metadata open forum 2008 iso/iec/iec 11179: metadata registries a tutorial from the national cancer...

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)

http://www.os.dhhs.gov/

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


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


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

http://ncicb.nci.nih.gov/NCICB/EVS




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


• 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)


• 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


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 – 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


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



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


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


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?


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


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


Your Questions

Thank you for your attention!

Please join us on a future caDSR Training teleconference, or send an email.

metadata open forum 2008 iso/iec/iec 11179: metadata registries a tutorial from the national cancer...

Documents

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data elementsisoiec

unit of data

basic isoiec

data descriptive pattern

metadata registration

metadata registrieswhat