australia’s virtual herbarium
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AUSTRALIA’S VIRTUAL HERBARIUM. A national collaborative model for integrated access to distributed biological information Jim Croft, Greg Whitbread Australian National Herbarium. Outline of presentation. Background to the AVH What is the AVH ? Aspects of the AVH Plant names, specimens - PowerPoint PPT PresentationTRANSCRIPT
AUSTRALIA’S VIRTUAL HERBARIUM
A national collaborative model for integrated access to distributed
biological information
Jim Croft, Greg WhitbreadAustralian National Herbarium
Outline of presentation
• Background to the AVH– What is the AVH ?
• Aspects of the AVH – Plant names, specimens– Plant images, plant identification tools
• Uses and users of the AVH– Botanical research– Community projects
• Summary
What is a Virtual Herbarium?
• The physical resources and biological information of a herbarium represented digitally
• On-line access to herbaria and to botanical information managed by herbaria
• Integrated access to botanical information from various sources in a herbarium and other on-line botanical information
What is the AVH?
• A collaborative project of the Australian Herbarium community–Digital–Collaborative–On-line–Integrated
• Partnership and shared access• Real-time access• Shared access to common authority files• Shared data-hosting, archiving and backup• Co-ownership
Where is the AVH?
• Spread across Australian herbaria
• Data distributed; resides with custodians
• Each herbarium has a portal to receive requests and to deliver data
• A common single query AVH interface in each herbarium polls all herbaria
Major Australian Herbaria
AVH Partners
State Herbarium of South Australia
Queensland Herbarium
Australian National Herbarium
Northern Territory Herbarium
Tasmanian Herbarium
Industry Partner:KE Software
National Herbarium of Victoria
National Herbarium of New South Wales
Western Australian Herbarium
Australian Biological Resources Study
Why is there an AVH?
• Pressure on Herbaria to work more efficiently
• Demand for access to larger amounts of data
• Demand to access data more quickly
• Demand to view data in different ways
• Pressure on herbaria to appear and to be more responsive to community needs
Potential users of the AVH
• The participating herbaria have access to all the data at the highest precision
• Public access filter restricts access to work in progress, sensitive locality data, etc.
• Research and education
• Public general interest
• Access to conservation agencies, land managers, environmental decision makers
There is some urgency …
• Historical ignorance
• Australia’s biodiversity has been damaged
• At risk from inappropriate land management practices
• We know a lot about what not to do
• Redressing the damage, and managing better for the future, requires sound information
• Sustainable natural resource management needs scientific knowledge– what was there and where it occurred– what is there now
There is some urgency …1907
2002
• > 20,000 species of higher plants• > 64,000 available names• Extensive synonymy (4 names per plant)• Many alternative taxonomic concepts
• 8 major government-funded herbaria• Similar number of university herbaria
• > 6,500,000 specimens in Aust. herbaria• 50-100 data elements per specimen• Several Kb per specimen (excl. images)
What is the problem?
Specimen data from major herbaria
Herbarium database status
• $10M over 5 years to database all major Australian herbarium collections
• $10 million: - $ 4 million Commonwealth- $ 4 million State/Territory- $ 2 million private
• Initial focus on capture of herbarium specimen data
• Ultimate aim a complete flora information system
The AVH Agreement
Australia’s Virtual Herbarium
On-line access to herbarium specimen information and botanical knowledge
What do we want to know?• What species does a plant belong to?
• What is its name?
• What other species is it related to?
• What does it look like?
• Where does it grow?
• Where might it grow?
• What other species grow with it?
• What species grow in a defined area?
• How did they get there?
Data refinement
datadata
informationinformation
knowledgeknowledge
actionaction
Increasing refinement & utility of data
the real worldthe real world
observationsobservations
Envir. decision making• conservation• restoration biology• resource mgmt• utilisation
Policy & strategy• government• corporate• individual
Botanical Literature
Herbarium Specimens
Specimen data
Collections data:
– Scientific name– Collection date– Collector name & number– Location– Soils– Habitat (incl. topography)– Vegetation community– Associated species– Plant features, e.g. colour
Core information is from herbarium specimens
Specimen Data Capture
A Herbarium Database Structure
Race to database
Need for semantic standard recognized
HISPID
Exchange Distributed query
Standard syntax
Need for common semantic schema recognized Botanica
l ontology?
Evolution of the AVH
How does the AVH work?
AVH General ArchitectureClientsCommon Web
portalsGatewaysDatabases
Australia’s Virtual Herbarium
Some views of the data
Australian Plant Name Australian Plant Name Index (APNI)Index (APNI)
www.anbg.gov.au/apni
http://www.chah.gov.au/avh.html
Acaciasalicina
Incu
rved
Incu
rved
Rec
urve
d
Plant distribution analysis
?Incurved Recurved
Pultenaea species in eastern Australia
?
Predictive Modelling
Predictive Modelling
• On-line Flora information systems
• Generally regionally based
• Integrating:
– Plant names– Descriptive Flora treatments– Illustrations– Distributions
Related Products
Flora Information Systems
Botanical illustrations
National Plant Photograph IndexSearch on-line
Some digital imagesavailable
35,000 images ofAustralian plantsand vegetation
Portraits of Plant species
www.anbg.gov.au/anbg/photo-collection/
High resolution image oftype specimen of Austrobaileyadownloaded over the Internetfrom the Herbarium of theNew York Botanical Garden
Type Images on demand
Interactive Plant Identification
Invasive Plant Notification
Why it is working
• Communication - CHAH, few herbaria
• Collaboration - long-standing, data sharing, overcoming Australia’s Federal/State system
• Champions - management, public
• Lobbying and profile of herbaria
• Relevance of product
• And now…we need to maintain commitment to project
Summary
Australia’s Virtual Herbarium:
• A collaborative national project
• Making botanical information available
• Using modern technology
• Using cheap readily available components
• A model for regional and global cooperation
Acknowledgements
State Herbarium of South Australia
Queensland Herbarium
Australian National Herbarium
Northern Territory Herbarium
Tasmanian Herbarium
Industry Partner:KE Software
National Herbarium of Victoria
National Herbarium of New South Wales
Western Australian Herbarium
Australian Biological Resources Study