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Terminology Metadata Extension of the Service Meta Model Salvatore Mungal Duke University

Terminology Metadata Extension of the Service Meta Model Salvatore Mungal Duke University May 20, 2008. “Metadata DownUnder” : 11th Open Forum on Metadata Registries Sydney, NSW Australia. Sharing and advancing knowledge and experience about standards, technologies and implementations. .

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Terminology Metadata Extension of the Service Meta Model Salvatore Mungal Duke University

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  1. Terminology Metadata Extension of the Service Meta Model Salvatore Mungal Duke University May 20, 2008 “Metadata DownUnder”:11th Open Forum on Metadata Registries Sydney, NSW Australia Sharing and advancing knowledge and experience about standards, technologies and implementations. 

  2. Agenda • Background (5 min) • Review Proposed Model (20 - 25 min) • Next Steps (5 min) • Discussion (10 - 15 min)

  3. Team Members • Brian Davis (3rd Millennium) • Frank Hartel (NCI) • Tom Johnson (Mayo) • George Komatsoulis (NCI) • Hua Min (Fox Chase) • Sal Mungal (Duke) • Scott Oster (OSU) • Mike Riben (MD Anderson) • Denise Warzel (NCI)

  4. Background - caBIGTM • Goals: • The cancer Biomedical Informatics Grid (caBIGTM) is an information technology program that develops software tools to support cancer research efforts by establishing a common infrastructure that can be used to share data and applications across organizations. • Interoperability is a key factor in caBIG’s infrastructure and is very dependent on terminologies.

  5. Background - caBIGTM • Goals: • The growing demand for service-oriented access to terminologies in the caBIG community is anticipated to result in increased publication of respective services on the caGrid. • Efficient discovery, administration and query of these resources require definition and use of consistent and reliable metadata from the cancer Data Standards Repository (caDSR) that can be queried at the service level.

  6. Background - Goals • Goals: • Identify metadata queryable at the index service level • Narrow focus for first model revision… • Initial model defined to satisfy discovery 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

  7. Background – Use Cases • Use Case Collection • Identification • Internationalization • Intended/Allowed Usage • Provenance • Administration

  8. Background - Use Cases • Samples • Browsing Ontologies • Viewing Differences • Administering the NCBO Ontology Library • Web of Trust

  9. Background - Use Cases (1) Browsing • 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” If there is a match: • 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 (preferred Name), description

  10. 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 (id), version

  11. Background - Use Cases (3) Discovery • 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

  12. 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

  13. 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.

  14. 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

  15. Background – Model Alignment

  16. Background – Model Alignment

  17. 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

  18. Model - Overview

  19. Model - AdministeredComponent • Administered Component - a common superclass based on the ISO 11179 standard providing typical attributes relevant to any component registered and maintained on the grid (e.g. id, preferredName, preferredDefinition)

  20. Model – Core Identification & Description • localName (1..n) • Name used to refer to the terminology within a localized context; often a mnemonic. • ICD-9-CM, ICD-9 • category (0..n) • Applicable domains or scientific fields. • e.g. anatomy, genomic, proteomic, phenotype…

  21. Model – Core Identification & Description • 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-hierarchicalstructure. • complex - supports multiple relationships and/or relationship types

  22. Model – Core Identification & Description • 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, …

  23. 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 …

  24. Model - Provenance • 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 source (0..1) • Origin or provider of content • National Center for Health Statistics (NCHS) • releaseLocation (0..1) • Location of resource in the releaseFormat. • ftp://ftp1.nci.nih.gov/pub/cacore/EVS/NCI_Thesaurus/Thesaurus_07.12a.OWL.zip • releaseVersion (0..1) • Represented version identifier. • 2007

  25. Model - Certification • type • e.g. Good housekeeping or caBIG’s level of compliance • value • e.g. Gold seal of approval or caBIG’s bronze, silver, gold

  26. Model - ReleasePackage • name • meta distribution containing the terminology as released. eg. UMLS • version • identifier of the composite ontology or meta distribution containing the terminology as released. eg. 2007AB

  27. Model - Contact • A common class used to maintain contact information (e.g. name, address, phone) as defined by the ISO 11179 standard

  28. Model – Anticipated Alignment against available classes Superclasses Based on 11179

  29. Next Steps • Model harmonization w/ recommended superclasses is complete but additional changes are anticipated in the registration process using caBIGTM tools • 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

  30. Questions/Discussion

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