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 interchangingbotanical data on-line

Jim CroftCentre for Plant Biodiversity

ResearchAustralian National Herbarium

jrc@anbg.gov.auhttp://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 accuracySurvey 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 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

Holdings of Aust. Herbaria

National Herbarium Collectiondatabase 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

GREENING THE

GRAINBELT Uses

Uses

ROTAP ferns and fern allies

ROTAP ferns and fern allies

Cyathea exilis

Tectaria devexa

Cyathea exilis

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...

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

BIG But...

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

AcknowledgementsState 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