1 / 11

eXtended Metadata Registry (XMDR): Contributions for an Open Ontology Repository

eXtended Metadata Registry (XMDR): Contributions for an Open Ontology Repository OOR Panel - “Getting OOR off the ground: Synergies and Gaps” August 22, 2008. Bruce Bargmeyer Lawrence Berkeley National Laboratory University of California, Berkeley Tel: +1 510-495-2905 bebargmeyer@lbl.gov.

neorah
Download Presentation

eXtended Metadata Registry (XMDR): Contributions for an Open Ontology Repository

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. eXtended Metadata Registry (XMDR): Contributions for an Open Ontology Repository OOR Panel - “Getting OOR off the ground: Synergies and Gaps” August 22, 2008 Bruce Bargmeyer Lawrence Berkeley National Laboratory University of California, Berkeley Tel: +1 510-495-2905 bebargmeyer@lbl.gov

  2. Things Needed for OOR • Use Cases • Model • Architecture & Software • User Interface – Go BioPortal! • Everything else • Content & Content Loading

  3. What XMDR Brings to the Table • Use cases - semantics challenges - and Requirements • Proposed specifications for ISO/IEC 11179 Edition 3 – Model, definitions, ontology • Modular software architecture and open source software modules • Open Source XMDR software • Test content

  4. Use Cases • What do we want to construct? • XMDR contributed use cases to the OOR web site. It would be good to update and flesh out the use cases. The XMDR use cases are based on proposals for ISO/IEC 11179 Edition 3. The intent is to use semantic artifacts, such as ontologies, to help manage data. • The core OOR functionality may be registering and disseminating ontologies. Do we want to extend our effort to the linkage of concept systems (e.g., ontologies) to metadata that describes data? • Do we want to be able to reason across the content of an OOR? XMDR enables this.

  5. Model – Ontology Region https://xmdr.lbl.gov/mediawiki/index.php/Latest_Diagrams

  6. Model – Registration Region

  7. Rational Rose? MagicDraw? Others? Sandpiper Visual Ontology Modeler? Model: XMI from 11179-ed3 UML is transformed to RDF/OWL for XML metamodel specification UML modeling & editing OWL ontology display,editing & validation Transformation to OWL ABSTRACT STEP UML interchange Logic index Reasoner Human compare / hand editing XMDR OPEN SOURCE TOOLS XSLT scripts Poseidon Protege Swoop Jena Pellet XMDR Metamodel (UML) XMDR Metamodel (XMI) XMDR Metamodel (preliminary RDF/OWL) XMDR Metamodel (final RDF/OWL) XMDR Metamodel asserted logic index XMDR Metamodel inferred logic index FILES (AND TYPES) POSSIBLE ALTERNATE TOOLS CMWR July 8, 2008 -v2.ppt

  8. Metadata Sources concept systems, data elements USERS Web Browsers…..Client Software Content Loading & Transformation (Lexgrid & custom) Application Program Interface (REST) Human User Interface (XML pages & javascript) Authentication Service Validation (XML Schema) Mapping Engine Search & Inference Queries (Jena, SPARQL) Metamodel specs (UML & Editing) (Poseidon, Protege) XMDR data model & exchange format XML, RDF, OWL Reasoner (Pellet) Text Search (Lucene) Registry Store(Subversion) standard XMDR files XMDR metamodel (OWL & xml schema) standard XMDR files Full Text Index Inferred LogicIndex Asserted LogicIndex standard XMDR files standard XMDR files XMDR Architecture & Open Source Software CMWR July 8, 2008 -v2.ppt

  9. Content loading, with XMDR metamodel used for inferred indexing and validation CONTENT TRANSFORMATION VALIDATION REGISTRY INFORMATION INDEXING Subversion Reasoner (Pellet) Inferred LogicIndex Terminology A XMDR Files A Terminology B XMDR Files B LexGrid Thesaurus C XMDR Files C Terminology D XMDR Files D XMDR metamodel In XML schema Search & Inference Framework (Jena) Assesed LogicIndex XSLT script E Data Element Source E XMDR Files E XSLT script F Terminology Source F XMDR Files F XSLT script G Ontology Source G XMDR Files G Text Indexing (Lucene) Full Text LogicIndex XSLT script G External Source H XMDR Files H (virtual)

  10. An Approach • Use BioPortal • Use LexGrid • Extend with XMDR

  11. Thanks & Acknowledgements • John McCarthy, LBNL • Kevin Keck, LBNL • Fred Gey, UCB • Anirban Sen, UCB • Frank Olken, LBNL • Harold Solbrig, Mayo Clinic • INCITS L8 and ISO/IEC JTC1/SC 32/WG 2 Standards Committees • Major XMDR Project Sponsors and Collaborators • National Science Foundation (Grant #0637122) • National Cancer Institute • U.S. Environmental Protection Agency • Department of Defense • U.S. Geological Survey • And others! for more info, see xmdr.org

More Related