1. Gail Hodge Information International Associates, Inc. US Geological Survey, Consultant Joel Sachs Ebiquity Lab, University of Maryland Baltimore County From Here to There: Case Studies on a Path to Semantic Web 2.0 22 March 2006  Kobe, Japan

2. Outline Describe the National Biological Information Infrastructure (NBII) Highlight challenges in biodiversity- and eco- informatics Describe the “to be” scenario Present several NBII-related Semantic Web projects in biodiversity and ecosystem domains

3. Thematic Infrastructure Regional NBII Node Structure

4. Part of Multi-Sectored Approach World Data Centers (WDC) Global Biodiversity Information Facility (GBIF) Clearinghouse Mechanism (CHM) Pacific Biodiversity Information Forum (PBIF) The Inter-American Biodiversity Information Network (IABIN) NBII (US), CBIN (Canada) ERIN (Australia) State Heritage Programs GAP Analysis County Park Information GLOBAL REGIONAL NATIONAL LOCAL

5. Information Management Challenges Linking levels of: –Biological organization –Spatial organization –Temporal organization Linking people across disciplines and organizations

6. Challenges Across Disciplines & Organizations Accessing data from diverse sourcesAccessing data from diverse sources Discipline - based practicesDiscipline - based practices Different terminologies and representations for conceptsDifferent terminologies and representations for concepts Sensitive dataSensitive data Conflicts of interestConflicts of interest GOVERNMENTS UNIVERSITIES MUSEUMS NGOs

7. “As-Is” Situation Interaction between information resources is often “hard coded” While partnerships are important they take time to develop Difficult to respond quickly to new research areas or practical needs Does not promote discovery and “new connections”

8. “To-Be” Situation Fluid and flexible Connections (“partnerships”) made on the fly Local, regional, national and global information able to be integrated Desired situation requires understanding of content including: –Assessment of provenance and trustworthiness –Understanding semantics (across disciplines, languages and cultures) –Understanding the resource’s behavior (what you can do with it)

9. The Vision for the Future

10. What Is Needed? Semantic Web approaches Distributed web services available through a registry Metadata to describe who, why and how Semantics to improve understanding and reuse

11. NBII Semantic Web Activities Semantic Prototypes in Research Ecoinformatics (SPIRE) NBII Terminology Web Services Involvement in Ecoterm

12. Semantic Prototypes in Research Ecoinformatics Background on the SPIRE Project Two SPIRE prototypes: ELVIS Swoogle Demo of SPARQL queries against integrated semantic web documents

13. Spire Semantic Prototypes In Ecoinformatics Spire Semantic Prototypes In Ecoinformatics UMBCEbiquityUMBCEbiquity UMDMINDSWAPUMDMINDSWAP NASAGSFCNASAGSFC RMBLPeaceRMBLPeace UC Davis ICE ICE NBIINBII Prototype Applications Information Retrieval Agents Invasive Species Forecasting System/Remote Sensing Data Semantic CAIN Dissemination Ontology Development Food Webs Ecological Interaction Ontologies Semantic Web Tools Infrastructure

14. ELVIS (The Ecosystem Location Visualization and Information System) ? ELVIS is a suite of tools motivated by the belief that food web structure plays a role in the success or failure of potential species invasions. Answer the question “what are likely prey and predator species of the invader in the new environment?”

15. ELVIS Components Species List Constructor –Click a location, get a species list –Data integrated from NatureServe; Gap Analysis; Park Inventories; etc. Food Web Constructor –Input a species list, get a food web –Uses a database of several hundred published food webs to predict likely trophic interactions Evidence Provider –Drill down on predicted trophic links to see the evidence for the prediction

16. Swoogle: Motivation (Google + Web) has made us all smarter Something similar is needed by people and software agents for finding information on the semantic web

17. Allows users to search for both ontologies and instance data in a number of ways. OntologyRank algorithm returns Semantic Web documents according to their “importance” to the semantic web. A “triple shop” allows a user to select amongst returned documents. Swoogle

18. Pulling it Together: Triple Shop Demo The SPIRE Triple Shop allows a user to specify the URLs of arbitrary semantic web documents, and to issue SPARQL queries against the union of those documents. –It is alpha-version, and is not robust in the general case. However … We have expressed each of our 259 food webs in OWL, using the SpireEcoConcepts ontology. We have expressed a number of species accounts from the Animal Diversity Web in OWL, using the ETHAN ontology. For efficiency, we have precomputed all triples entailed by the original OWL files identified for this demo. –We are experimenting with ways to do the reasoning in real time. The user can issue SPARQL queries over the integrated data.

19. Slide with Relevant URLs http://thesaurus.nbii.gov/SearchNBIIThesaurus/ http://spire.umbc.edu/ont/sparql_demo/query.php?demo=1 What kind of food do herons eat? http://spire.umbc.edu/ont/sparql_demo/query.php?demo=2 What kind of pond-living or marsh-living fish do herons eat? Show known behavioral characteristics of those kinds of fish http://spire.umbc.edu/ont/sparql_demo/query.php?demo=4 What kind of pond-living or marsh-living fish do herons eat? http://spire.umbc.edu/ont/sparql_demo/query.php?demo=3

20. What kind of food do herons eat?

21. Bufo-americanus = American Toad Carassius-auratus = Goldfish

22. What kinds of fish do herons eat?

23. Cyprinus-carpio = Common Carp

24. What kinds of pond-living or marsh-living fish do herons eat?

25. Cyprinus-carpio = Common Carp Pimephales-notatus = Bluntnosed Minnow

26. What kind of pond-living or marsh-living fish do herons eat? Show known behavioral characteristics of those kinds of fish.

28. NBII Web Services Web service for the Biocomplexity Thesaurus Prototype developed between Biocomplexity Thesaurus and GEMET Web service for the Integrated Taxonomic Information System – authority file of biological organisms and their taxonomies

29. NBII Services Overview

30. Biocomplexity Thesaurus Web Services http://thesaurus.nbii.gov/SearchNBIIThesaurus/

31. “endangered species”

32. http://thesaurus.nbii.gov/SearchNBIIThesaurus/ “endangered species”

33. Involvement in Ecoterm –Subgroup of the Interagency/International Collaboration on Ecoinformatics Technical Working Group –Multilingual issues –Multi-discipline/domain issues –Prototypes in terminology registries, metadata and exchange formats –Using NBII Web Service Registry to describe web services across the Ecoterm organizations –May 2006 meeting will focus on identification and definition of standard environmental relationships

34. SKOS Example

35. Looking Forward: Microformats and the Semantic Web Microformats are a mechanism for embedding semantics in XHTML documents, using existing XHTML elements and attributes. –Much easier to modify existing authoring applications to incorporate microformats than RDF. –Already a larger user base (primarily bloggers) than for RDF. SPIRE is experimenting with microformats to express ecological field data.

36. Example of Microformat Markup Open Forum 2006 March 20 - 22, at the International Conference Center Kobe, Port Island, Kobe City, Japan

37. Where have we been? Where are we now?… & where are we planning to go? System manuals Data dictionaries 11179 E1 11179 E3 Terminologies, ontologies, etc. XML & related standards Semantic grids Semantics management for data Semantics services (SSOA) Complex semantics management Data engineering/XML Data Data Standards/Data Administration XMDR Project 11179 E2

38. 38 Contact Information Gail Hodge Information International Associates, Inc. 312 Walnut Place Havertown, PA 19083 USA Phone: +1 865-742-5430 E-mail: ghodge@iiaweb.com or gailhodge@aol.comghodge@iiaweb.comgailhodge@aol.com Joel Sachs University of Maryland Baltimore County Toronto, Canada Phone: +1 613-447-8653 E-mail: jsachs@cs.umbc.edujsachs@cs.umbc.edu