1. Steven Perry Dave Vieglais

2. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Overview WASABI is a framework for building scientific data networks based on RDF, OWL, and open data access protocols.

3. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Objective Build a data access network that… – Can handle many types objects – Is resilient to changes in data models – Refers to objects with GUIDs – Allows fast & efficient searches – Allows incremental harvesting – Simplifies creation of client software

4. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics RDF and OWL RDF described by OWL allows… – Machine readable controlled vocabularies – Distinction between classes and properties – Data objects as resources identified with globally unique LSIDs – Query languages to examine patterns of relationships between objects

5. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Framework Components Provides access to RDF data sets through multiple protocols

6. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Framework Components Provides access to RDF data sets through multiple protocols Libraries for building client applications

7. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Framework Components Provides access to RDF data sets through multiple protocols Libraries for building client applications Web-based client for accessing data on a wasabi network

8. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics A Simple Network

9. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics

10. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Server Server – Stores a cached copy of source data in RDF format called a data set – Each data set is bound to one or more protocols handlers – Standard protocols include OAI, SimpleLSID, and SPARQL

11. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Server

12. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Loading Data

13. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Loading Data Loading RDF Data – RDF data can be loaded from one or more files directly into Wasabi – Wasabi will not assign new LSIDs – Wasabi checks to see if any data objects are new or have changed and can scan for deleted data objects

14. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Loading Data

15. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Loading Data Loading Non-RDF Data – Wasabi uses a synchronizer program to generate RDF from SQL output or delimited files – Synch program must know about your source data format – Wasabi can assign LSIDs if needed – Wasabi checks to see if any data objects are new or have changed and can scan for deleted data objects

16. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics OAI-PMH

17. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics OAI-PMH Open Archive Initiative Protocol for Metadata Harvesting – Wasabi implementation allows efficient harvesting – Supports incremental harvesting “What objects have changed since Oct-02-2006?” – Notifies clients about deletions

18. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics LSID Resolution

19. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics LSID Resolution Life Science Identifier Metadata Resolution – Wasabi supports a simple HTTP-GET LSID metadata resolution service – Supports metadata resolution “What is the RDF metadata for urn:lsid:auth.org:ns:23?” – Compliant LSID resolution through plug-in for IBM LSID resolver.

20. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics LSID Resolution

21. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics SPARQL

22. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics SPARQL SPARQL Protocol – SPARQL is the W3C candidate for querying RDF – SPARQL protocol bound to HTTP-GET – ASK and SELECT queries return SPARQL XML results – DESCRIBE and CONSTRUCT queries return RDF/XML results

23. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics SPARQL SPARQL Query Language Example – “What is urn:lsid:auth.org:person:3424?” DESCRIBE <rdf:RDF xmlns:j.0=“http://tdwg.org/onto/bdi/person.owl#” xmlns:rdf:”http://www.w3.org/1999/02/22-rdf-syntax-ns#”> Steven Perry

24. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics SPARQL SPARQL Query Language Example – “What is the genus of the specimen urn:lsid:auth.org:spec:657?” SELECT ?genus WHERE { ?txname ?txname ?genus } ?genus = “Heteractis”

25. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Server OAI, SPARQL, and LSID are standard protocols, so Wasabi services can be used by non-Wasabi clients.

26. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics

27. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Client Library

28. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Client Library Client Library – Contains implementations of clients for protocols used by Wasabi – Can be included in projects that need to communicate with Wasabi servers – Programmatic access to services (hides XML messaging layer) – Provides status and progress listeners – Can be used to query non-Wasabi implementations of OAI or SPARQL

29. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics

30. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Indexer

31. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Indexer Indexer – Harvests from 1 or more RDF sources – Sources can be Wasabi servers (via OAI) sets of RDF files, etc. – Multiple types of indices can be fed from a single set of descriptions – Indexers can filter by object type, etc. – Indexers should understand incremental updates and deletions

32. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Indexer

33. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Indexer

34. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Indexer

35. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics

36. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Portal

37. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Portal Portal – Customizable human interface that allows access to 1 or more Wasabi servers – Default portal requires a Lucene index of harvested data. Most portal queries are against the index – To retrieve and display data objects, the portal makes repeated LSID resolution calls so servers can log access

38. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Wasabi Portal Portal – Portal automatically configures search forms and renderers based on downloaded OWL ontologies – Provides simple search, advanced search, ontology browsing, and export of downloaded data to CSV or RDF files

39. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics A More Realistic Network

40. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Implementation – http://wasabi.ecoforge.net – Java 1.5 with Spring, Jena, Lucene, and more – Server requires servlet container (Tomcat, WebLogic, etc.) – Server requires JDBC database (MySQL, PostgreSQL, etc.)

41. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Current State – Server, Client Library and Indexer components are feature complete – Portal is still under development – Using experimental OWL data models; awaiting TDWG ontology.

42. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Future Plans – Complete portal – Construct the FishNet2 network (25+ servers) – Construct the PlantCollections network (15+ servers)

43. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Conclusion WASABI is a framework for building scientific data networks based on RDF, OWL, and open data access protocols.

44. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Conclusion RDF allows us to share complex data models OWL allows machines to understand the data models and provides opportunities for extending models over time Standard protocols (OAI, LSID, & SPARQL) allow for integration across data networks and with the semantic web

45. W a s a b i Web Applications for the Semantic Architecture of Biodiversity Informatics Support Development of Wasabi is supported by the National Science Foundation as part of the Integrated Community Infrastructure (ICI) project.