Definitions

1
AVH - Australias Virtual Herbarium Logo
Jim Croft Centre for Plant Biodiversity
Research Australian National Herbarium
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Australias Virtual Herbariumstoring and
interchanging botanical data on-line

• Jim Croft
• Centre for Plant Biodiversity Research
• Australian National Herbarium
• jrc_at_anbg.gov.au
• http//www.anbg.gov.au/jrc/

3
Storage Industry speak

• Role of Industry / Cost of storage infrastructure
  relative to project / Business competetiveness /
  Strategic business advantage / Justify investment
  / Return on Information (ROI) / Ever-changing
  environment / Interoperability / Linking
  geographically dispersed sites/ Availability all
  the time, everywhere, forever / Storage strategy
  / Effective storage management / Right storage
  architecture / Faster storage environment /
  Advanced database technologies / Optimising
  availability, performance, placement, recovery /
  Flexible future-proof IT infrastructure / Data
  storage to assist RD / Replication for disaster
  recovery / Benefits of central disaster recovery
  / Necessity to plan ahead / Staged implementation
  approach / Lead organizational change

4
Herbarium botany speak

• Herbarium / Plants / Regional floristics /
  Preserved botanical specimens / Taxonomic
  hierarchy and taxon ranks / Nomenclature,
  synonymy / Alternative phylogenies and
  classifications / International Code of Botanical
  Nomencalture / Identification keys / Original,
  derived and modifided data / Localities, geocodes
  / Data accuracy and precision / Habitat,
  altitude, depth, substrate / Biological images /
  Geospatial modeling and visualization /
  Environmental modeling and prediction / Species
  distributions and occurrence / Biological
  descriptive frameworks / Interactive
  identification / Flora Information systems /
  Landcover species / Curatorial standards /
  Cryptogams / Gymnosperms / Platyzomataceae /
  Eucalyptus camaldulensis

5
AVH - The Big Questions

• The 6 Ws
• Who?
• What
• Where?
• When?
• Why?
• hoW?

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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?

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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

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Platyzoma micropyllum
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Platyzoma micropyllum
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Platyzoma micropyllum
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Platyzoma micropyllum
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Herbarium Specimens
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Compactus storage units
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Compactus storage units
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Botanical Library
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Botanical literature
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Specimen Data Capture
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Public Reference Herbarium
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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

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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

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The pilot distribution of Acacia aneura, mulga
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Acacia aneura Distribution of specimens from
each herbarium
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Overlays
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Geocode accuracy Survey data
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A Herbarium Database Structure
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(No Transcript)
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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

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What is the Problem?

• gt 18,000 species of higher plants
• gt 64,000 available names
• Extensive synonymy (4 names per plant)
• 8 major government-funded herbaria
• Similar number of university herbaria
• gt 6,500,000 specimens Aust. herbaria
• 50-100 data elements per specimen
• Several Kb per specimen

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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

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Where is the data?

• Images compound the problem
• Several Kb and up for 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 should be done

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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

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Major Australian Herbaria
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Who are the participants?
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
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Holdings of Aust. Herbaria
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(No Transcript)
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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)

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Aust. NZ Environment Conservation Council

• 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

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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)

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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

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GREENING THE GRAINBELT
Uses
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Uses
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When did the AVH happen?

• Basically this year
• But we have been working towards it for over 12
  years
• And there have been the occasional dead ends and
  setbacks, waiting for technology, capacity,
  support, etc.

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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 - Negotiating cost lobbying

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Recent Activity

• Major item at October 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

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Evolution of the AVH
Need for common semantic schema recognized
Standard syntax
Race to database
HISPID
Botanical ontology?
Need for semantic standard recognized
Exchange
Distributed query
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hoW does the AVH work?

• On a number of different levels
• Politically
• Administratively
• Technically
• Scientifically

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AVH General Architecture
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(No Transcript)
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Standards
URL
XSL
T
XPATH
RDF
XML
SVG
BNF
UML
ITF
UDDI
Z39.50
URI
XHTML
SOAP
Dublin Core
Z39.19
HTTP
DOM
RDFS
PNG
HISPID
ASN.1
SAX
CSS
WAIS
XML schema
cgi
RMI
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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

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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)

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Botanical illustrations
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Plus
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But...
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Integrated strategies for tackling fungal
biodiversity
But...

• 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

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Australian eFloras and other digital products
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Australian eFloras and other digital products
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Australian eFloras and other digital products
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Why it will work

• Communication - CHAH, few herbaria
• Collaboration - long-standing, data sharing,
  overcoming Australias Federal/State system
• Champions - management, public
• Lobbying and profile of herbaria
• Relevance of product
• And nowwe need to maintain commitment to project
  (e.g. impact on research outputs and other
  organisational initiatives)

60
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

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Participants
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