Australia’s Virtual Herbarium:

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

37. 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

38. 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

39. “Greening the Grainbelt” Uses

40. Uses

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

42. ROTAP ferns and fern allies

43. Cyathea exilis

44. Cyathea exilis Tectaria devexa

45. 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

46. 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)

47. Plus Botanical illustrations

48. Plus

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

50. But...