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

Repository

OOR Panel - “Getting OOR off the ground: Synergies and Gaps”

 August 22, 2008

Bruce BargmeyerLawrence Berkeley National LaboratoryUniversity of California, BerkeleyTel: +1 510-495-2905bebargmeyer@lbl.gov

Things Needed for OOR

Use Cases Model Architecture & Software

User Interface – Go BioPortal! Everything else

Content & Content Loading

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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

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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.

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Model – Ontology Region

6https://xmdr.lbl.gov/mediawiki/index.php/Latest_Diagrams

Model – Registration Region

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page 8 of xxx CMWR July 8, 2008 -v2.ppt

Model: XMI from 11179-ed3 UML is transformed to RDF/OWL for XML metamodel specification

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Sandpiper Visual Ontology Modeler?

XMDRMetamodelasserted

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Others?Rational Rose?

Poseidon XSLTscripts

Protege Swoop Jena Pellet

MagicDraw?

page 9 of xxx CMWR July 8, 2008 -v2.ppt

Authentication ServiceValidation

(XML Schema)

MappingEngine

Full TextIndex

AssertedLogicIndex

InferredLogicIndex

Reasoner(Pellet)

Text Search(Lucene)

Registry Store (Subversion)

XMDR metamodel (OWL & xml schema)

Metamodel specs(UML & Editing)

(Poseidon, Protege)

XMDR Architecture & Open Source Software

Search & Inference Queries (Jena, SPARQL)

Human User Interface(XML pages & javascript)

USERSWeb Browsers…..Client

Software

Application Program Interface (REST)

standard XMDR filesstandard XMDR files

standard XMDR filesstandard XMDR files

Content Loading & Transformation

(Lexgrid & custom)

Metadata Sources concept systems,

data elements

XMDR data model & exchange format

XML, RDF, OWL

page 10 of xxx

Content loading, with XMDR metamodel used for inferred indexing and validation

CONTENT

Terminology A

Terminology D

Terminology B

Thesaurus C

Data ElementSource E

TerminologySource F

OntologySource G

ExternalSource H

VALIDATIONTRANSFORMATION REGISTRY INFORMATION INDEXING

LexGrid

Reasoner(Pellet)

TextIndexing(Lucene)

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Framework(Jena)XSLT

script E

XSLTscript F

XSLTscript G

XSLTscript G

XMDR Files A

XMDR Files D

XMDR Files B

XMDR Files C

XMDR Files E

XMDR Files F

XMDR Files G

XMDR Files H (virtual)

Subversion

XMDR metamodel

In XML schema

An Approach

Use BioPortal Use LexGrid Extend with XMDR

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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