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A u s t r a l i a ’ s G r o w i n g F u t u r e Greg Whitbread, Australian National Herbarium; Shunde Zhang and Paul Coddington, South Australian Partnership.

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Presentation on theme: "A u s t r a l i a ’ s G r o w i n g F u t u r e Greg Whitbread, Australian National Herbarium; Shunde Zhang and Paul Coddington, South Australian Partnership."— Presentation transcript:

1 A u s t r a l i a ’ s G r o w i n g F u t u r e Greg Whitbread, Australian National Herbarium; Shunde Zhang and Paul Coddington, South Australian Partnership for Advanced Computing TAPIR networks in Australia’s Virtual Herbarium and the Atlas of Living Australia

2 A u s t r a l i a ’ s G r o w i n g F u t u r e Australia’s Virtual Herbarium: The first, and currently the major, iteration of Australia's Virtual Herbarium (AVH) uses a very simple protocol designed for a single task, – to assemble partial HISPID documents from a number of providers and display species occurrence on a map. It is web-based, easy to implement, fully distributed, and both praised and lamented by the community it serves.






8 A u s t r a l i a ’ s G r o w i n g F u t u r e Australia’s Virtual Herbarium: A collaborative national project Making botanical information easily available Using modern technology Using cheap, readily available components A model for regional cooperation

9 Australia’s Virtual Herbarium 2.0 Improved code structure and maintainability, all open source –complete rewrite of AVH code –coding work is specific to AVH Improved reliability Additional functionality Single version with consistent functionality across providers Early Warning System for weeds

10 A u s t r a l i a ’ s G r o w i n g F u t u r e Australia’s Virtual Herbarium 2.0 Accommodate full data interchange between Herbaria and enable development of products to meet increased local expectations and support provider participation in global markets for biodiversity information. The story is: a network based on TDWG standards. ABCD and BioCASE AVH and GBIF data providers

11 Same architecture as before –Web portal for queries, with results as text data or map –adopts a central index and database –Distributed queries across multiple databases Many improvements made over prototype system –More complex queries supported –Web mapping program used to generate maps (MapServer) –HISPID format data –Caching of query results for faster queries Australia’s Virtual Herbarium 2.0

12 A u s t r a l i a ’ s G r o w i n g F u t u r e AVH 2.0 Implementation Being developed by SAPAC –Paul Coddington, Shunde Zhang –,Gerson Galang, Donglai Zhang Code has been completely rewritten –Using Java and JSP –Based on some code for prototype written by SA DEH Free, open source software –Apache and Tomcat for web server –mySQL for index database –eXist XML database for storing ABCD records –Continue to use MapServer for mapping

13 A u s t r a l i a ’ s G r o w i n g F u t u r e … System architecture diagram

14 Features of TAPIRUS Supports TAPIR and BioCASE protocols, extensible to handle other protocols Documentation, examples and a tutorial Supports web proxies Log output by Log4J XML configuration Session management and event driven post processor Better performance Features of TAPIRUS

15 A u s t r a l i a ’ s G r o w i n g F u t u r e Integration of AVH and TAPIRUS AVH database Resource tableSpecimen table Provider3Provider1Provider2 1. Get all resources that need to be indexed TAPIRUS incremental index process (runs once a day overnight) 2. Send requests to providers 3. Parse XML and save data

16 Australia’s Virtual Herbarium: State Herbarium of South Australia Queensland Herbarium Australian National Herbarium Northern Territory Herbarium Tasmanian Herbarium National Herbarium of Victoria National Herbarium of New South Wales Western Australian Herbarium Australian Biological Resources Study

17 National Collaborative Research Infrastructure Strategy (NCRIS) Australian Government initiative of $542M over 5yrs NCRIS principles: Focus on infrastructure investment Develop major research facilities –National collaborative basis Improve access to infrastructure Investments under 16 major capability areas, incl. –Integrated biological systems, which includes biological collections – the ALA

18 Atlas of Living Australia Proposed Budget: –$7.5m over 5 years from NCRIS –Tools and information management infrastructure –Possibility for some taxonomic data capture Mapping Australian Plant Census –Non-NCRIS cash contribution $6.3m over 5 years –In-kind contribution $26.2m over 5 years –In total: c. $40m project

19 Atlas of Living Australia A web-based encyclopaedia of all Australian life Unlock over $1billion worth of biodiversity resources held in biological collections around Australia Data provided by over 60 biological collections –State Museums and Herbaria –State Departments –CSIRO –Universities –Microbial Collections Free and easy access for any user

20  Victorian Agricultural Insect Collection INSTITUTIONS – Tasmania Hobart  Australian National Fish Collection (CSIRO)  Tasmanian Museum and Art Gallery, Zoology  Tasmanian Herbarium  Tasmanian Environmental Invertebrate Collection  Tasmanian Forest Insect Collection  Australian Collection of Antarctic Microorganisms (University of Tasmania)  Culture Collection of Microalgae (CSIRO) Devonport  DPIW Insect Reference Collection Launceston  Queen Victoria Museum and Art Gallery, Zoology Section Adelaide Perth INSTITUTIONS – Victoria Melbourne  Museum Victoria  National Herbarium of Victoria  University of Melbourne Herbarium Melbourne Hobart Launceston Townsville Devonport Armidale Darwin Brisbane Lismore Orange Sydney Canberra INSTITUTIONS – South Australia Adelaide  South Australian Museum  South Australia Herbarium  Waite Insect & Nematode Collection  Mycology Culture Collection (Women’s and Children’s Hospital)  Clinical Microbiology Culture Collection (IMVS)  Australian Wine Research Institute INSTITUTIONS – Western Australia Perth  Western Australian Museum  Western Australian Herbarium  King Edward Memorial Hospital/PMH Culture Collection  Western Australian Department of Agriculture and Food, Invertebrate Reference Collection and Plant Research Division Culture Collection  CALM Forest Insect Reference Collection  University of Western Australia Microbiology Culture Collection  Murdoch University Algal Collection INSTITUTIONS – Northern Territory Darwin  Museum & Art Gallery of the Northern Territory  Northern Territory Herbarium  Northern Territory Economic Insect Collection  Phytoplasma DNA Collection (Charles Darwin University)  Biocatalytic Microbe Collection (CSIRO)  Microbiological Diagnostic Unit, Public Health Laboratory, The University of Melbourne Maroochydore Gosford INSTITUTIONS – Australian Capital Territory  Australian National Insect Collection (CSIRO)  Australian National Herbarium (CSIRO)  Australian National Wildlife Collection (CSIRO)  GAUBA Herbarium  Australian Biological Resources Study Canberra Lismore  Australian Plant DNA Bank Armidale  N.C.W. Beadle Herbarium  Australian Museum  National Herbarium of NSW  Downing Herbarium (Macquarie University)  John Ray Herbarium (University of Sydney)  The John T. Waterhouse Herbarium (UNSW)  Forestry Commission of NSW Insect Collection (FCNI)  Macleay Entomology Collection (MAMU)  Food Research Collection (CSIRO)  Microbiology Culture Collection (University of NSW)  Plant Pathology Herbarium (DPI)  NSW Agricultural Scientific Collections Unit  Australian Collection of Plant Pathogenic Bacteria INSTITUTIONS – New South Wales Sydney Orange Gosford  Australian Legume Innoculants Research Unit (DPI)  Queensland Museum  Queensland Herbarium  DPI&F Plant Pathology Herbarium  DPI&F Insect Collection  University of Queensland Insect Collection  BSES Insect Collection  Australian Collection of Microorganisms (University of Queensland) INSTITUTIONS – Queensland Townsville  AIMS Marine Bioresources Library  Microbial Gene Research and Resources Facility (Griffith University Brisbane Maroochydore  University of the Sunshine Coast Microbial Library Biological Collections contributing to ALA

21 Atlas of Living Australia Data provision infrastructure which facilitates the mobilization of the many biodiversity collections into a cohesive and robust data provision network. Data integration platform using globally accepted and supported data sharing standards and protocols. Data access and analysis infrastructure that will provide powerful tools for data capture, management and analysis.

22 Taxonomic names Data from taxonomic names lists eg. APNI, AFD, ITIS, Species2000 Specimen data includes observational data Data about specimens from museum & herbarium and culture collections, vouchered DNA specimens, observational datasets Molecular /sequence data DNA sequence data held in DNAbanks, and barcodes from CBOL projects Phenotypic data e.g. morphology, biochemistry Character datasets e.g.: morphology, biochemistry, growth, enzymes Multimedia Data from image banks and repositories Darwin Core GenBank schema Structured Descriptive Data Images using URI, XMP, EXIF metadata Links Links from: Phylogenies (Tree of Life) Endangered species (IUCN Red List) CITES Literature Tools Tools: Data visualisation (eg mapping) Data validation Modelling Biodiversity measures (eg endemism) Data out to users GBIF OBIS Taxonomic Concept Schema I n t e r n e t

23 Atlas of Living Australia Data Provision (or Mobilisation) Infrastructure –Provider services –Support Data Integration Infrastructure –Cache –Nomenclatural and taxonomic services Data Access and Analysis infrastructure –Web site and portal –Tools


25 Atlas of Living Australia An integrating force Include Social infrastructure Focus for Australia’s international biodiversity informatics activity A national infrastructure built on TDWG standards –TAPIR network –Packaged solutions New components to be developed within the the TDWG framework –Push ? …

26 Atlas of Living Australia Thank you

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