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

A u s t r a l i a ’ s G r o w i n g F u t u r eAustralia’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.

A u s t r a l i a ’ s G r o w i n g F u t u r eAustralia’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

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

A u s t r a l i a ’ s G r o w i n g F u t u r eAustralia’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

• 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

A u s t r a l i a ’ s G r o w i n g F u t u r eAVH 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

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

Web InterfaceModule

Indexing Module

Converting Module

Data InitialisingModule

MySQL eXist

DAO Module XMLDB Module

Users BioCASE Providers

MapServer UnitLoader

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

A u s t r a l i a ’ s G r o w i n g F u t u r eIntegration of AVH and TAPIRUS

AVH database

Resource table Specimen table

Provider3Provider1 Provider2

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

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

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

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

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

Victorian Agricultural Insect Collection

INSTITUTIONS – TasmaniaHobart

Australian National Fish Collection (CSIRO)

Tasmanian Museum and Art Gallery, ZoologyTasmanian Herbarium

Tasmanian Environmental Invertebrate Collection Tasmanian Forest Insect Collection

Australian Collection of Antarctic Microorganisms (University of Tasmania)

Culture Collection of Microalgae (CSIRO)

DevonportDPIW Insect Reference CollectionLauncestonQueen Victoria Museum and Art Gallery, Zoology Section

Adelaide

Perth

INSTITUTIONS – Victoria MelbourneMuseum VictoriaNational Herbarium of VictoriaUniversity of Melbourne Herbarium

Melbourne

Hobart

Launceston

Townsville

Devonport

Armidale

Darwin

BrisbaneLismore

Orange

SydneyCanberra

INSTITUTIONS – South Australia AdelaideSouth Australian MuseumSouth 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 PerthWestern Australian MuseumWestern 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 TerritoryDarwinMuseum & Art Gallery of the Northern TerritoryNorthern Territory HerbariumNorthern Territory Economic Insect CollectionPhytoplasma 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 HerbariumAustralian Biological Resources Study

Canberra

LismoreAustralian Plant DNA Bank

ArmidaleN.C.W. Beadle Herbarium

Australian MuseumNational Herbarium of NSWDowning 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 UnitAustralian Collection of Plant Pathogenic Bacteria

INSTITUTIONS – New South Wales

Sydney

Orange

GosfordAustralian Legume Innoculants Research Unit (DPI)

Queensland MuseumQueensland HerbariumDPI&F Plant Pathology HerbariumDPI&F Insect CollectionUniversity of Queensland Insect CollectionBSES Insect CollectionAustralian Collection of Microorganisms (University of Queensland)

INSTITUTIONS – Queensland

TownsvilleAIMS Marine Bioresources Library

Microbial Gene Research and Resources Facility (Griffith University

Brisbane

MaroochydoreUniversity of the Sunshine Coast Microbial Library

Biological Collections contributing to ALA

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.

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 CoreGenBank schema

Structured Descriptive Data

Images using URI, XMP, EXIF metadata

LinksLinks 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

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

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 ?

• …

Atlas of Living Australia

Thank you