Gail Hodge

1
From Here to There Case Studies on a Path to
Semantic Web 2.0
22 March 2006 ? Kobe, Japan

• Gail Hodge
• Information International Associates, Inc.
• US Geological Survey, Consultant
• Joel Sachs
• Ebiquity Lab, University of Maryland Baltimore
  County

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
NBII Node Structure

• Regional

• Thematic

• Infrastructure

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
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 sources
• Discipline - based practices
• Different terminologies and representations for
  concepts
• Sensitive data
• Conflicts of interest

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 resources 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
UMBC Ebiquity
Spire Semantic Prototypes In Ecoinformatics
Prototype Applications Information
Retrieval Agents
UMD MINDSWAP
UC Davis ICE
Semantic CAIN Dissemination Ontology Development
NBII
Semantic Web Tools Infrastructure
NASA GSFC
RMBL Peace
Invasive Species Forecasting System/Remote
Sensing Data
Food Webs Ecological Interaction Ontologies
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
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.

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//spire.umbc.edu/ont/sparql_demo/query.php?de
mo1
What kind of food do herons eat?
What kind of food do herons eat?
http//spire.umbc.edu/ont/sparql_demo/query.php?de
mo2
What kind of pond-living or marsh-living fish do
herons eat?
http//spire.umbc.edu/ont/sparql_demo/query.php?de
mo3
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?de
mo4
http//thesaurus.nbii.gov/SearchNBIIThesaurus/
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What kind of food do herons eat?
21
Carassius-auratus Goldfish
Bufo-americanus American Toad
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.
27
(No Transcript)
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
http//thesaurus.nbii.gov/SearchNBIIThesaurus/
32
endangered species
http//thesaurus.nbii.gov/SearchNBIIThesaurus/
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

• ltspan class"vevent"gt
• lta class"url" href"http//www.tiu.ac.jp/org/open
  forum2006/"gt
• ltspan class"summary"gtOpen Forum 2006lt/spangt
• ltabbr class"dtstart" title"2006-03-20"gtMarch
  20lt/abbrgt-
• ltabbr class"dtend" title"2006-02-22"gt22lt/abbrgt,
  
• at the ltspan class"location"gtInternational
  Conference Center Kobe, Port Island , Kobe City,
  Japanlt/spangt
• lt/agt
• lt/spangt

37
Where have we been? Where are we now? where
are we planning to go?
Semantic grids
System manuals
Semantics services (SSOA)
11179 E3
Data dictionaries
11179 E1
XML related standards
XMDR Project
11179 E2
Terminologies, ontologies, etc.
Complex semantics management
Data engineering/XML Data
Semantics management for data
Data Standards/Data Administration
38
Contact Information

• Gail Hodge
• Information International Associates, Inc.
• 312 Walnut Place
• Havertown, PA 19083 USA
• Phone [phone]
• E-mail ghodge_at_iiaweb.com or gailhodge_at_aol.com

Joel Sachs University of Maryland Baltimore
County Toronto, Canada Phone 1
613-447-8653 E-mail jsachs_at_cs.umbc.edu