadata life-cycle and governance processes

• Created, maintained by NCI Contractors and Open Development model

• Available as an open-source download

* Training ** Training *

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* Training ** 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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• 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

Curation Tool

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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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• 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“CONTEXTBrowsing”

“CONTEXTBrowsing”

Basic SearchBasic Search

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• 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.

CDE Browser

Advanced SearchAdvanced 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

OC caDSR DEFAULT VALUES: Workflow status = "Released" Alw ays. Version = 1.0 Alw ays. Create Date =Date loaded by Loader. Created by = EVS. Long Name = EVS Preferred name

EVS Preferred Name Definition Definition Source Database Context Preferred NameEffective Begin Date Change Note Alternate Name Type

VARCHAR2 (20) VARCHAR2 (2000) VARCHAR2 (2000) VARCHAR2 (255) VARCHAR2 (20) VARCHAR2 (30) VARCHAR2 (2000) VARCHAR2 (20) Mapped to Long Name and Preferred Name

PreferredDefinition Definition Source Database Requestors Context YY.MM.B Text AlternateName.Type

Not Null Not Null Null Not Null Not Null Null Null Not Null

Celsius Scale The temperature scale defined by the values 0 degree Celsius for the freezing point of water and 100 degrees Celsius for the boiling point of water.  The Celsius degree (C) is the same size as a Kelvin and equal to (F - 32)/1.8.  To convert Celsius to Fah

NCI NCI Thesaurus caBIG 11/18/2004 Requested by Dianne Reeves

NCI_Concept_Code

HEENT HEENT is the Head, Ears, Eyes, Nose and Throat, and is referred to as a body system on a physical or medical examination.  The term is typically used as 'HEENT' in a physician or caregiver notes.

NCI NCI Thesaurus caBIG 11/18/2004 Requested by Dianne Reeves

NCI_Concept_Code

Gracely Pain Unpleasantness Scale

The Gracely Pain Unpleasantness Scale is a visual analog scale of 0 to 20 used by a subject to define their pain unpleasantness experience.  Together with the intensity scale these tools serve to differentiate the patient's sensory perception of pain inte

NCI NCI Thesaurus caBIG 11/18/2004 Requested by Dianne Reeves

NCI_Concept_Code

• 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 ItemAdministration 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

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/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

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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

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Questions?