australia’s virtual herbarium:

Australia’s Virtual Herbarium:

Medium to long-term benefits

from distributed biodiversity

information systems

Austalia’s Virtual Herbarium

• Is an idea

• Is a tool for data access

• Is not the answer

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

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

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.)

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.

Collecting specimens

The work of herbaria

Herbarium Specimens

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 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

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

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

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?

• > 20,000 species of higher plants• > 64,000 available names• Extensive synonymy (3 - 4 names per

species)

• 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)

Holdings of Aust. Herbaria

National Herbarium Collectiondatabase status

‘Us’

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

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

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)

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)

“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)

How does the AVH work?

• On a number of different levels:

•Politically•Administratively•Technically•Scientifically•Emotionally

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?

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

AVH General Architecture

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

Example HISPID data export in XML

A Herbarium Database Structure

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

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

“Greening the Grainbelt” Uses

Uses

ROTAP ferns and fern allies

Insufficiently known

Rare

Vulnerable

Endangered

Presumed extinct

ROTAP ferns and fern allies

Cyathea exilis

Tectaria devexa

Cyathea exilis

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 – the “Consensus Census”

• Stage 2+: images, descriptions, identification tools

• Multiple resources and options (cf. library)

Botanical illustrationsPlus

Plus

High resolution image oftype specimen of Austrobaileyadownloaded over the Internetfrom the Herbarium of theNew York Botanical Garden

Type Images on demand

But...

Tackling fungal biodiversity

• 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

BIG But...

Australian eFloras and other digital products

Australian eFloras and other digital products

Some challenges

• Identifications patchy• Inadequate specimens• Work in progress / Curation lag

• Lack of a national “Consensus Census”• Interstate differences• “Problem” families and genera

• > 35% herbarium unsuitable / unusable• Unidentifiable / qualified identifications• Vague / imprecise locality data

• Records represent presence only data

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

Why it will work

• Communication - CHAH, few herbaria• Collaboration - long-standing, data

and specimen sharing, overcoming Australia’s Federal/State system

• Champions – government, management, staff, public

• Lobbying and profile of herbaria• Relevance and utility of product• And now…we need to maintain

commitment to project

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)

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…

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