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Metadata Open Forum 2008
ISO/IEC/IEC 11179: Metadata Registries A Tutorial from the National Cancer Institute
Dianne M. Reeves, RN, MSNNational Cancer Institute CBIIT
Tommie G. Curtis, MSScience Applications International Corporation (SAIC)
Metadata Open Forum 2008 - Goals
• Explain the role of ISO/IESC 11179 in capturing structured metadata
• Discuss the added value of binding vocabulary/terminology, to ISO/IEC administered items
• Estimate the level of effort needed to collect and maintain metadata
• Assess and justify metadata registration needs for an organization
Metadata Open Forum 2008 – Activities
• Review and discuss the ISO/IEC 11179 standard• Examine a registry implementation of ISO/IEC 11179• Map source metadata to registry content• Utilize semantics to bind to metadata• Assess the value and role of an ISO/IEC 11179 registry
in an organization
Metadata Open Forum 2008 – ISO/IEC 11179 Metadata Registries
What is the Standard?• Six-part standard defining various aspects of
metadata development and metadata registry management
• Common way of representing metadata• A “Grammar” for describing data
– Descriptive (pattern for creating meaning)– Prescriptive (pre-existing rules for the pattern)
Metadata Open Forum 2008 – ISO/IEC 11179 Information technology StandardISO/IEC 11179 Information technology Standard
• ISO/IEC 11179 Part 1: Framework
• ISO/IEC 11179 Part 2: Classification
• ISO/IEC 11179 Part 3: Registry metamodel and basic attributes
• ISO/IEC 11179 Part 4: Formulation of data definitions
• ISO/IEC 11179 Part 5: Naming and Identification Principles for Data Elements
• ISO/IEC 11179 Part 6: Registration
• Publicly Available from: http://metadata-standards.org/11179/
Metadata Open Forum 2008 – Basic ISO/IEC 11179 Metamodel ComponentsBasic ISO/IEC 11179 Metamodel Components
Data_Element_Concept
1..10..*
+specifing1..1
+having0..*
data_element_concept_conceptual_domain_relationship
0..*
1..1
+providing_representation_to0..*
+represented_by1..1
expression
0..* 1..1+represented_with
0..*
+providing_representation_for1..1
representation
0..*
1..1
+representing
0..*
+specified_by1..1
specification
Data Element Concept
Conceptual_Domain
Conceptual Domain
Data_Element
Data Element
Value_Domain
Value Domain
Perception
Representation
Metadata Open Forum 2008 – Terms and Definitions for ISO/IEC 11179
Data Element: A unit of data for which the definition, identification, representation, and permissible values are specified by means of a set of attributes.
Data Element Concept: An idea that can be represented in the form of a data element, described independently of any particular representation.
Conceptual Domain: A set of valid Value Meanings.
Representation Class: A classification of data elements based upon the type of representational form.
Value Domain: A set of attributes describing representational characteristics of instance data with or without enumerated permissible values.
Value Meaning: A member of the set of finite allowed inventory of notions that can be categorized for a conceptual domain.
Permissible Value: An expression of a Value Meaning expressed in a Value Domain.
Data Element
Data Element Concept
Value Domain
Value Meaning Permissible Value
Conceptual Domain
Representation Class
Metadata Open Forum 2008 –Terms and Definitions for ISO/IEC 11179
Data Element Concept: An idea that can be represented in the form of a data element, described independently of any particular representation.
- The suggested pattern for creating the meaning of a DEC is further described using Object Class and Property
Object Class: The part of the DEC ‘pattern’ pertaining to the thing in the real world. A person, a gene, a vehicle.
Property: The part of the DEC ‘pattern’ pertaining to an observable or recordable characteristic of the thing in the real world. These characteristics, or attributes, are those things that help to differentiate instances of one thing of the same type or kind, from another. For example characteristics of a person that differentiate one person from another: Hair color, Eye color, Height, Weight, BSA
Data Element Concept
Object Class
Qualifiers
Qualifiers
Property
Metadata Open Forum 2008 – ISO 11179 - caDSR Implementation Diagram
Object ClassChemopreventative Agent
Object ClassChemopreventative Agent
PropertyName
PropertyName
Conceptual DomainAgent
Conceptual DomainAgent
Data Element ConceptChemopreventive
Agent Name
Data Element ConceptChemopreventive
Agent Name
Data ElementChemopreventive
Agent Name
Data ElementChemopreventive
Agent Name
Value DomainCTEP Drug Names
Value DomainCTEP Drug Names
RepresentationName
RepresentationName
Valid ValuesCyclooxygenase
InhibitorDoxercalciferol
Eflornithine…
Ursodiol
Valid ValuesCyclooxygenase
InhibitorDoxercalciferol
Eflornithine…
Ursodiol
Metadata Open Forum 2008 – NCI CBIIT Extensions
• Mandatory Object Class and Property– NCI Compliance ensures that the parts of the semantics are clearly,
unambiguously identified– Simplifies development of programs and interfaces that can reliably
detect similar or different content (uses the ‘grammar’ to interpret metadata)
• Value Meanings as Administered Items– Alternate names and definitions– Reference documents– Origins
• Forms and parts of forms as administered items– Unique identifier– Versioning– Simplify creating and sharing Data Elements– Promote reuse of standards
Metadata Open Forum 2008 – NCI CBIIT Extensions
• Concepts as Administered Items– Provides links to external vocabularies and code systems– Minimal concept information extracted from external vocabulary systems
to populate the Administered Item Record to simplify reuse of NCI standardized concepts
• Preferred name, definition, concept identifier, source vocabulary identification
• Concepts bound to Controlled Vocabulary – Binding registry semantics to immutable external vocabulary concepts– Provides access to extensive synonymy and semantics represented in
ontologies, taxonomies and code systems where the concepts are more fully described
• Extended use of Concepts: Property, Representation, Value Meanings, Value Domains, Conceptual Domain, etc.– Enhances programmatic interpretation of semantics– (*ISO/IEC 11179 Ed. 2 specifies concepts as optionally associated with Object
Class)
Metadata Open Forum 2008 – NCI CBIIT Extensions
• Applied business rules to make the addition of semantics mandatory for Object Class, Property, Representation, Qualifiers, and Value Meanings
• Include Preferred Question Text
Next steps:
Forms as administered items CSI as administered items
Metadata Open Forum 2008 – NCI CBIIT Business Rules for Metadata Development and Maintenance
• Metadata Development– Naming and Definitions– Semantic Assignment– Completeness Criteria– Ownership and Usage– Status Assignment
• Metadata Maintenance– Updating/Modifying– Versioning– Status assignment
Metadata Open Forum 2008 – NCI CBIIT Best Practices
• Describe common processes• Improve quality and encourage reuse• Facilitate training and understanding• Documented in FAQs and documents• Encourage use of data standards
Metadata Open Forum 2008 – Enterprise Vocabulary Services - Thesaurus
• Controlled vocabulary resources for caCORE and the cancer research community
• Vocabulary Products and Services– NCI Thesaurus– NCI Metathesaurus– External vocabularies
• NCI Thesaurus - controlled vocabulary source for metadata– Has excellent coverage of cancer terminology– Expands based on needs for additional terminology– Based on concepts rather than terms– Each concept has a unique identifier or CUI with definitions and
synonym
Preferred Name
Synonyms
Definition
Relationships
Concept Code
Metadata Open Forum 2008 – Enterprise Vocabulary Services - Thesaurus
Metadata Open Forum 2008 – Curation: Manual Curation
Use a suite of caDSR Tools:• CDE Browser to locate existing metadata• Curation tool to create metadata
– Applies 11179 rules for well formed metadata• Administration tool to create classifications, classification
scheme items
Metadata Open Forum 2008 – ISO/IEC 11179 Implementation in NCI CBIIT- Browser
Metadata Open Forum 2008 – ISO/IEC 11179 Implementation in NCI CBIIT - Browser
Metadata Open Forum 2008 – ISO/IEC 11179 Implementation in NCI CBIIT- Browser
Common Data Element (CDE) Browser
Data Element Search Pane: This is the main search window. Users looking for Data Elements can enter a key word or phrase.
caDSR Search Tree: Displays all the current caDSR Contexts. Users can search for groups of DEs by navigating the tree. CDE_Browser_Training_Final.ppt
Jennifer Brush, Dianne Reeves
Metadata Open Forum 2008 – NCI CBIIT and caBIG™ Data Standards
Metadata Open Forum 2008 – NCI CBIIT and caBIG™ Data Standards - Details
Metadata Open Forum 2008 –
CDE Browser – Advance Search
Long name:
Permissible Value:
Workflow Status:
Metadata Open Forum 2008 – Curation Tool
Metadata Open Forum 2008 – Curation Tool
Metadata Open Forum 2008 – Curation Tool
Metadata Open Forum 2008 – Curation Tool
Example – Searching for a Representation Term in the Curation Tool brings up The list of 37 preferred Representation terms.
Metadata Open Forum 2008 – Preferred Representation Terms
• Anatomic Site
• Category
• Code
• Count
• Date
• Date/Time
• Dose
• Duration
• Float
• Frequency
• Grade
• Identifier
• Ind-2
• Ind-3
• Indicator• Integer• Interval• Measurement• Name• Number• Range• Rate • Reason
• Result• Scale• Score• Source• Specify• Stage• Status• Text• Time• Type• Unit of Measure• Value
Metadata Open Forum 2008 – Curation Tool
Metadata Open Forum 2008 – Curation Tool
Metadata Open Forum 2008 – Curation Tool
Metadata Open Forum 2008 – Curation Tool
Metadata Open Forum 2008 – Administration Tool
Metadata Open Forum 2008 – Administration Tool
Metadata Open Forum 2008 – Administration Tool
Metadata Open Forum 2008 – Administration Tool
Metadata Open Forum 2008 – Ways to Register Metadata into the caDSR
• Manual Curation• Model Loading• Batch Loader
Metadata Open Forum 2008 – Sources of Metadata
UML ModelcaDSR / ISO 11179 EVSLegacyApplication
FormQuestionnaire
1. Name: _______2. Birth Date: __/__/__3. Age: _______4. St. Address: _______5. City: _______6. State: _______7. Zip code: _______
8. Dx Cancer: ____9. Family History?Y / N10. Age at onset: ____
1025131
Questionnaire
1. Name: _______2. Birth Date: __/__/__3. Age: _______4. St. Address: _______5. City: _______6. State: _______7. Zip code: _______
8. Dx Cancer: ____9. Family History?Y / N10. Age at onset: ____
102513110251311025131
Metadata Open Forum 2008 – ISO/IEC 11179 Implementation in NCICBIIT
caDSR Implementation of ISO/IEC 11179:Data Element Fundamentals
NCI Thesaurus NCI Metathesaurus
Enterprise Vocabulary Services
ObjectClass
Property
DataElementConcept
Representation
ValueDomain+
What is it? How do you want torepresent it?
=Data
ElementConcept
ValueDomain
DataElement
Common Data Element+ =
caDSR & ISO 11179 TrainingJennifer Brush, Dianne Reeves
Metadata Open Forum 2008 –
ISO/IEC 11179 Implementation in NCICBIIT
Metadata Example: Patient Age in Years
caDSRmetadatarepository
Data
Describes the data in
What is your age?:
Metadata
33 Localdatabase
stored in
Person Self Reported Age(data element)
Person Self Reported Age(data element concept)
Age Values(value domain)
Person(object class)
Self Reported Age(property)
Datatype: NumericMax length: 10Version: 2.0High Value: 999Low Value: 0Type: Non-enumerated
stored in
caDSR & ISO 11179 TrainingJennifer Brush, Dianne Reeves
Metadata Open Forum 2008 –
Curation of Content: Data Element
caDSR Implementation of ISO/IEC 11179:Data Element Fundamentals
NCI Thesaurus NCI Metathesaurus
Enterprise Vocabulary Services
ObjectClass
Property
DataElementConcept
Representation
ValueDomain+
What is it? How do you want torepresent it?
=Data
ElementConcept
ValueDomain
DataElement
Common Data Element+ =
Age ValuePerson Self Reported Age Person Self ReportedAge Value
caDSR & ISO 11179 TrainingJennifer Brush, Dianne Reeves
Metadata Open Forum 2008 – Curation: Loading a Model into caDSR
caCORE SDK Workflow
1. Design system and draw model(UML tool)
2. Perform Semantic Integration (SIW - Semantic Integration Workbench)
3. Register metadata (UML Loader)
4. Generate and deploy system (Code Generator)
UML Model XMI File
Verified EVSReport
Code Generator
VerifiedAnnotated Fixed XMI
caDSRSTAGEPublic APIs
EVS
NO
Fixed XMI
Metadata Retrieval
Stage
caDSRProduction
Terminology Services
SuccessfulTest?
Compatibility Review
YES
ApprovedAnnotated Fixed XMI
caDSR ServicesUsing
CodeGen?
YES
NO
Semantic Integration Workbench
(SIW)
Load to Stage
UML LoaderUML
Loader
Metadata Open Forum 2008 – ISO/IEC 11179 Administered Items
Metadata Open Forum 2008 – ISO/IEC 11179 Administration Record
Metadata Open Forum 2008 – Creation of Metadata: Data Element Concept
What guidance does the ISO/IEC 11179 Standard give for DEC creation?
• Conceptual Domain• Object + Qualifiers (optional)• Property + Qualifiers (optional)• Administration Record:
– Data Identifier (‘Public ID’)– Version– Long, Short, and alternate names– Definitions (we use 3 types)– Effective date– Until date– Classifications– Origin– Administrative status– Registration status– And more characteristics…
Metadata Open Forum 2008 – Creation of Metadata: Value Domain
What guidance does ISO/IEC 11179 give for VD creation?• Conceptual Domain• Representation term + Qualifiers• Data Identifier (‘Public ID’)• Version• Long, Short, and alternate names• Definitions• Effective date• Until date• Classifications• Origin• Administrative Status• Registration Status• Data type• Field length• UOM• Permissible values/Value meanings/Concepts/Value meaning Descriptions• Reference Documents
Metadata Open Forum 2008 – Creation of Content: Data Element
What guidance does ISO/IEC 11179 give for DE creation?• DE• VD• Document Text – Question used on a form• Definition• Effective Date• Until Date• Data Identifier• Version• Classifications• Documents• Origin• Administrative status• Registration Status• Reference Documents
Metadata Open Forum 2008 – caDSR Organization of Content
Organization of Metadata in caDSR• By Context or owning group• By Model (UML Browser)• By Classification (CS) / Classification Scheme Item (CSI)
– Different ‘types’ of CS’s represent Business Categories, Data or Web Services, Items used together, etc.
• By Form
Metadata Open Forum 2008 – Organization of Metadata in caDSR: Contexts
A context is a group owning metadata• Context administrator• Business rules for aspects of metadata curation and
maintenance• Privileges for an identified set of users/curators
Metadata Open Forum 2008 – NCI CBIIT Data Quality Metrics
• Analyze the current content and identify issues• Clean-up quality of content in the caDSR by addressing
incomplete, inconsistent, and redundant metadata in the caDSR
• Establish best practices and business rules to prevent the creation of data quality problems in the future
• Strengthen the reuse of metadata across user communities
Metadata Open Forum 2008 – Cleanup Activities
• Identify incomplete, redundant, and inconsistent CDEs and their components
• Reduce duplication• Remove orphans• Ensure conformance with current business
rules• Continue to monitor content over time
Metadata Open Forum 2008 –
Example Metrics Report - Concepts – Baseline Update
Number of Concepts by Workflow Statuses
3/19/2008 4/16/2008
RELEASED 11,518 11,603
RETIRED ARCHIVED 7 8
RETIRED DELETED 4 4
RETIRED PHASED OUT 17 17
RETIRED WITHDRAWN 37 37
Total Number of Concepts 11,583 11,669
Metadata Open Forum 2008 – caDSR Users: Training Courses
Metadata Open Forum 2008 – Role: Context Administrator
Metadata Open Forum 2008 – Role: Subject Matter Expert/Content Expert
Metadata Open Forum 2008 – Training Course Materials
Metadata Open Forum 2008 – What is the value of using ISO/IEC 11179?
• Standardize structure and content• Promote reuse of standards• Enhance the ability to successfully search metadata
Metadata Open Forum 2008 – What organizations are using ISO/IEC 11179?
• Australian Institute of Health & Welfare • Nordic Common Data Elements Registry • UDEF (Universal Data Element Framework)• UK – cgMDR (Cancer Grid Metadata Registry)• US - National Cancer Institute• US - Department of Justice• US - Environmental Protection Agency or EPA • US – United States Health Information Knowledge Base
• Others?
Metadata Open Forum 2008 –
What is Needed for a Metadata Program?
• Management support• Commitment of resources• A registry tool• Business Rules• Best Practices• Quality Measurement Plan• Training program
Metadata Open Forum 2008 – Resources/References
caDSR SDK Guide: ftp://ftp1.nci.nih.gov/pub/cacore/SDK/v3.2.1/caCORE_SDK_3.2.1_Programmers_Guide.pdf
caCORE User Application Manual: ftp://ftp1.nci.nih.gov/pub/cacore/NCICBapplications/NCICBAppManual.pdf
caCORE Technical Guide: ftp://ftp1.nci.nih.gov/pub/cacore/caCORE3.2_Tech_Guide.pdf
• caDSR Homepage: http://ncicb.nci.nih.gov/core/caDSR
Metadata Open Forum 2008 –
Contact Information
NCI CBIIT Instructor: Dianne Reeves ([email protected])
caDSR Home Page:http://ncicb.nci.nih.gov/NCICB/infrastructure/
cacore_overview/cadsrcaDSR Training Home Page:
http://ncicb.nci.nih.gov/NCICB/training/cadsr_trainingcaDSR Training ListServ:
https://list.nih.gov/archives/cadsr_training-l.htmlhttp://list.nih.gov
Metadata Open Forum 2008 –
Your Questions
Thank you for your attention!
Please join us on a future caDSR Training teleconference, or send an email.