Speeding up ontology creation of scientific terms. Luis Bermudez, John Graybeal, Montery Bay...
Transcript of Speeding up ontology creation of scientific terms. Luis Bermudez, John Graybeal, Montery Bay...
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Speeding up ontology creation of scientific terms.
Luis Bermudez , John Graybeal,Montery Bay Aquarium Research Institute
http://marinemetadata.org
December 7, 2005
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Why are ontologies importantAt AGU we
have 31 abstracts and 2 entire sessions related to ontologies
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Problem: Semantic Interoperability
SSDS
AOSN
get me Data for Variable ocean_temperature (C)
get me Data for Parameter temperature_1(deg C)
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Need for controlled vocabulary
A set of restricted words, used by an information community when describing resources or discovering data. The controlled vocabulary prevents misspellings and avoids the use of arbitrary, duplicative, or confusing words that cause inconsistencies when cataloging data.
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Controlled Vocabularies: Discovery of Data
GCMD HTMLhttp://gcmd.gsfc.nasa.gov/Resources/valids
BODC Discovery
Comma Separated Value
http://wwwtest.bodc.ac.uk/data/ codes_and_formats/parameter_codes/bodc_para_dict.html
AGU Index Terms HTMLhttp://www.agu.org/pubs/ gaplist.html
MEL HTMLhttps://mel.dmso.mil/docs/metadata_guide/section_6.htm
NOAA CoRIS Thesauri PDF
http://www.coris.noaa.gov/backmatter/keywords/discovery_ thesaurus.pdf
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Controlled Vocabularies: Usage (tag the data collected)
BODC
Comma Separated Value
http://wwwtest.bodc.ac.uk/data/ codes_and_formats/parameter_codes/bodc_para_dict.html
U.S. JGOFS Dictionary of parameters HTML
http://usjgofs.whoi.edu/datasys/ param_master.html
IOC GF3 parameter codes HTML
http://ioc.unesco.org/oceanteacher/ resourcekit/M3/Formats/Integrated/GF3/GF3.htm
SEACOOS
Comma Separated value
http://twiki.sura.org/twiki/pub/Main/DataStandards/seacoos_draft_data_ dictionary_v2.0.csv
CF XMLhttp://www.cgd.ucar.edu/cms/eaton/cf-metadata/standard_name.xml
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Problem: Semantic Interoperability
semantics semantics
Standard vocabularies
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Harmonization
DTDDTD
Comma Comma Separated Separated
ValuesValues
HTMLHTML
Tab Tab Separated Separated
ValuesValues
Relational Relational DatabaseDatabase
XML/XSDXML/XSD
RDFRDF
Web OntologyWeb Ontology Language (OWL)Language (OWL)
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Web Ontology Language: OWL
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, Pangloss, Kuwari, VINE, Voc2OWL
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Fast introduction to OWL
RDF TriplesRDF ResourcesClasses - individuals - propertiesRDF Graph
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RDF: Triples, triples, triples
id description unitsocean_
temperatureOcean
Temperature C
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RDF: Resource
Resources
A resource is anything on the Web that has a unique identifier. Examples:
URI: urn:aosn.mbari.org.recordVariable.id:1900 URL: http://mmi.org/2005/08/gcmd-keyw#Chlorophyll URL: ftp://mmi.org/data-example
Literal
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Parameters
id description units
Temperature_1water temperature from unit 00471 deg C
Temperature_2water temperature from unit 00822 deg C
Looks like a class
Looks like individuals of (members of) the class Parameter
Classes Individuals Properties
Property (Attributes)
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How are ontologies created?
Conceptual direction strategy:
Up - down
Bottom - up
Automation approach:
Manual
Automatic
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Up - down approach
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Bottom - up approach
Body of Water Class
RiverLake
Has water
Is inland body
Has a relative defined channel
Lake RiverExample:1. Properties of real
world objects are identified.
2. Similarities are identified.
3. Concepts are created
4. and are expressed as a class.
5. Classes are related.
Subclass
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id description unitsTemperature deg C
temperature
Temperature inside the OASIS can, in degrees C
Temperature
temperature measured inside the MMC controller
Temperature CelsiusTemperature degrees CTemperature water temperature deg C
Temperature_1water temperature from unit 00471 deg C
Temperature_2water temperature from unit 03533 deg C
Bottom - up approach
id description unitsocean_temperature Ocean Temperature Cocean_temperature_2 Ocean Temperature 2 C
ocean_temperature_allOcean TemperatureAll
C
ocean_temperature_qcflag
Ocean TemperatureQcflag
0=good,1=missing,2=marginal,3=bad
ocean_temperature_rawOcean TemperatureRaw
counts
sea_surface_temperatureSea SurfaceTemperature
C
ssds:Parameter
aosn:Variable
Example:1.Real word objects:
parameters in observatory systems.
2.They all have similar properties (id, description and units).
3. Make them a resource: instance of a class Parameter
rdf:type
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Bottom - up approach (cont.)
ssds:Parameter
aosn:Variable
mmi:Parameter
sweet:Property
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Manual (Ontology editor)
List of more than 50 editors: http://www.xml.com/2002/11/06/Ontology_Editor_Survey.html
Protégé
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Automatic
Ontology in Ontology in OWLOWL
Software Program
transformationProperties file
id description unitsocean_temperature Ocean Temperature Cocean_temperature_2 Ocean Temperature 2 C
ocean_temperature_allOcean TemperatureAll
C
ocean_temperature_qcflag
Ocean TemperatureQcflag
0=good,1=missing,2=marginal,3=bad
ocean_temperature_rawOcean TemperatureRaw
counts
sea_surface_temperatureSea SurfaceTemperature
C
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Automatic
Advantages Fast Preserves a connection with the source
( back - compatibility ) Avoids typing and copy/paste errors
Disadvantage Only works with simple vocabularies
( Flat vocabularies, and some taxonomies)
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VOC2OWL
Tool created by MMIAllows to create automatic - bottom -up
ontologies from two basic structures of simple vocabularies: Flat vocabularies (e.g. phone directory) Hierarchical vocabularies (e.g.
taxonomies)JAVA - Eclipse standalone application
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Metadata
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Conversion Properties I/OFormat of the ASCII file to transform: tab or csv
Location of the ASCII file
Location where the ontology in OWL will be saved
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Ontology Conversion Properties
Namespace of the resources
Column from where the local names of the resources (individuals) will be created.
One class (at least) is always created.
More than one class can be created
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ResultParameters
id description units
Temperature_1water temperature from unit 00471 deg C
Temperature_2water temperature from unit 00822 deg C
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Ontology Conversion Properties
If treated as a hierarchy, there is no such primary class. All the lines in the ASCII file represent a hierarchy
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Example Hierarchy (GCMD)
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Has been tested !
About 50 vocabularies were converted to OWL for the MMI workshop “ Advancing Domain Vocabularies” (Aug, 2005)
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Why do we need all these ontologies ?
Workshop was about relating terms from one controlled vocabulary to another one.
Microsoft Excel was to hard to use for this purpose -:)
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Mapping results
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
47 participants and 12 hours of mapping time
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VINE : Vocabulary Integration Environment
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More…
• Advance the Marine Knowledge: 250,000 RDF triples (Ontologies + mappings)• They are available as:
• SOAP web services at: http://marinemetadata.org/webservices• Ontology files at: http://marinemetadata.org/ns
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Conclusions
• Solving semantic interoperability issues is fun.• We need to relate data producers vocabularies with standard vocabularies.• OWL is growing and growing in popularity more and more tools will be available.• VOC2OWL can help you !
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Our Guides
Roy Lowry, BODC Robert Arko, LDEO Julie Bosch, NOAA Ben Domenico, Unidata Karen Stocks, SDSC Steve Hankin, NOAA -
Ocean.US/DMAC
Mark Musen, Stanford Univ Michael Parke, Univ of Hawaii Lola Olsen, NASA Goddard Bob Weller, WHOI Dawn Wright, Oregon State
University
Steering Committee
Executive Committee
John Graybeal, MBARI. (PI) Philip Bogden, SURA/SCOOP
Stephen Miller, SIO. Francisco Chavez, MBARI.
Stephanie Watson, Texas A&M
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MMI:Your Handy Reference GuideMMI: http://marinemetadata.org
Voc2OWL: http://marinemetadata.org/voc2owl
Vine: http://marinemetadata.org/vine
Help Line: [email protected]
Ontologies: http://marinemetadata.org/ns
Term Search:
http://mmi.mbari.org:9600/mmi2/search.jsp
Tethys: http://marinemetadata.org/tethys