gail hodge information international associates, inc. us geological survey, consultant joel sachs...
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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
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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
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Thematic
Infrastructure
Regional
NBII Node Structure
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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
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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
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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
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“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”
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“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)
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The Vision for the Future
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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
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NBII Semantic Web Activities
• Semantic Prototypes in Research Ecoinformatics (SPIRE)
• NBII Terminology Web Services
• Involvement in Ecoterm
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Semantic Prototypes in Research Ecoinformatics
• Background on the SPIRE Project
• Two SPIRE prototypes:• ELVIS• Swoogle
• Demo of SPARQL queries against integrated semantic web documents
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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
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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?”
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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
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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
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• 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
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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.
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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
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What kind of food do herons eat?
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Bufo-americanus = American Toad
Carassius-auratus = Goldfish
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What kinds of fish do herons eat?
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Cyprinus-carpio = Common Carp
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What kinds of pond-living or marsh-living fish do herons eat?
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Cyprinus-carpio = Common Carp
Pimephales-notatus = Bluntnosed Minnow
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What kind of pond-living or marsh-living fish do herons eat? Show known behavioral characteristics of those kinds of fish.
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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
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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
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Biocomplexity Thesaurus Web Services
http://thesaurus.nbii.gov/SearchNBIIThesaurus/
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http://thesaurus.nbii.gov/SearchNBIIThesaurus/
“endangered species”“endangered species”
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http://thesaurus.nbii.gov/SearchNBIIThesaurus/http://thesaurus.nbii.gov/SearchNBIIThesaurus/
“endangered species”“endangered species”
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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
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SKOS Example
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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.
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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>
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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
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Contact InformationGail HodgeGail Hodge
Information International Associates, Inc.312 Walnut Place
Havertown, PA 19083 USAPhone: +1 865-742-5430
E-mail: [email protected] or [email protected]
Joel SachsJoel SachsUniversity of Maryland Baltimore County
Toronto, CanadaPhone: +1 613-447-8653
E-mail: [email protected]