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Australia’s Virtual Herbarium: PowerPoint Presentation
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Australia’s Virtual Herbarium:

Australia’s Virtual Herbarium:

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Australia’s Virtual Herbarium:

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  1. Australia’s Virtual Herbarium: Medium to long-term benefits fromdistributed biodiversity informationsystems

  2. Austalia’s Virtual Herbarium • Is an idea • Is a tool for data access • Is not the answer

  3. 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

  4. 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

  5. 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.)

  6. 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.

  7. Collecting specimens The work of herbaria

  8. Herbarium Specimens

  9. Botanical literature

  10. Specimen Data Capture

  11. Public Reference Herbarium

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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)

  18. Holdings of Aust. Herbaria

  19. National Herbarium Collectiondatabase status ‘Us’

  20. 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

  21. 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

  22. 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)

  23. 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)

  24. “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)

  25. How does the AVH work? • On a number of different levels: • Politically • Administratively • Technically • Scientifically • Emotionally

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

  27. 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

  28. AVH General Architecture

  29. The pilot: distribution of Acacia aneura, mulga

  30. The pilot: distribution of Acacia aneura, mulga

  31. Acacia aneura: Distribution of specimens from each herbarium

  32. Overlays

  33. Geocode accuracy Survey data

  34. Example HISPID data export in XML

  35. A Herbarium Database Structure

  36. 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

  37. 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

  38. “Greening the Grainbelt” Uses

  39. Uses

  40. ROTAP ferns and fern allies Insufficiently known Rare Vulnerable Endangered Presumed extinct

  41. ROTAP ferns and fern allies

  42. Cyathea exilis

  43. Cyathea exilis Tectaria devexa

  44. 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

  45. 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)

  46. Plus Botanical illustrations

  47. Plus

  48. Type Images on demand High resolution image oftype specimen of Austrobaileyadownloaded over the Internetfrom the Herbarium of theNew York Botanical Garden

  49. But...