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Illinois Educational Digital Natural History Museum P. Bryan Heidorn University of Illinois at Urbana-Champaign pheidorn@uiuc.edu National Science Digital Library Biobrowser Biological Information Browsing Environment (BIBE) NSF Biological Databases and Informatics

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Illinois Educational Digital Natural History Museum


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illinois educational digital natural history museum

Illinois Educational Digital Natural History Museum

P. Bryan Heidorn

University of Illinois at Urbana-Champaign

pheidorn@uiuc.edu

biological information browsing environment bibe
Biological Information Browsing Environment (BIBE)
  • NSF Biological Databases and Informatics
  • Indexing, searching and visualizing biological information
  • Augmenting dichotomous keys
self repairing biodiversity database
Self-repairing Biodiversity Database
  • NSF Information Technology Research
  • Wireless access to flora and fauna in the field
  • Synchronous Collaboration with experts
  • Mapping Distributions of species
slide7

Entomologist

Botanist

BaseServer

Internet

FieldServer

Field Wireless

workshop on biodiversity digital library design
Workshop on Biodiversity Digital Library Design
  • Five Components
    • Survey Support Services
    • Collection searching
    • Federation of EcoSystem species data
    • Remote Sensing and Geographic Information Systems
    • Decision Support Analysis and Publishing
dl software requirements
DL Software Requirements
  • Needs to meet biodiversity needs
  • Low Cost for citizen groups and governments
  • Ease of use
  • Management tools
  • Information sharing
  • Collaborative development and use
remote sensing and gis
Remote Sensing and GIS
  • Activities
    • Identification of sites
    • Historical/Seasonal conditions
    • Distributions
    • Monitoring abiotics (siltation, tepidity, pH, water temperature,
    • Socioecosystem overlays, land use, weather
    • Reports and Proposals
rs requirements
RS Requirements
  • Sufficient resolution: 1m?
  • Timeliness
  • Reliability
  • Continuity of service
  • Costs
  • Redistribution of images
  • Image processing / Classification
    • clustering, false color, forest-type, wetland
  • Repackaging for reports
rs requirements12
RS Requirements
  • Tools need to meet needs
  • Water cover
  • Forest cover
  • Leaf-out time
gis requirements
GIS Requirements
  • Land use reports
  • Geopolitical Units
  • Point distribution and GPS
  • Extrapolation / GAP-like
  • Predictive modeling
self publishing
Self Publishing
  • Sharing Findings
  • Post Aerial images
  • Post Classification / Image processing
training
Training
  • Evaluation Procedures
  • Verification
  • Use of RS & GIS
community biology collections
Community Biology Collections
  • Virtual, distributed natural history collections (one per school or community)
  • Specimen data
  • Species data
  • Ecology: distribution and interactions
  • Teacher enhancement
  • Biology information library and portal
  • NSDL infrastructure
features of community biology collections
Features of Community Biology Collections
  • Inquiry-based (observation and research)
  • Multimedia (physical collection optional)
  • Low-cost creation and viewing tools
  • Permanent collections
  • Quality verification
advantages
Advantages
  • Inquiry-Based Learning
    • Ask activity-oriented
    • Investigate students conduct field and library research
    • Create fact sheets
    • Discuss with peers and professionals
    • Reflect permanent keys of local flora and fauna
  • Research
curriculum integration
Curriculum Integration
  • Teacher certification
  • New teacher training
  • Science club and advanced placement programs
  • Student mobility
  • Cross-curricular activities
    • Biology
    • Earth science
    • Social science
specimen data
Specimen Data
  • Name
  • Location
  • Collector
  • Description
  • References
  • Images, Sounds
specimen data example
Specimen Data Example
  • Name: Danaus plexippus/Monarch butterfly
  • Location: Open weedy area
  • Collector: Jim McKay
  • Description: Orange and black, four inch wing span
  • References: Opler, P. (1992). A field guide to eastern butterflies. Boston: Houghton Mifflin.
taxon fact sheets
Size

Food

Flight habits

Taxon Fact Sheets
  • Summary information about a species
  • Name
  • Editor
  • Description
  • Distribution
  • References
  • Images, Sounds
taxon fact sheet example
Size: 3 3/8 - 4 7/8 inches

Food: Flower nectar

Flight habits: Slow, gliding

Taxon Fact Sheet Example
  • Name: Danaus plexippus/Monarch butterfly
  • Editor: Jim McKay
  • School: Pekin High
  • Description: Black and orange, scent patch on underside
  • Distribution: Statewide
  • References: Opler, P. (1992). A field guide to eastern butterflies. Boston: Houghton Mifflin.
taxon fact sheet example24
Taxon Fact Sheet Example

Danaus plexippus/Monarch butterfly

quality control
Quality Control
  • On-line reports with quality tags
  • Peer review
  • Teacher review
  • State review
    • Environmental biology internships
    • Illinois Natural History Survey
infrastructure
Infrastructure
  • Web-based and Java for accessibility
  • Research, state, local servers
  • Connection to NSF/NSDL as peer
  • Borrow heavily from Tropicos and VAH
  • Learning technology hubs
  • Z39.50 federation
some features
Some features
  • Based on observation and research
  • Multimedia without physical collection
  • Low cost creation and viewing tools
  • Persistent components
  • Quality verification
what is it good for
What is it good for?
  • Learning
    • Active, product oriented learning
    • Students conduct field and library research
    • Peer and professional evaluation
    • Part of professional project
    • Student Publishing - Keys, Local Flora/Fauna
  • Research
specimen data29
Specimen Data
  • Name
  • Location
  • Collector
  • Description
  • References
  • Images, sounds
taxon fact sheets30
Conservation status

Allies

Natural history notes

….

Taxon Fact Sheets
  • Summary information about a species
  • Name
  • Editor
  • Description
  • Distribution
  • References
  • Keys
  • Images, Sounds
quality control31
Quality Control
  • Most reports stay on line but with Quality tags.
  • Peer review
  • Teacher review
  • School review
  • State Review
tasks
Tasks
  • Participants
    • Teachers and Schools
    • Herbaria
  • Framework for Treatments
  • Input Screens
  • Database Structure
  • Services (dot maps, compendia caching, account management, …)
webvibe web base information browsing

WebVIBE: Web-Base Information Browsing

Vector model retrieval

Point Of Interest (POI)

Document Clustering

Remote Collections

projects
Projects
  • Opler, Paul A., Harry Pavulaan, and Ray E. Stanford (coordinators). 1995. Butterflies of North America. Jamestown, ND Northern Prairie Wildlife Research Center Home Page. http://www.npwrc.usgs.gov/resource/distr/lepid/bflyusa/bflyusa.htm. Where we indexed some butterflies.
databases
Databases
  • Missouri botanical IMLS http://hoya.mobot.org/imls/
  • The New York Botanical Garden http://www.nybg.org/bsci/herb/ Type imaging project
  • The CalFlora Species Database
  • http://elib.cs.berkeley.edu/calflora/about.html
slide37
USDA
  • THE USDA Plants Database http://plants.usda.gov/plants/
  • Integrated Taxonomic Information System (ITIS)http://www.itis.usda.gov/index.html
features
Features
  • Retrieval Set Size
  • Stack Size
  • Disambiguation
    • Motion
    • Highlighted influencing POIs
  • Lasso collections of Icons
features under development or underdeveloped features
Features under Development (or underdeveloped features)
  • Faceted Retrieval
  • Similarity Based Retrieval
  • Data Mining
  • Data Fusion
  • Federated Search
faceted retrieval
Faceted Retrieval
  • Semi-structured field search
  • Trees, to 25 m, crowns narrow. Bark of young trunks and branches reddish brown, when mature becoming pinkish white to light red (starkly white in interior Alaska; D. F.Murray, pers. comm.), smooth, exfoliating in thin sheets. Twigs glabrous, covered with conspicuous resinous glands…..
similarity based retrieval
Similarity Based Retrieval

Statistical Similarity - such as the cosine measure.

data mining
Data Mining
  • Conversion of free text to another format
  • “Trees, to 25 m, crowns narrow”
  • Plant height in meters, color, texture..
  • Free text to DELTA
  • Intelligent similarity
    • round > oval > lancolate
data fusion
Data Fusion
  • Multiple sources
  • FNA, CalFlora, USDA Plants, NYBG Herbarium…
federated search
Federated Search
  • Across collection and locations
  • ZBIG - Z39.50
  • Biological XML Data Interchange Standard
  • Taxonomic Data Working Group