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AVH - Australia’s Virtual Herbarium Logo Jim Croft Centre for Plant Biodiversity Research Australian 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 Australia’s Virtual Herbarium: storing and interchanging botanical data on-line Jim Croft Centre for Plant Biodiversity Research Australian National Herbarium jrc@anbg. gov. au http: //www. anbg. gov. au/jrc/

Storage Industry speak • Role of Industry / Cost of storage infrastructure relative to Storage Industry speak • Role of Industry / Cost of storage infrastructure relative to project / Business competetiveness / Strategic business advantage / Justify investment / Return on Information (ROI) / Ever-changing environment / Interoperability / Linking geographically dispersed sites/ Availability all the time, everywhere, forever / Storage strategy / Effective storage management / Right storage architecture / Faster storage environment / Advanced database technologies / Optimising availability, performance, placement, recovery / Flexible futureproof IT infrastructure / Data storage to assist R&D / Replication for disaster recovery / Benefits of central disaster recovery / Necessity to plan ahead / Staged implementation approach / Lead organizational change

Herbarium botany speak • Herbarium / Plants / Regional floristics / Preserved botanical specimens Herbarium botany speak • Herbarium / Plants / Regional floristics / Preserved botanical specimens / Taxonomic hierarchy and taxon ranks / Nomenclature, synonymy / Alternative phylogenies and classifications / International Code of Botanical Nomencalture / Identification keys / Original, derived and modifided data / Localities, geocodes / Data accuracy and precision / Habitat, altitude, depth, substrate / Biological images / Geospatial modeling and visualization / Environmental modeling and prediction / Species distributions and occurrence / Biological descriptive frameworks / Interactive identification / Flora Information systems / Landcover species / Curatorial standards / Cryptogams / Gymnosperms / Platyzomataceae / Eucalyptus camaldulensis

AVH - The Big Questions The 6 Ws: Who? What Where? When? Why? ho. AVH - The Big Questions The 6 Ws: Who? What Where? When? Why? ho. W?

AVH - The Big Questions What is the AVH? Why should the AVH happen? 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? ho. W does the AVH happen? Whence the AVH?

What is a Herbarium? • A physically and administratively secure building • A managed 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

Platyzoma micropyllum Platyzoma micropyllum

Platyzoma micropyllum Platyzoma micropyllum

Platyzoma micropyllum Platyzoma micropyllum

Herbarium Specimens Herbarium Specimens

Compactus storage units Compactus storage units

Compactus storage units Compactus storage units

Botanical Library Botanical Library

Botanical literature Botanical literature

Specimen Data Capture Specimen Data Capture

Public Reference Herbarium Public Reference Herbarium

What is a Virtual Herbarium? • The physical resources and biological information of a 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: 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 Acacia aneura: Distribution of specimens from each herbarium

Overlays Overlays

Geocode accuracy Survey data Geocode accuracy Survey data

A Herbarium Database Structure A Herbarium Database Structure

Why is there an AVH? • Pressure on Herbaria to work more efficiently • 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 > 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

Where is the data? • In each herbarium (largest 1. 3 million specimens) • 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 Where is the data? • Images compound the problem • Several Kb and up for 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 should be done

Where is the AVH? • Spread across Australian herbaria • Data distributed; resides with 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 Major Australian Herbaria

Who are the participants? State Herbarium of South Australia National Herbarium of Victoria Queensland Who are the participants? State Herbarium of South Australia National Herbarium of Victoria Queensland Herbarium National Herbarium of New South Wales Australian National Herbarium Northern Territory Herbarium Tasmanian Herbarium Industry Partner: KE Software Western Australian Herbarium Australian Biological Resources Study

Holdings of Aust. Herbaria Holdings of Aust. Herbaria

Who runs the AVH? • The Council of Heads of Australian Herbaria (CHAH). • 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 • Government committee of Commonwealth and State/Territory Aust. & NZ Environment & Conservation Council • 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 “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 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

Uses GREENING THE GRAINBELT Uses GREENING THE GRAINBELT

Uses Uses

When did the AVH happen? • Basically this year • But we have been When did the AVH happen? • Basically this year • But we have been working towards it for over 12 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 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 - Negotiating cost & lobbying

Recent Activity • Major item at October CHAH meeting - Agreement on what information Recent Activity • Major item at October 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

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

ho. W does the AVH work? • On a number of different levels – ho. W does the AVH work? • On a number of different levels – Politically – Administratively – Technically – Scientifically

AVH General Architecture AVH General Architecture

Standards URL XPATH XSLT SVG XML RDF ITF UML UDDIXHTML URI SOAP Dublin Core Standards URL XPATH XSLT SVG XML RDF ITF UML UDDIXHTML URI SOAP Dublin Core Z 39. 19 RDFS Z 39. 50 BNF HTTP DOM SAX HISPID CSS XML schema RMI ASN. 1 PNG WAIS cgi

Whence the AVH? • A new era of integrated access to botanical information • 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) • 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 Botanical illustrations

Plus Plus

But. . . But. . .

But. . . Integrated strategies for tackling fungal biodiversity < Problem: 250, 000 spp. But. . . Integrated 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

Australian e. Floras and other digital products Australian e. Floras and other digital products

Australian e. Floras and other digital products Australian e. Floras and other digital products

Australian e. Floras and other digital products Australian e. Floras and other digital products

Why it will work • Communication - CHAH, few herbaria • Collaboration - long-standing, 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 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 data access and delivery analysis and visualization knowledge discovery

Participants State Herbarium of South Australia National Herbarium of Victoria Queensland Herbarium National Herbarium Participants State Herbarium of South Australia National Herbarium of Victoria Queensland Herbarium National Herbarium of New South Wales Australian National Herbarium Northern Territory Herbarium Tasmanian Herbarium Industry Partner: KE Software Western Australian Herbarium Australian Biological Resources Study