avh_san

Slide 1: 

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 : 

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 : 

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 future-proof 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 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 : 

AVH - The Big Questions The 6 Ws: Who? What Where? When? Why? hoW?

AVH - The Big Questions : 

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? : 

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

Slide 8: 

Platyzoma micropyllum

Slide 9: 

Platyzoma micropyllum

Slide 10: 

Platyzoma micropyllum

Slide 11: 

Platyzoma micropyllum

Slide 12: 

Herbarium Specimens

Slide 13: 

Compactus storage units

Slide 14: 

Compactus storage units

Slide 15: 

Botanical Library

Slide 16: 

Botanical literature

Slide 17: 

Specimen Data Capture

Slide 18: 

Public Reference Herbarium

What is a Virtual 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? : 

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

Slide 21: 

The pilot: distribution of Acacia aneura, mulga

Slide 22: 

Acacia aneura: Distribution of specimens from each herbarium

Slide 23: 

Overlays

Slide 24: 

Geocode accuracy Survey data

Slide 25: 

A Herbarium Database Structure

Why is there an AVH? : 

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? : 

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? : 

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? : 

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? : 

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

Slide 32: 

Major Australian Herbaria

Slide 33: 

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

Slide 34: 

Holdings of Aust. Herbaria

Who runs the AVH? : 

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 : 

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” : 

“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? : 

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 : 

GREENING THE GRAINBELT Uses

Slide 41: 

Uses

When did the AVH happen? : 

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 : 

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 : 

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

Slide 45: 

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

hoW does the AVH work? : 

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

Slide 47: 

AVH General Architecture

Slide 49: 

URL UML XML URI XHTML HTTP UDDI XSL T 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? : 

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 : 

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)

Slide 52: 

Botanical illustrations

Slide 53: 

Plus

Slide 54: 

But...

Integrated strategies for tackling fungal biodiversity : 

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 But...

Slide 56: 

Australian eFloras and other digital products

Slide 57: 

Australian eFloras and other digital products

Slide 58: 

Australian eFloras and other digital products

Why it will work : 

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 : 

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

Slide 61: 

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