1. Speeding up ontology creation of scientific terms. Luis Bermudez, John Graybeal, Montery Bay Aquarium Research Institute http://marinemetadata.org December 7, 2005

2. Marine Metadata Interoperability Initiative 1 Why are ontologies important At AGU we have 31 abstracts and 2 entire sessions related to ontologies

3. Marine Metadata Interoperability Initiative 2 Problem: Semantic Interoperability SSDS AOSN get me Data for Variable ocean_temperature (C) get me Data for Parameter temperature_1 (deg C)

4. Marine Metadata Interoperability Initiative 3 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.

5. Marine Metadata Interoperability Initiative 4 Controlled Vocabularies: Discovery of Data

6. Marine Metadata Interoperability Initiative 5 Controlled Vocabularies: Usage (tag the data collected)

7. Marine Metadata Interoperability Initiative 6 Problem: Semantic Interoperability semantics Standard vocabularies

8. Marine Metadata Interoperability Initiative 7 Harmonization DTD CommaSeparatedValues HTML TabSeparatedValues RelationalDatabase XML/XSD RDF Web Ontology Language (OWL) Language (OWL)

9. Marine Metadata Interoperability Initiative 8 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

10. Marine Metadata Interoperability Initiative 9 Fast introduction to OWL RDF Triples RDF Resources Classes - individuals - properties RDF Graph

11. Marine Metadata Interoperability Initiative 10 RDF: Triples, triples, triples

12. Marine Metadata Interoperability Initiative 11 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#Chlorophyllhttp://mmi.org/2005/08/gcmd-keyw#Chlorophyll URL: ftp://mmi.org/data-exampleftp://mmi.org/data-example Literal

13. Marine Metadata Interoperability Initiative 12 Looks like a class Looks like individuals of (members of) the class Parameter Classes Individuals Properties Property (Attributes)

14. Marine Metadata Interoperability Initiative 13 How are ontologies created? Conceptual direction strategy: Up - down Bottom - up Automation approach: Manual Automatic

15. Marine Metadata Interoperability Initiative 14 Up - down approach

16. Marine Metadata Interoperability Initiative 15 Bottom - up approach Body of Water Class RiverLake Has water Is inland body Has a relative defined channel LakeRiver Example: 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

17. Marine Metadata Interoperability Initiative 16 Bottom - up approach 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

18. Marine Metadata Interoperability Initiative 17 Bottom - up approach (cont.) ssds:Parameter aosn:Variable mmi:Parameter sweet:Property

19. Marine Metadata Interoperability Initiative 18 Manual (Ontology editor) List of more than 50 editors: http://www.xml.com/2002/11/06/Ontology_Editor_Survey.html Protégé

20. Marine Metadata Interoperability Initiative 19 Automatic Ontology in OWL Software Program transformation Properties file

21. Marine Metadata Interoperability Initiative 20 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)

22. Marine Metadata Interoperability Initiative 21 VOC2OWL Tool created by MMI Allows 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

23. Marine Metadata Interoperability Initiative 22

24. Marine Metadata Interoperability Initiative 23 Metadata

25. Marine Metadata Interoperability Initiative 24 Conversion Properties I/O Format of the ASCII file to transform: tab or csv Location of the ASCII file Location where the ontology in OWL will be saved

26. Marine Metadata Interoperability Initiative 25 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

27. Marine Metadata Interoperability Initiative 26 Result

28. Marine Metadata Interoperability Initiative 27 Ontology Conversion Properties If treated as a hierarchy, there is no such primary class. All the lines in the ASCII file represent a hierarchy

29. Marine Metadata Interoperability Initiative 28 Example Hierarchy (GCMD)

30. Marine Metadata Interoperability Initiative 29 Has been tested ! About 50 vocabularies were converted to OWL for the MMI workshop “ Advancing Domain Vocabularies” (Aug, 2005)

31. Marine Metadata Interoperability Initiative 30 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 -:)

32. Marine Metadata Interoperability Initiative 31 Mapping results 47 participants and 12 hours of mapping time

33. Marine Metadata Interoperability Initiative 32 VINE : Vocabulary Integration Environment

34. Marine Metadata Interoperability Initiative 33 More… Advance the Marine Knowledge: 250,000 RDF triples (Ontologies + mappings) They are available as: SOAP web services at: http://marinemetadata.org/webservices http://marinemetadata.org/webservices Ontology files at: http://marinemetadata.org/ns http://marinemetadata.org/ns

35. Marine Metadata Interoperability Initiative 34 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 !

36. Marine Metadata Interoperability Initiative 35 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

37. Marine Metadata Interoperability Initiative 36 MMI: Your Handy Reference Guide MMI: http://marinemetadata.orghttp://marinemetadata.org Voc2OWL: http://marinemetadata.org/voc2owlhttp://marinemetadata.org/voc2owl Vine: http://marinemetadata.org/vinehttp://marinemetadata.org/vine Help Line: ask@marinemetadata.orgask@marinemetadata.org Ontologies: http://marinemetadata.org/nshttp://marinemetadata.org/ns Term Search: http://mmi.mbari.org:9600/mmi2/search.jsp Tethys: http://marinemetadata.org/tethyshttp://marinemetadata.org/tethys