Gail HodgeGail HodgeInformation International Associates, Inc.Information International Associates, Inc.

US Geological Survey, ConsultantUS Geological Survey, Consultant

Joel SachsJoel SachsEbiquity Lab, University of Maryland Baltimore CountyEbiquity Lab, University of Maryland Baltimore County

From Here to There: Case Studies on a Path to

Semantic Web 2.0

From Here to There: Case Studies on a Path to

Semantic Web 2.0

22 March 2006 22 March 2006 Kobe, Japan Kobe, Japan

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

Thematic

Infrastructure

Regional

NBII Node Structure

Part of Multi-Sectored Approach

World Data Centers (WDC)World Data Centers (WDC)

Global Biodiversity Information Facility (GBIF)Global Biodiversity Information Facility (GBIF)

Clearinghouse Mechanism (CHM)Clearinghouse Mechanism (CHM)

Pacific Biodiversity Information Forum (PBIF)Pacific Biodiversity Information Forum (PBIF)

The Inter-American Biodiversity Information Network The Inter-American Biodiversity Information Network (IABIN)(IABIN)

NBII (US), CBIN (Canada)NBII (US), CBIN (Canada)

ERIN (Australia)ERIN (Australia)

State Heritage ProgramsState Heritage ProgramsGAP AnalysisGAP Analysis

County Park InformationCounty Park Information

GLOBAL

REGIONAL

NATIONAL

LOCAL

Information Management Challenges

Linking levels of:Linking levels of:

–Biological organizationBiological organization–Spatial organizationSpatial organization–Temporal organizationTemporal organization

Linking people across disciplines and organizationsLinking people across disciplines and organizations

Challenges Across Disciplines & Organizations

• Accessing data from diverse sources Accessing data from diverse sources

• Discipline - based practicesDiscipline - based practices

• Different terminologies and Different terminologies and

representations for conceptsrepresentations for concepts

• Sensitive dataSensitive data

• Conflicts of interestConflicts of interest

GOVERNMENTSGOVERNMENTS

UNIVERSITIESUNIVERSITIES

MUSEUMS

NGOsNGOs

“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”

“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)

The Vision for the Future

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

NBII Semantic Web Activities

• Semantic Prototypes in Research Ecoinformatics (SPIRE)

• NBII Terminology Web Services

• Involvement in Ecoterm

Semantic Prototypes in Research Ecoinformatics

• Background on the SPIRE Project

• Two SPIRE prototypes:• ELVIS• Swoogle

• Demo of SPARQL queries against integrated semantic web documents

Spire

Semantic Prototypes In Ecoinformatics

Spire

Semantic Prototypes In Ecoinformatics

UMBCUMBCEbiquityEbiquity

UMBCUMBCEbiquityEbiquity

UMD UMD MINDSWAPMINDSWAP

UMD UMD MINDSWAPMINDSWAP

NASANASAGSFCGSFC

NASANASAGSFCGSFC RMBLRMBL

Peace Peace

RMBLRMBLPeace Peace

UC DavisUC DavisICEICE

UC DavisUC DavisICEICE

NBIINBIINBIINBII

Prototype ApplicationsInformation RetrievalAgents

Invasive Species Forecasting System/Remote Sensing Data

Semantic CAIN DisseminationOntology Development

Food WebsEcological Interaction Ontologies

Semantic Web ToolsInfrastructure

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?”

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

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

• 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

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.

Slide with Relevant URLs

http://thesaurus.nbii.gov/SearchNBIIThesaurus/

http://spire.umbc.edu/ont/sparql_demo/query.php?demo=1What kind of food do herons eat?

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

What kind of food do herons eat?

Bufo-americanus = American Toad

Carassius-auratus = Goldfish

What kinds of fish do herons eat?

Cyprinus-carpio = Common Carp

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

Cyprinus-carpio = Common Carp

Pimephales-notatus = Bluntnosed Minnow

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

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

NBII Services Overview

text

Describe and Discover

www.NBII.gov

PORTAL

My.NBII.gov

Content Management Integrated/Federated SearchCollaboration Services

Database and Web Services Model ServicesGeospatial Services

ITIS DIGR CatalogThesaurus Mapping Geoparsing CatalogGeo-referencing

Discovery CatalogOperations

Dublin Core (plus)

UDDI / WSDL ??OGC/ISO FGDC/ISO

Distributed Applications Databases Websites Tools and Models

Consume

Integrated View

DistributedServices

Resource and Service Catalogs

DistributedResources

Resource Catalog

Geospatial Services Catalog

Geospatial Dataset

Resource Clearinghouse

Database and Web Services

Catalog

Model ServicesCatalog

Biocomplexity Thesaurus Web Services

http://thesaurus.nbii.gov/SearchNBIIThesaurus/

http://thesaurus.nbii.gov/SearchNBIIThesaurus/

“endangered species”“endangered species”

http://thesaurus.nbii.gov/SearchNBIIThesaurus/http://thesaurus.nbii.gov/SearchNBIIThesaurus/

“endangered species”“endangered species”

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

SKOS Example

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.

Example of Microformat Markup

<span class="vevent"> <a class="url" href="http://www.tiu.ac.jp/org/openforum2006/"> <span class="summary">Open Forum 2006</span><abbr class="dtstart" title="2006-03-20">March 20</abbr>- <abbr class="dtend" title="2006-02-22">22</abbr>, at the <span class="location">International Conference Center

Kobe, Port Island , Kobe City, Japan</span></a></span>

Where have we been? Where are we now?… & where are we planning to go?

System manuals

Data dictionaries

11179 E1

11179 E3

Termin

ologies, o

ntolo

gies, 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 Project11179 E2

38

Contact InformationGail HodgeGail Hodge

Information International Associates, Inc.312 Walnut Place

Havertown, PA 19083 USAPhone: +1 865-742-5430

E-mail: ghodge@iiaweb.com or gailhodge@aol.com

Joel SachsJoel SachsUniversity of Maryland Baltimore County

Toronto, CanadaPhone: +1 613-447-8653

E-mail: jsachs@cs.umbc.edu