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					     AVH - Australia’s Virtual Herbarium
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                Jim Croft
Centre for Plant Biodiversity Research
   Australian National Herbarium
Australia’s Virtual Herbarium:
      storing and interchanging
        botanical data on-line

                Jim Croft
 Centre for Plant Biodiversity Research
    Australian National Herbarium
            jrc@anbg.gov.au
    http://www.anbg.gov.au/jrc/
  AVH - The Big Questions
The 6 Ws:
            Who?
             What
            Where?
            When?
            Why?
            hoW?
AVH - The Big Questions
     What is the AVH?
Why should the AVH happen?
Where does the AVH happen?
Who does the AVH happen for?
When does the AVH happen?
 hoW does the AVH happen?
     Whence the AVH?
    What is a Herbarium?
• A physically and administratively secure
  building
• A managed archival scientific collection of
  preserved plant specimens
• A research environment and resource for
  botanical systematic and taxonomic resource
• A taxonomic, spatial and temporal
  information base for botanical research,
  environmental decision-making and public
  information
Collecting specimens
Platyzoma micropyllum
Platyzoma micropyllum
Herbarium Specimens
Herbarium Specimens
Compactus storage units
Compactus storage units
Botanical Library
Botanical literature
Specimen Data Capture
Public Reference Herbarium
        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, providing:
  – Partnership and shared access to each
    others data
  – Real-time access to current working data
  – Shared access to common authority files
  – A shared development environment
  – Opportunity to shared data-hosting,
    archiving and off-site backup.
  – Co-ownership of the final product
The pilot: distribution of Acacia aneura, mulga
The pilot: distribution of Acacia aneura, mulga
Acacia aneura: Distribution of specimens from each herbarium
Overlays
Geocode accuracy
Survey data
A Herbarium Database Structure
    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 be and appear
  more responsive to community needs
      What is the Problem?
•   > 18,000 species of higher plants
•   > 64,000 available names
•   Extensive synonymy (4 names per plant)
•   8 major government-funded herbaria
•   Similar number of university herbaria
•   > 6,500,000 specimens Aust. herbaria
•   50-100 data elements per specimen
•   Several Kb per specimen (excl. images)
      Where is the data?
• In each herbarium (largest 1.3 million
  specimens)
• Pooling data centrally not acceptable for
  operational, political and emotional
  reasons.
• Therefore we need a distributed data
  management and access solution,
  maintaining and ensuring custodial
  responsibility
      Where is the data?
• Images compound the problem
• Several Kb and up for live plant images
  (possibly 100,000 available)
• Specimen images need high resolution, up
  to 20 Mb or more
• Need to be sub-sampled for web display
• At least 100,000 type specimens
• Ideally all 6.5 million specimens should be
  done
       Where is the AVH?
• Spread across Australian herbaria
• Data distributed; resides with custodians
• Each herbarium has a portal to receive
  requests to and deliver data from its
  database
• Each herbarium hosts a common AVH
  query interface that polls all herbaria and
  integrates and returns data as a single
  query
Major Australian Herbaria
Who are the participants?
  State Herbarium of     National Herbarium of
  South Australia        Victoria

  Queensland Herbarium   National Herbarium of
                         New South Wales
  Australian National
  Herbarium              Western Australian
                         Herbarium
  Northern Territory
  Herbarium              Australian Biological
                         Resources Study
  Tasmanian Herbarium


  Industry Partner:
  KE Software
Holdings of Aust. Herbaria
National Herbarium Collection
      database status
      Who runs the AVH?
• The Council of Heads of Australian
  Herbaria (CHAH).
• The Herbarium Information Systems
  Committee (HISCOM)
• IT staff at each herbarium (technology)
• Botanical staff at each herbarium (content)
• Scientific staff at each herbarium
  (validation)
   Aust. & NZ Environment &
 Conservation Council (ANZECC)

• Government committee of Commonwealth
  and State/Territory Environment Ministers
• Accepted that the community wanted the
  product
• Funding options and regional support
• Working group
• Project design input - new name
        “The Agreement”

• $10 million project over five years
• Capture new data and validate old
• State/Territory to contribute amount relative
  to specimens to be databased/validated
• $4 million Commonwealth + $4 million
  State/Territory + $2 million private
• Sharing data critical to cost (cf. $16 million)
      Who uses the AVH?
• The participating herbaria get access to all
  the data at the highest precision.
• Public access filter restricts access to work
  in progress, sensitive locality data, etc.
• Access to conservation agencies,
  environmental decision makers
• Research and education
• Public general interest
Uses   GREENING THE GRAINBELT
Uses
ROTAP ferns and fern allies
ROTAP ferns and fern allies
Cyathea exilis
                  Cyathea exilis




Tectaria devexa
       When did the AVH
          happen?

• Basically last year and this year

• But we have been working towards it for
  over 13 years

• And there have been the occasional dead
  ends and setbacks, waiting for technology,
  capacity, support, etc.
    Brief History of the AVH

• 1995 - HISCOM recommends the AVH
  concept (a distributed database) to CHAH
• 1997 - Canvassed at Systematics meeting
• 1999 - Proof of concept with Acacia
• 2000 - Government Minister shows interest
• 2000 - Interest from industry/foundations
• 2000/01 - Negotiating cost & lobbying
         Recent Activity
• Major item at October 2001 CHAH meeting
  - Agreement on what information we
  provide to community
  - Priority groups and ‘Who does what?’
• Trust to oversee financial arrangements
• Liaison and Advisory Committee
• Funds identified in budgets
• Herbaria recruit staff and start work
 hoW does the AVH work?
• On a number of different levels
  – Politically
  – Administratively
  – Technically
  – Scientifically
  – Emotionally
AVH General Architecture
       Whence the AVH?
• A new era of integrated access to
  botanical information
• New ways of visualizing data form
  different sources
• New ways on managing and validating
  data across remote databases
• More automation, more speed, higher
  throughput
Added extras - the real AVH
• Stage 1: databasing (dots on maps)
• Plus map overlays, precision flags, spatial
  queries, pretty interfaces, etc.
• Conflicting taxonomies - towards a
  National Census
• Stage 2+: images, descriptions,
  identification tools
• Multiple resources and options (cf. library)
Botanical illustrations
Plus
But...
BIG But...
       Strategies for tackling
         fungal biodiversity
    Problem: 250,000 spp., 5% known, few
     herbarium collections
    Solution: Fungimap
    Community mapping of 100 common species
     by 600 volunteers
    Distribution and habitat data leads to better
     conservation and systematics
Australian eFloras and other digital products
Australian eFloras and other digital products
Australian eFloras and other digital products
         Why it will work
• 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 (e.g. impact on research outputs
  and other organisational initiatives)
        Future technology
• Currently very simple architecture and
  technology
• Increase in complexity and ‘bulk’ is
  inevitable
• Can not avoid engaging computer
  scientists and the computer industry
  – Optimize   data storage
  – Optimize   data access and delivery
  – Optimize   analysis and visualization
  – Optimize   knowledge discovery
  Acknowledgements
State Herbarium of     National Herbarium of
South Australia        Victoria

Queensland Herbarium   National Herbarium of
                       New South Wales
Australian National
Herbarium              Western Australian
                       Herbarium
Northern Territory
Herbarium              Australian Biological
                       Resources Study
Tasmanian Herbarium

Industry Partner:
KE Software

				
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