AVH - Australia’s Virtual Herbarium Logo Jim Croft Centre for Plant Biodiversity Research Australian National Herbarium

Australia’s Virtual Herbarium: storing and interchanging botanical data on-line Jim Croft Centre for Plant Biodiversity Research Australian National Herbarium

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

Herbarium Specimens

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

Acacia aneura: Distribution of specimens from each herbarium

Overlays

Geocode accuracy Survey 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 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 Collection database 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

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 HISCOM recommends the AVH concept (a distributed database) to CHAH Canvassed at Systematics meeting Proof of concept with Acacia Government Minister shows interest 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

Evolution of the AVH Race to database Need for semantic standard recognized HISPID ExchangeDistributed query Standard syntax Need for common semantic schema recognized Botanical ontology?

hoW does the AVH work? On a number of different levels –Politically –Administratively –Technically –Scientifically –Emotionally

AVH General Architecture

URL UML XML URI XHTML HTTP UDDI XSLT XPATH RDF PNG SVG DOM CSS SAX HISPID ITF BNF Z39.50 WAIS ASN.1 XML schema Standards Dublin Core RDFS Z39.19 SOAP cgi RMI

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

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

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