1. AUSTRALIA’S VIRTUAL HERBARIUM
A national collaborative model for integrated access to distributed biological information
Jim Croft, Greg Whitbread
Australian National Herbarium
Key Innovations in Biodiversity Informatics: Integrating Biodiversity Data
Australia's Virtual Herbarium: a national collaborative model for integrated access to distributed biological information
Jim Croft &.Greg Whitbread (15-20 minutes)
Australian National Herbarium, Centre for Plant Biodiversity Research, Canberra
The Australia's Virtual Herbarium (AVH) is a collaborative project of the Australian botanical community providing integrated access to on-line botanical information from the scientific collections and resources of Australian herbaria in a national partnership with a formal agreement between participants. With new funding of $Aus 10 million over 5 years, the initial phase of the AVH project is to database and make available taxonomic, distribution and occurrence information associated with all 6.5 million herbarium specimens held across the country through a simple on-line GIS application; the ultimate aim is to provide a complete integrated flora information system as a tool for scientific research, environmental decision-making and public information.
The AVH is based on a distributed heterogeneous database information system, so that the data resides with and is managed and controlled by the custodians and each herbarium has a portal to receive requests and to deliver data from its institutional databases. A shared common AVH query interface in each herbarium polls all participating herbaria and delivers a single integrated result. The design philosophy of the AVH is based on information standards developed by and for the botanical community, open architecture, public domain software and free availability of the application and information management structures for use in other biodiversity documentation projects. It is the intention of the AVH to adapt its architecture and information standards to those being adopted or endorsed internationally in biodiversity informatics frameworks such as TDWG and GBIF.
The AVH marks an unprecedented level of cooperation between institutions at a national level and has been driven by a collective desire on the part of the herbarium community to be more responsive to community needs in providing access to larger amounts of data more rapidly and the need for herbaria to work more efficiently within a declining resource framework. The acceptance and thus success of the project lies in the relevance of the product for a wide range of users, including applications for research, industry and education, for conservation agencies, land managers and environmental decision makers.

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. There is some urgency …
1907
2002
In concluding our presentation this afternoon I want to bring you back to think about the importance of collaborative efforts and of disseminating the results of our research
When this picture, from a 1907 land sale catalogue, was being used as a positive image, well meaning govt subsidies had resulted in what you see here – ringbarked trees and cleared land, although one selling point was that it was yellowbox country – with the implication that it was good country.
Now – with govt money in the NHT and the NAP we are now replanting these same landscapes [Murray’s slide of planting sites]
We need to do this intelligently using the best information and knowledge we can
So that the decisions are not made in isolation of that knowledge, we as researchers need to make it accessible for our partners and to synthesise it for others to use and apply.
In this way we see that the collections and national botanical databases will contribute significantly to the Healthy Country Flagship program with biodiversity informatics playing a strong underpinning role in such areas as restoration biology.
And hopefully we can win back far more of the resources than the division commits to the BHAG.
I hope we’ve given you a snapshot of how we are going about that via biodiversity informatics.

11. What is the problem? > 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
data elements per specimen
Several Kb per specimen (excl. images)

12. Specimen data from major herbaria

13. Herbarium database status

14. The AVH Agreement - $ 4 million State/Territory - $ 2 million private
$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

15. Australia’s Virtual Herbarium
On-line access to herbarium specimen information and botanical knowledge

16. 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?

17. Data refinement Envir. decision making Policy & strategy
conservation
restoration biology
resource mgmt
utilisation
Policy & strategy
government
corporate
individual
action
knowledge
information
Increasing refinement & utility of data
data
The real world - The natural and modified landscape
Observations of the real world - Measurements, occurrences, photographs
Collections from the real world - Herbarium specimens, living specimens
Collated into datasets which are analysed in various ways to develop information and results which are interpreted and through that knowledge we can take decisions, we can implement and take actions
Analysis of observations
Visualization of analyses
Interpretation of results
observations
the real world

18. Botanical Literature

19. Herbarium Specimens

20. Specimen data Core information is from herbarium specimens
Collections data:
Scientific name
Collection date
Collector name & number
Location
Soils
Habitat (incl. topography)
Vegetation community
Associated species
Plant features, e.g. colour
So there are many data elements associated with each collection
What will become clear as we talk this afternoon is that in addition to the specimens being used for taxonomic research, the associated data is now being used for very different purposes from which it was originally collected – largely for taxonomic purposes.
Among the many questions being asked –
What species does a plant belong to?
What is its name?
What other species is it related to?
What does it look like?
How does it grow?
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?

21. Specimen Data Capture

22. A Herbarium Database Structure

25. 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

26. AVH General Architecture
Databases
Gateways
Common Web portals
Clients

27. Australia’s Virtual Herbarium
Some views of the data

28. Australian Plant Name Index (APNI)

33. Acacia
salicina

41. Plant distribution analysis
Pultenaea species in eastern Australia
Incurved
Recurved
20 classes and excluding those cells with 2 or less species. Highly similar groups were grouped again..with the resultant zones with taxonomic affinities.
Zones with shared species emerged, which were not apparent when groups were considered together.
Incurved group:
Similarity values were relatively low ( ) – but six different zones with taxonomic affinities were identified. 6 clear groups were apparent.
Recurved group:
Similarity values were much higher in this group. ( ). 3 clear groups were identified
The question is what do these classes relate to?
Groups of species with shared ecologies—environmental requirements? OR or groups of species with shared evolutionary histories? OR a combination of both.
Information on the later possibility can be gleaned by comparing the classes to phylogenetic info—showing the genetic r’ships between species.
Can see from this cladogram, most species in the incurved group Zone4 in SA and most of Vic all cluster in the top part of the phylogenetic tree as a similar group. That is are all related species.
Also that species in the yellow incurved yellow group form a clear phylogenetic cluster.
It suggests that at least in the incurved group the major taxonomic patterns in the landscape might be reflecting evolutionary histories of these groups—some of the classes probably represent environmental preferences. The taxon zones of recurved species however do not correspond with closely related groups of species on the cladogram. This may indicate that distributions represent the environmental domains of the groups rather than any historical evolutionary patterns. More work is required to test these hypotheses. ? ?
Incurved
Recurved

42. Predictive Modelling

43. Predictive Modelling

44. Related Products On-line Flora information systems
Generally regionally based
Integrating:
Plant names
Descriptive Flora treatments
Illustrations
Distributions

45. Flora Information Systems

46. Botanical illustrations

47. Portraits of Plant species
National Plant Photograph Index
Search on-line
Some digital images available
35,000 images of Australian plants and vegetation
A number of potential candidates, more or less fitting, these criteria have been identified.
And of them I’ve started looking at spatial distribution patterns of the bush Peas Pultenaea—and I’m going to present some of the initial findings of that work.

50. Type Images on demand
High resolution image of type specimen of Austrobaileya downloaded over the Internet from the Herbarium of the New York Botanical Garden

51. Interactive Plant Identification

52. Invasive Plant Notification

53. 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

54. 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

55. 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