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 … discoveryInitial 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

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 /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

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

Model – Core Identification & Description uri (1) Unique persistent identifier. urn:oid: 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…

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

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

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

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 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_Thes aurus/Thesaurus_07.12a.OWL.zip

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

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 registrationStatus (1) Designation of terminology status in life cycle. Possible values from 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

Model – Anticipated Alignment against available classes Superclasses Based on 11179

Vote Vote will be for … Approval of the identified criteria Acknowledgement that model will be aligned with existing (e.g 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