1. Australia’s Virtual Herbarium: Medium to long-term benefits from distributed biodiversity information systems

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

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

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

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

42. ROTAP ferns and fern allies

43. Cyathea exilis

44. Tectaria devexa Cyathea exilis

45. New Project Distribution of primitive vascular plants 3-year postdoc Biogeography of pteridophytes, gymnosperms Based on resources of the AVH Establish GIS capabilities for the Centre Collaboration with other CSIRO divisions, government agencies, universities Implement technology, provide data for Centre projects and the AVH Model for future spatial projects

46. 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

47. 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)

48. Botanical illustrations Plus

50. High resolution image of type specimen of Austrobaileya downloaded over the Internet from the Herbarium of the New York Botanical Garden Type Images on demand

51. But...

52. Tackling fungal biodiversity Problem: 250,000 spp., 5% known, few herbarium collections A solution: Fungimap Community mapping of 100 common species by 600 volunteers Distribution and habitat data leads to better conservation and systematics BIG But...

53. Australian eFloras and other digital products

57. Some challenges Identifications patchy Inadequate specimens Work in progress / Curation lag Lack of a national “Consensus Census” Interstate differences “Problem” families and genera > 35% herbarium unsuitable / unusable Unidentifiable / qualified identifications Vague / imprecise locality data Records represent presence only data

58. CPBR projects benefiting Basically anything spatial needing defensible dots or blobs on maps Rare plants; Conservation Australian flora distributions General biogeography; Weed biogeography Remnant vegetation; Revegetation Phylogeography of Australian plants Outreach On-line Floras Interactive Keys

59. Why it will work Communication - CHAH, few herbaria Collaboration - long-standing, data and specimen sharing, overcoming Australia’s Federal/State system Champions – government, management, staff, public Lobbying and profile of herbaria Relevance and utility of product And now…we need to maintain commitment to project

60. Current Developments need to join communities into larger “federations” ultimately part of GBIF distributed generic portals (DiGIR) utilizing discovery (UDDI) of published web services –for specimens, taxonomy, coverages, etc.… exchanging complex queries and result sets encapsulated as XML (SOAP/XMLP)

61. Current Developments rely on the existance of an extended community schema –abcd, a common subset (Darwin core) of elements –simple thesauri Incorporation and discovery of ontologies and semantic networks will have to wait a while…

62. 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