22 March 2006

Kobe, Japan
From Here to There:
Case Studies on a Path to
Semantic Web 2.0
Gail Hodge
Information International Associates, Inc.
US Geological Survey, Consultant
Joel Sachs
Ebiquity Lab, University of Maryland Baltimore County
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
NBII Node Structure


Regional
Thematic

Infrastructure
Part of Multi-Sectored Approach
GLOBAL
REGIONAL
World Data Centers (WDC)
Global Biodiversity Information Facility (GBIF)
Clearinghouse Mechanism (CHM)
Pacific Biodiversity Information Forum (PBIF)
The Inter-American Biodiversity Information Network
(IABIN)
NATIONAL
NBII (US), CBIN (Canada)
ERIN (Australia)
LOCAL
State Heritage Programs
GAP Analysis
County Park Information
Information Management Challenges
Linking levels of:
–Biological organization
–Spatial organization
–Temporal organization
Linking people across disciplines and organizations
Challenges Across Disciplines &
Organizations
• Accessing data from diverse sources
NGOs
• Discipline - based practices
• Different terminologies and
representations for concepts
MUSEUMS
• Sensitive data
GOVERNMENTS
UNIVERSITIES
• Conflicts of interest
“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
UMBC Prototype Applications
Ebiquity Information Retrieval
Agents
Spire
UMD
MINDSWAP
Semantic Web Tools
Infrastructure
NASA
GSFC
UC Davis
ICE
Semantic CAIN Dissemination
Ontology Development
NBII
Semantic Prototypes In
Ecoinformatics
Invasive Species Forecasting
System/Remote Sensing Data
RMBL
Peace
Food Webs
Ecological Interaction Ontologies
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
Swoogle
• 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.
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
What kind of food do herons eat?
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?
http://spire.umbc.edu/ont/sparql_demo/query.php?demo=3
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
http://thesaurus.nbii.gov/SearchNBIIThesaurus/
What kind of food do herons eat?
Carassius-auratus = Goldfish
Bufo-americanus = American Toad
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
www.NBII.gov
My.NBII.gov
PORTAL
Integrated View
Distributed
Services
ITIS
Content Management
Collaboration Services
Integrated/Federated Search
Database and Web
Services
Geospatial Services
Model Services
Thesaurus
DIGR
Catalog
Mapping
Georeferencing
Geoparsing
Catalog
Discovery
Operations
Catalog
Resource
Catalog
Resource and
Service Catalogs
Distributed
Resources
Dublin Core(plus)
Geospatial
Services
Catalog
Geospatial
text
Dataset
Resource
Clearinghouse
Database and
Web Services
Catalog
Model
Services
Catalog
OGC/ISO
FGDC/ISO
UDDI/ WSDL
??
Describe and Discover
Distributed Applications
Consume
Databases
Websites
Tools and Models
Biocomplexity Thesaurus Web Services
http://thesaurus.nbii.gov/SearchNBIIThesaurus/
“endangered species”
http://thesaurus.nbii.gov/SearchNBIIThesaurus/
“endangered species”
http://thesaurus.nbii.gov/SearchNBIIThesaurus/
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
11179 E3
Data dictionaries
11179 E1
XML & related standards
XMDR Project
11179 E2
Complex semantics management
Data engineering/XML Data
Data Standards/Data Administration
Semantics management for data
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.com
Joel Sachs
University of Maryland Baltimore County
Toronto, Canada
Phone: +1 613-447-8653
E-mail: jsachs@cs.umbc.edu
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