Australia

1
Australias Virtual Herbarium

• Medium to long-term benefits
• from distributed biodiversity
• information systems

2
Austalias Virtual Herbarium

• Is an idea
• Is a tool for data access
• Is not the answer

3
The AVH as a framework

• Will dominate herbarium activity and priorities
  for the next 5 years
• Data management
• Data exchange
• Curation priorities
• Specimen management
• Loans and exchanges

4
The AVH as a framework

• Will involve all major Australian herbaria
• Common information standards
• Specimen data exchange
• Common national census
• Division of labour
• New visualization tools
• New analysis tools
• New botanical products and services

5
The AVH

• a prototype
• not terribly sophisticated technically
• replicated query engine (portal)
• interrogating distributed data providers (URLs)
• implementing common schema through a limited set
  of access points (gen./sp.)

6
The AVH

• Illustrates how federated systems might evolve in
  heterogenous environments
• the development and application of community
  standards
• HISPID, XML
• the adoption of open source solutions
• Mapserver,  Perl, PHP etc.
• Similar solutions are being used to federate
  ENHSIN, SpeciesAnalyst, DIGIR, etc.

7
Collecting specimens
The work of herbaria
8
Herbarium Specimens
9
Botanical literature
10
Specimen Data Capture
11
Public Reference Herbarium
12
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

13
What is the AVH?

• A collaborative project of the Australian
  Herbarium community, providing
• Partnership and shared access to 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

14
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
• A common single query AVH interface in each
  herbarium polls all herbaria

Major Australian Herbaria
15
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
16
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

17
What is the Problem?

• gt 20,000 species of higher plants
• gt 64,000 available names
• Extensive synonymy (3 - 4 names per species)
• 8 major government-funded herbaria
• Similar number of university herbaria
• gt 6,500,000 specimens in Aust. herbaria
• 50-100 data elements per specimen
• Several Kb per specimen (excl. images)

18
Holdings of Aust. Herbaria
19
National Herbarium Collectiondatabase status
Us
20
Where is the data?

• In each herbarium (largest 1.3 million specimens)
• Pooling data centrally not acceptable for
  operational, political and emotional reasons.
• We need a distributed data management and access
  solution, maintaining and ensuring custodial
  responsibility

21
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

22
Who runs the AVH?

• The Council of Heads of Australian Herbaria
  (CHAH).
• The Herbarium Information Systems Committee
  (HISCOM)
• IT staff at herbaria (technology)
• Botanical staff at herbaria (content)
• Data entry staff at herbaria (content)
• Scientific staff at herbaria (validation)

23
Aust. NZ Environment Conservation Council
(ANZECC)

• Government committee of Commonwealth and
  State/Territory Environment Ministers
• Accepted community wanted the product
• Funding options and regional support
• Working group
• AVH Board and Trust
• (management through Environment Australia)

24
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 to do each specimen)

25
How does the AVH work?

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

26
How does the AVH work?
Need for common semantic schema recognized
Standard syntax
Race to database
HISPID
Botanical ontology?
Need for semantic standard recognized
Exchange
Distributed query
Evolution of the AVH
27
The 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

28
AVH General Architecture
29
The pilot distribution of Acacia aneura, mulga
30
The pilot distribution of Acacia aneura, mulga
31
Acacia aneura Distribution of specimens from
each herbarium
32
Overlays
33
Geocode accuracy Survey data
34
Example HISPID data export in XML
35
A Herbarium Database Structure
36
(No Transcript)
37
Who uses the AVH?

• The participating herbaria get access to all the
  data at the highest precision.
• Custodians retain rights on data release
• General agreement to minimize restriction
• Public access filter restricts access to work in
  progress, sensitive locality data, etc.
• Password controlled locally
• Simple httpd access control
• No encryption

38
Who uses the AVH?

• Basic public access available to
• Access to conservation agencies, environmental
  decision makers, etc
• Research and education
• Public general interest
• Detailed access to large chunks of data
• One stop shop
• Application through project proposal to CHAH
• Applications to individual herbaria discouraged
• Respecting data custodianship

39
Greening the Grainbelt
Uses
40
Uses
41
ROTAP ferns and fern allies
Insufficiently known
Rare
Vulnerable
Endangered
Presumed extinct
42
ROTAP ferns and fern allies
43
Cyathea exilis
44
Cyathea exilis
Tectaria devexa
45
New Project

• Distribution of primitive vascular plants
• 3-year postdoc
• Biogeography of pteridophytes, gymnosperms
• Based on resources of the AVH
• Establish GIS capabilities for the Centre
• Collaboration with other CSIRO divisions,
  government agencies, universities
• Implement technology, provide data for Centre
  projects and the AVH
• Model for future spatial projects

46
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

47
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 the Consensus Census
• Stage 2 images, descriptions, identification
  tools
• Multiple resources and options (cf. library)

48
Plus
Botanical illustrations
49
Plus
50
Type Images on demand
High resolution image oftype specimen of
Austrobaileyadownloaded over the Internetfrom
the Herbarium of theNew York Botanical Garden
51
But...
52
Tackling fungal biodiversity
BIG But...

• Problem 250,000 spp., 5 known, few herbarium
  collections
• A solution Fungimap
• Community mapping of 100 common species by 600
  volunteers
• Distribution and habitat data leads to better
  conservation and systematics

53
Australian eFloras and other digital products
54
Australian eFloras and other digital products
55
(No Transcript)
56
(No Transcript)
57
Some challenges

• Identifications patchy
• Inadequate specimens
• Work in progress / Curation lag
• Lack of a national Consensus Census
• Interstate differences
• Problem families and genera
• gt 35 herbarium unsuitable / unusable
• Unidentifiable / qualified identifications
• Vague / imprecise locality data
• Records represent presence only data

58
CPBR projects benefiting

• Basically anything spatial needing defensible
  dots or blobs on maps
• Rare plants Conservation
• Australian flora distributions
• General biogeography Weed biogeography
• Remnant vegetation Revegetation
• Phylogeography of Australian plants
• Outreach
• On-line Floras
• Interactive Keys

59
Why it will work

• Communication - CHAH, few herbaria
• Collaboration - long-standing, data and specimen
  sharing, overcoming Australias Federal/State
  system
• Champions government, management, staff, public
• Lobbying and profile of herbaria
• Relevance and utility of product
• And nowwe need to maintain commitment to project

60
Current Developments

• need to join communities into larger
  federations
• ultimately part of GBIF
• distributed generic portals (DiGIR)
• utilizing discovery (UDDI) of published web
  services
• for specimens, taxonomy, coverages, etc.
• exchanging complex queries and result sets
  encapsulated as XML (SOAP/XMLP)

61
Current Developments

• rely on the existance of an extended community
  schema
• abcd, a common subset (Darwin core) of elements
• simple thesauri
• Incorporation and discovery of ontologies and
  semantic networks will have to wait a while ?

62
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
63
(No Transcript)
64
(No Transcript)
65
(No Transcript)
66
(No Transcript)
67
(No Transcript)
68
(No Transcript)
69
(No Transcript)
70
(No Transcript)
71
(No Transcript)
72
(No Transcript)
73
(No Transcript)