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Biodiversity Informatics

Biodiversity Informatics. Biodiversity informatics and the manipulation of biolog ic al information Jim Croft jrc@anbg.gov.au. Outline. ‘Biodiversity Informatics’ Australia’s Virtual Herbarium as a model of use and management of biodiversity knowledge

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Biodiversity Informatics

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  1. Biodiversity Informatics Biodiversity informatics and the manipulation of biological information Jim Croft jrc@anbg.gov.au

  2. Outline • ‘Biodiversity Informatics’ • Australia’s Virtual Herbarium as a model of use and management of biodiversity knowledge • New ways of managing biological knowledge • Information management issues • Current trends and future directions in biodiversity knowledge management

  3. Biodiversity Informatics Management of our knowledge of biodiversity using modern techniques of data and information management

  4. Taxonomy of Database Interoperability Multi-database systems [Autonomous] Non-federated Federated Loosely coupled Tightly coupled Multiple schemas Unified schema Sheth & Larson (1990)

  5. Tightly Coupled • Central administration • Semantic consistency • Schemas • Authority files • Common technology • Difficult to implement • Proprietary solutions tolerated • Expensive

  6. Loosely Coupled • Closer to Reality • Independent management • Suited to scientific systems • Common publication syntax • Export schema • Less functionality … Doable • Need open standards

  7. Intermediate Coupling • Scientific Independence • Common syntax & semantics for the exchange of information. • Import/export • HISPID, Darwin Core, TDWG/CODATA abcd • Leverage Existing Open Standards • Participation in wider, more loosely coupled federations • Simplicity • Distribution of effort

  8. Policy & strategy • government • corporate • individual • Envir. decision making • conservation • restoration biology • resource mgmt • utilization Data Refinement action knowledge information Increasing refinement & utility of data data observations the real world

  9. Herbarium Specimens

  10. Specimen Data Capture

  11. Specimen Data • The core information is from herbarium specimens • Beyond taxonomy & names • Collections data: • Scientific name • Collection date • Collector name& number • Location • Soils • Habitat (incl. topography) • Vegetation community • Associated species

  12. A Herbarium Database Structure

  13. What do we want to know? • What species does a plant belong to? • What is its name? • What other species is it related to? • What does it look like? • Where does it grow? • Where might it grow? • What other species grow with it? • What species grow in a defined area? • How did they get there?

  14. What is a Virtual Herbarium? An on-line digital representation of a scientific collection of preserved plant specimens and botanical information

  15. What is the AVH? • Spread across Australian herbaria • Data distributed; resides with custodians • Each herbarium has a portal to receive requests and to deliver data • A common single query AVH interface in each herbarium polls all herbaria Major Australian Herbaria

  16. AVH Partners 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

  17. 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 appear and to be more responsive to community needs

  18. What is the AVH task? • > 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 in Aust. herbaria • 50 -100 data elements per specimen • Several Kb per specimen (excl. images)

  19. Herbarium database status

  20. The AVH Agreement • $10M over 5 years to database all major Australian herbarium collections • $10 million: - $ 4 million Commonwealth - $ 4 million State/Territory - $ 2 million private • Initial focus on capture of herbarium specimen data • Ultimate aim a complete flora information system

  21. Australia’s Virtual Herbarium On-line access to herbarium specimen information and botanical knowledge

  22. Australian Plant Name Index (APNI)

  23. www.anbg.gov.au/apni

  24. www.anbg.gov.au/win

  25. http://www.chah.gov.au/avh.html

  26. Acacia salicina

  27. Incurved Incurved Recurved Research Potential:Plant distribution analysis Pultenaea distribution classes in eastern Australia ? ? Recurved Incurved

  28. Flora Information Systems • On-line systems • Often regionally based • Integrating: • Plant names and synonyms • Descriptive Flora treatments • Illustrations • Distributions • etc.

  29. Flora Information Systems

  30. Botanical illustrations

  31. National Plant Photograph Index Search all records on-line Digital images available (‘best of class’) 35,000 images of Australian plants and vegetation www.anbg.gov.au/anbg/photo-collection/

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

  33. Flora & Revision Databases New ways of managing and delivering botanical information

  34. A Flora in XML Example in HTML <p><b>Platyzomamicrophyllum</b>R.Br., <i>Prodr.</i> 160 (1810)</p> <p ><i>Gleichenia platyzoma</i> F.Muell., <i>Veg. Chatham.-Isl.</i> 63 (1864).T: Facing Island, Qld, <i>R.Brown Iter Austral. 102</i> ; lecto: BM.</p> <p>Illus.: S.B.Andrews…</p> <p>Rhizome short-creeping… Sporangia in zones in distal half of frond.Fig. 55</p> <p>Widespread across northern Australia… Grows in sandy or swampy soils....Map 135.</p> <p>W.A.: 14.4 km NW of Mt…</p> Example in XML <taxon><name>Platyzomamicrophyllum</name><author>R.Br</author>, <publication><title>Prodr.</title><page>160</page><date>1810</date></publication> <synonym> <name>Gleichenia platyzoma</name><author> F.Muell. </author><publication>Veg. Chatham.-Isl.</publication><page>63<page><date>1864</date><type>T: Facing Island, Qld, …</type></synonym> <illustration>Illus.: S.B.Andrews…</illustration> <description>Rhizome short-creeping… Sporangia in zones in distal half of frond. </description><figure>Fig. 55 </figure> <locality>Widespread across northern Australia… </locality><habitat>Grows in sandy or swampy soils...</habitat> <map>Map 135.</map> <specimens>W.A.: 14.4 km NW ofMt…</specimens></taxon>

  35. A Flora XML Schema fragment

  36. A Flora database structure

  37. A Flora database report

  38. An old process of publication Botanist W-P file Editors W-P file Publisher C-R Copy Book, etc.

  39. An new process of publication Botanist W-P file Editors W-P file Publisher Outputs XML file C-R Copy Outputs Database XML file Book, etc.

  40. A future process of publication Botanist Database Editors Publisher Outputs XML file C-R Copy Outputs Database Book, etc.

  41. Interactive Identification Using computers to identify and name plant species and display information about them

  42. Interactive Plant Identification

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