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