terminology metadata
DESCRIPTION
Terminology Metadata. Extension of the Service Meta Model. SWG Proposal January 2008. Agenda. Background (5 min) Review Proposed Model (15 min) Discussion (5 min) Vote Next Steps (5 min). Team Members. Tom Johnson (Mayo) Frank Hartel (NCI) George Komatsoulis (NCI) Sal Mungal (Duke) - PowerPoint PPT PresentationTRANSCRIPT
Terminology Metadata
Extension of the Service Meta Model
SWG Proposal
January 2008
Agenda
• Background (5 min)• Review Proposed Model (15 min)• Discussion (5 min)• Vote• Next Steps (5 min)
Team Members
• Tom Johnson (Mayo)• Frank Hartel (NCI)• George Komatsoulis (NCI)• Sal Mungal (Duke)• Hua Min (Fox Chase)• Scott Oster (OSU)• Mike Riben (MD Anderson)• Brian Davis (3rd Millennium)
Background - Goals
• Goals: • Identify metadata queryable at the index service level• Narrow focus for first revision …
• Initial model defined to satisfy discoverydiscovery use cases
• Support development of enhanced grid discovery client• Resolve runtime services for terminologies of interest• Additional metadata available through runtime services
• Allow/anticipate future expansion
Background – Use Cases
• Use Case Collection & Classification of Attributes• Identification• Internationalization• Intended/Allowed Usage• Provenance• Administration
Background - Use Cases
• Samples• Browse Existing Ontologies• Viewing Differences• Detecting Recently Added Ontologies• Web of Trust
(1) Browse Existing Ontologies• An ontology developer is interested in creating an ontology
for a domain (e.g., radiographic anatomy).
• Determine if there are already similar ontologies in that domain. • Evaluates assigned categories for registered ontologies. • Discovers match for “anatomy”
• Views available titles and descriptions• Finds listings for “human” and “mouse” anatomy, but not “radiology” • Looks at the human anatomy ontology to see if it fits the need
Attributes: category, title, description
Background - Use Cases
(2) Viewing Differences • An ontology developer wants to view what has changed
between two versions of an ontology.
• Retrieve listing of registered terminology services• Sort by URI, then version• Select and resolve grid services for differing versions• Invokes runtime services to resolve and compare content
Attributes: uri, version
Background - Use Cases
(3) Detecting Recently Added Ontologies• A user wants to contact the providers for new ontologies
registered within the last quarter.
• Query registered ontologies by registration date• Pull point of contact information (source, curator, registration
authority) from listed items
Attributes: registration date, registration authority, source, curator
Background - Use Cases
(4) Web of Trust• Quality of ontologies:
• User is aware that there are several anatomy ontologies, and is unclear which to use.
• Trusts certain ontology sources (anatomists) more than others • Views ontology source to determine content origin• Views intended and example use to consider alignment with
application• Considers caBIG certification level
Attributes: source, intended use, example use, certification level
Background - Use Cases
Background – Model
• Focus of work on …• Model alignment
• External … Incorporate feedback from review and alignment with relevant specifications and standards.
• Internal … Take better advantage of previously registered models and classes.
• Incorporating specific feedback on model classes and attributes.
Background - Alignment
• Specifications/standards considered …• Dublin Core• ISO 11179-2/3/6: classification, registries, admin• LexGrid/LexBIG model• National Center for Biomedical Ontology (NCBO) BioPortal• Public Health Information Network (CDC/PHIN)• Simple Knowledge Organization System (SKOS core)• UMLS Rich Release Format (RRF)• CTS/CTS2
Background – Model Alignment
Background – Model Alignment
Background – Model Alignment
• Findings …• No silver bullet• General alignment for defined items
• All SWG items and definitions represented conceptually in one or more specifications
• Adequate, but not perfect, alignment of semantics
• Some name changes
• Some new attributes identified• Supplement existing use case
• Generally not found to be required unless we add use cases
Model - Overview
class Domain Objects
The Domain class model captures essential information about objects in the domain.
TerminologyMetaData
+ category: String [0..n]+ defaultLanguage: String = eng+ description: String [0..1]+ keyword: String [0..n]+ localName: String [1..n]- structure: StructureType+ supportedContentType: String [1..n]+ supportedLanguage: String [1..n]+ title: String+ type: typeEnum [0..1]+ uri: String
TerminologyUsage
+ exampleUse: String [0..n]+ intendedUse: String [0..n]+ isRestricted: isRestrictedType+ rights: String [0..n]+ rightsHolder
TerminologyProv enance
+ curator [0..1]+ releaseDate: Date+ releaseFormat: String+ releaseLocation: String+ releasePackage: String+ releaseVersion: String+ source [0..1]
TerminologyAdmin
+ certification: certificationType [0..1]+ registrationAuthority+ registrationDate: Date+ registrationStatus: registrationStatusType+ registrationTag: String [0..n]
+terminologyMetaData
1
hasStatus
+terminologyAdmin 1+terminologyMetaData 1
hasProvenance
+terminologyProvenance 1
+terminologyMetaData
1
hasUsage
+terminologyUsage 1
Model – Core Identification& Description
• uri (1)• Unique persistent identifier.• urn:oid:2.16.840.1.113883.6.2
• title (1)• Formal or published name for display.• International Classification of Disease, 9th…
• localName (1..n)• Name used to refer to the terminology within a
localized context; often a mnemonic.• ICD-9-CM, ICD-9
• description (0..1)• Human-readable explanation or narrative.• The International Classification of …
• category (0..n)• Applicable domains or scientific fields.• e.g. anatomy, genomic, proteomic,
phenotype…
class Logical Model
TerminologyMetaData
+ category: String [0..n]+ defaultLanguage: String = eng+ description: String [0..1]+ keyword: String [0..n]+ localName: String [1..n]- structure: StructureType+ supportedContentType: String [1..n]+ supportedLanguage: String [1..n]+ title: String+ type: typeEnum [0..1]+ uri: String
• type (0..1)• Nature of content relative to the category.• application – describes domain in an application
dependent manner• core – describes domain in an application
independent manner• domain – describes the most important
concepts in a domain• task – describes generic types of tasks or
activities (e.g. selling, selecting)• upperLevel – describes general, domain
independent concepts (e.g. space, time)
• structure (1)• Indicates complexity of maintained relationships• flat – no hierarchy• simple - supports a single inheritance mono-
hierarchical structure.• complex - supports multiple relationships and/or
relationship types
Model – Core Identification& Description
class Logical Model
TerminologyMetaData
+ category: String [0..n]+ defaultLanguage: String = eng+ description: String [0..1]+ keyword: String [0..n]+ localName: String [1..n]- structure: StructureType+ supportedContentType: String [1..n]+ supportedLanguage: String [1..n]+ title: String+ type: typeEnum [0..1]+ uri: String
• defaultLanguage (1)• Language for text unless otherwise specified• eng
• supportedLanguage (1..n)• Languages supported for text-based content• eng, spa, …
• supportedContentType (1..n)• Supported type of text or imbedded multimedia• e.g. mime type (text/plain, image)
• keyword (0..n)• Words or phrases of special significance.• patient record, nursing protocol, …
Model – Core Identification& Description
class Logical Model
TerminologyMetaData
+ category: String [0..n]+ defaultLanguage: String = eng+ description: String [0..1]+ keyword: String [0..n]+ localName: String [1..n]- structure: StructureType+ supportedContentType: String [1..n]+ supportedLanguage: String [1..n]+ title: String+ type: typeEnum [0..1]+ uri: String
Model - Usage
• intendedUse (0..n)• Human-readable description of intended use.• data integration
• exampleUse (0..n)• Human-readable example of use.• Integration of protein data.
• isRestricted (1)• Indication of intellectual property boundaries.• true
• rights (0..n)• Human-readable description of IP rights.• NCI Thesaurus terms of use …
• rightsHolder (point of contact) (0..1)• Contact point for intellectual property rights.• National Cancer Institute
class Logical Model
TerminologyUsage
+ exampleUse: String [0..n]+ intendedUse: String [0..n]+ isRestricted: isRestrictedType+ rights: String [0..n]+ rightsHolder
Model - Provenance
• source (0..1)• Origin or provider of content• National Center for Health Statistics (NCHS)
• curator (0..1)• Maintains the content in the release format (e.g.
OWL, OBO, RRF)• National Library of Medicine
• releaseDate (0..1)• Date of availability in released format.• 2007-08-30
• releaseFormat (0..1)• Format as released by the curator.• e.g. OWL, OBO, RRF
• releaseLocation (0..1)• Location of resource in the releaseFormat.• ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
NCI_Thesaurus/Thesaurus_07.12a.OWL.zip
class Logical Model
TerminologyProv enance
+ curator [0..1]+ releaseDate: Date+ releaseFormat: String+ releaseLocation: String+ releasePackage: String+ releaseVersion: String+ source [0..1]
Model - Provenance
• releasePackage (0..1)• Name of the composite ontology or meta
distribution containing the terminology as released.
• e.g. UMLS, NCI_MetaThesaurus, BiomedGT
• releaseVersion (0..1)• Represented version identifier.
• 2007
class Logical Model
TerminologyProv enance
+ curator [0..1]+ releaseDate: Date+ releaseFormat: String+ releaseLocation: String+ releasePackage: String+ releaseVersion: String+ source [0..1]
Model - Administration
• registrationAuthority (1)• Responsible for maintaining content on the grid• National Cancer Institute
• registrationDate (1)• Date of grid availability or last change of
registration status.• 2007-09-30
• registrationStatus (1)• Designation of terminology status in life cycle.• Possible values from 11179-3 registration life
cycle status category.
• registrationTag (0..1)• Supports lookup by version-agnostic designation• development, test, production
• certification (0..1)• caBIG level of compliance.• bronze, silver, gold
class Logical Model
TerminologyAdmin
+ certification: certificationType [0..1]+ registrationAuthority+ registrationDate: Date+ registrationStatus: registrationStatusType+ registrationTag: String [0..n]
«enumeration»registrationStatusType
candidate incomplete preferredStandard qualified recorded retired standard superceded
Model – Anticipated Alignmentagainst available classes
class Domain Objects
The Domain class model captures essential information about objects in the domain.
TerminologyMetaData
+ abbreviation: java.lang.String [1..n]+ category: java.lang.String [0..n]+ defaultLanguage: java.lang.String = eng+ description: java.lang.String [0..1]+ keyword: java.lang.String [0..n]- structure: StructureType+ supportedContentType: java.lang.String [1..n]+ supportedLanguage: java.lang.String [1..n]+ title: java.lang.String+ type: typeEnum [0..1]+ uri: java.lang.String
TerminologyUsage
+ exampleUse: java.lang.String [0..n]+ intendedUse: intendedUseType+ isRestricted: isRestrictedType+ rights: java.lang.String [0..n]+ rightsHolder: java.lang.String
TerminologyProv enance
+ curator: java.lang.String [0..1]+ releaseDate: Date+ releaseFormat: java.lang.String+ releaseLocation: java.lang.String+ releaseVersion: java.lang.String+ source: java.lang.String [0..1]
TerminologyAdmin
+ certification: java.lang.String [0..1]+ registrationAuthority+ registrationDate: Date+ registrationStatus: registrationStatusType+ registrationTag: java.lang.String [0..n]
+terminologyMetaData
1
hasStatus
+terminologyAdmin 1+terminologyMetaData 1
hasProvenance
+terminologyProvenance 1
+terminologyMetaData
1
hasUsage
+terminologyUsage 1
SuperclassesBased on 11179
Vote
• Vote will be for …• Approval of the identified criteria• Acknowledgement that model will be aligned with
existing (e.g. 11179-based) superclasses, with model and attribute details to be addressed as required.
Questions/Discussion before Vote
Next Steps
• Model harmonization w/ recommended superclasses• Change caGRID tooling to capture additional metadata
when registering terminology• Create custom discovery client for terminology services, to
take advantage of additional metadata in support of identified use cases