Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Vocabulary Integration Environment: VINE

Luis E. Bermudez

Monterey Bay Aquarium

Research Institute

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

The Marine Metadata Initiative

• NSF starter funding, with SURA(ONR) in-kind support, NOAA CSC bridge funds

• International contributions and support• Main deliverables: web site, and a community• Goal for future: Solve the metadata problem

– At least, creating effective processes to improve it

– Asking world wide contributors, to work with us– Identifying strategies and partners for

operations

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Data complexity and heterogeneity from observed data source in the MUSE Project http://www.mbari.org/MUSE/

Complexity of Observing Systems

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Semantic Conflicts in Metadata Annotations

Search for sea

water temperature

data Water Temperature

sea_water_temperature

TEMP

BODC

GCMD

CF

Only matches

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

“Advancing Domain Vocabularies”MMI workshop Aug 2005

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

About 60 ontologies available

http://marinemetadata.org/allont

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

“Advancing Domain Vocabularies”MMI workshop Aug 2005

Topic Direct

mappings Inferred mappings

Total mappings

Plant Pigments 405 1,022 1,427

PaCOOS 131 375 506

Waves 93 181 274

Currents 90 153 243

CTD 81 432 513

Habitats 23 37 60

Total 823 2,200 3,023

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Framework to make marine vocabularies interoperable

• Identification

• Harmonization

• Mapping

• Publication

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Controlled Vocabulary

• Formally managed, community-specific terminology that collectively represents a specialized vocabulary for a community. Benefits:– helps to avoid misspellings and avoid the

use of arbitrary words that cause inconsistencies,

– helps to solve semantic incompatibilities among distributed systems.

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Achieving Semantic Interoperability

DTDDTD

Comma Comma Separated Separated

ValuesValues

HTMLHTML

Tab Tab Separated Separated

ValuesValues

Relational Relational DatabaseDatabase

XML/XSDXML/XSD

RDFRDF

OWLOWL

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Web Ontology Language: OWL

<owl:Class rdf:ID=“Body_of_Water”></owl:Class>

<owl:Class rdf:ID=“River”> <rdfs:subClassOf rdf:resource=“# Body_of_Water”/></owl:Class>

Body of Water

River

• 2003 World Wide Web Consortium recommendation to formally express ontologies.

• Based on the Resource Description Framework (RDF).

• Can be serialized in XML.• Supporting tools: JENA, Protégé,

SWOOP, Sesame, Kuwari, VINE, …

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Semantic Web

The internet is an electronic Library of Congress without a cataloguing system. R Johnson (1998): Historical Research Online. A new ball game.

DataData

InformatioInformation n

Resources Resources (Metadata)(Metadata)

Knowledge Knowledge ResourcesResources

(RDF)(RDF)

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Resource Description Framework

r a d a r

r a i n

m e a s u r e s

D r e x e l

d b Z

i s i n

D I X

i s a

P h i l a d e l p h i a

c o v e r s

0

V a l u e i s

p u b l i s h e s

N O A Ao p e r a t e s

M o s t r e c e n t a v e r a g e

H a s u n i t s

R a i n i n g

R e l a t e d n o u n

N o R a i n i n g

N e g a t i o n o f

m e a s u r e s

V a l u e i s

H a s u n i t s

S u b j e c tO b j e c tp r e d i c a t e

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

RDF Simple Graph Model

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Graphs = knowledge

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

URI“The most fundamental specification of Web

architecture, while one of the simpler, is that of the URI. The principle that anything, absolutely anything, “on the web” should be identified distinctly by an otherwise opaque string of characters is core to the universality”. Tim Bernee Lee.

Proven paradigm: mail, IP, Web, SIN, Telephone number, P2P, banking transaction

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Ontology definition

Is an RDF Graph which uses URIs as unique identifiers, useful to construct knowledge of domains, identifying, defining and relating control vocabularies.

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Mapping

Term BTerm A

Controlled vocabulary

Controlled vocabulary

mapping

A == BA subclass of BA is a type of BA isNarrowerThan B…

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Mapping relations at MMI

• Main relations:– Same as (owl:sameAs)

• Inverse, symmetric and transitive– Narrower Than (map:narrowerThan)

• Transitive, Inverse of map:broaderThan)– Broader Than (map:broaderThan)

Transitive, Inverse of map:narrowerThan)• SKOS (W3C) is defining similar realtions.

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

sameAs relation: direct and inference statements

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Free - Flexible Tool

• JAVA tool

• Available at Sourceforge

• Is an Eclipse Rich Client Platform (RCP)

• GPL License

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Simplified Statement

temperature parameter

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Smart Deep Graph Search

Ontology simplified statements:• tkel1 temperature in kelvin• tke1ctd temperature in kelvin ctd• tke2 temp k

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Main Widgets

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Main Interfaces

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Model View Controller

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Comparison with other tools

• VINE allows any arbitrary relation to be created. Other tools are more enforced and will not let you to create any relation between RDF resources. For example: Protégé and SWOOP. OWL Full is not a problem.• VINE allows to do a “friendly search” for any term in an ontology. It will take into account the first graph of a term and creates a simplify statement to improve efficiency. Other tools search in the local name; however, SPARQL queries are becoming more available in pupular tools, like Protégé.

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

ACKNOWLEDGMENTS

MMI is supported by the National Science Foundation, the Monterey Bay Aquarium Research Institute (MBARI) and the David and Lucile Packard Foundation.

Marine M

etadata Interoperability Initiative

Congreso Colombiano de Computación - CCC 2007 Abril 18 al 20 de 2007 Pontificia Universidad Javeriana, D.C

Thank You

http://marinemetadata.org

Luis Bermudez

bermudez@mbari.org