Biodiversity Information Systems (HB)

Collaborative projects

Australia's Virtual Herbarium

Australia's Virtual Herbarium is a collaborative project of the Commonwealth, State and Territory herbaria to make botanical information available on-line in an integrated format so that a query will harvest relevant information from all herbaria in real time and present the result as a single seamless report. It presents information from herbarium collections, nomenclatural and taxonomic databases, State and Territory checklists, flora information systems, image databases and archives, and other on-line sources of botanical data. There are c. 6 million botanical collections in the major Australian herbaria, yet only 40% of these were recorded in databases when the project was initiated. Managers and information technology staff from the State, Territory and Commonwealth herbaria have been collaborating on this project with a vision of completing the data capture of all botanical specimens by 2007. Centre staff have been actively involved in the development of the AVH and are supervising a contract to enhance the prototype interface and data delivery mechanism, and in coordinating funding proposals with representatives of State, Territory and Commonwealth governments, and ANZECC. Agreement has been reached to fund the data capture first phase of the AVH with funding from State, Territory and Commonwealth Governments and from private foundations. The data design work the Centre is doing in collaboration with ABRS to deliver text and graphical flora information on-line will feed into the AVH.

• Access to AVH is at: www.chah.gov.au/avh/about.jsp

HISCOM

Centre staff are active participants in the Australian Herbarium Information Systems Committee (HISCOM), a subcommittee of the Council of Heads of Australian Herbaria (CHAH), where botanical data exchange protocols (such as HISPID) are developed, established and installed in the major Australian Herbaria. Through this collaboration data associated with loans and exchange specimens as well as data from research collections has been exchanged with state herbaria and universities. Online web interfaces have been developed to deliver this data in a number of formats, including the agreed HISPID format, text data, tabular data, spreadsheet data, summary maps and recently XML format. HISPID is the foundation data description for Australia's Virtual Herbarium.
More information about HISCOM is available at:

• http://plantnet.rbgsyd.nsw.gov.au/HISCOM/

Australian Biological Information Facility (ABIF-Flora)

The Australian Biological Information Facility is a program to deliver Commonwealth information on the countries flora and fauna to the public via the Internet. Centre staff are collaborating with ABIF-Flora staff of ABRS to incorporate Flora of Australia information into a database format and to prepare flexible Internet gateways to query and deliver this information in a variety of formats. Several simple tools have been developed, using the Centre's Oracle relational data base and XML as the data loading and internet delivery format.

• Links to ABIF can be found at: http://www.abif.org/index.htm

Global Biodiversity Information Facility (GBIF)

The Global Biodiversity Information Facility is an international organisation that aims to make the world's biodiversity data freely accessible anywhere in the world. GBIF's members include countries and international organisations who have agreed to share biodiversity data and to contribute to the development of increasingly effective mechanisms for making those data available via the Internet. Australia is a financial contributing member of GBIF and staff from the Australian National Herbarium participate in a number of GBIF technical and operational activities. ABIF is the Australian node of GBIF. Australian National Herbarium data on plant names and specimen records are made available to GBIF through the Australia's Virtual Herbarium and through ABIF using international biodiversity information management standards.

GBIF's activities are organized around seven integrated thematic areas:

• Data Access and Database Interoperability, designed to facilitate the full use of biodiversity and other databases by facilitating "data-mining;"
• Digitisation of Natural History Collections Data, in order to expand biodiversity knowledge on the Internet;
• Electronic Catalogue of the Names of Known Organisms, to improve searching of biodiversity data and enable combining of data from different disciplines;
• Outreach and Capacity Building, to ensure that people in every country have access to and can easily and freely use the world's biodiversity information
• SpeciesBank, to provide a complete compendium of knowledge about particular species drawn from online information sources; and
• Digital Biodiversity Literature Resources, to open up Web access to digitised versions of the published literature.
• A network or national and regional GBIF nodes that facilitate access and exchange and of GBIF data between participants.
  
  
• Links to ABIF can be found at: http://www.gbif.org/

International Plant Names Project (IPNI)

As custodians of the Australian Plant Name Index (APNI) and developmental work on plant nomenclatural and taxonomic databases, the Centre continues participation in an international collaborative project involving the Royal Botanic Gardens Kew and the Harvard University Herbaria to integrate the work of the Index Kewensis, the Harvard Gray Cards and APNI into a single database of world plant names to be accessible to researchers via the Internet. After an initial grant obtained from the US National Science Foundation (NSF) for the development of a proof of concept application relating to author names, a larger NSF proposal for funding for three years to complete the project was successful.

• This application, known as the International Plant Name Index (IPNI) can be seen at: http://www.ipni.org/

The Australian National Herbarium is a collaborator with other Australian herbaria and museums in the NCRIS Atlas of Living Australia project. This NCRIS project is to develop and provide the infrastructure that will enable herbaria and museums to share and exchange biodiversity data and information and to provide the research community and the general public with integrated access to these resources and to provide tools to query, display, report on, analyze and visualize the data. The Atlas of Living Australia will be a vehicle for data from the Australia's Virtual Herbarium (AVH) project and we provide data to the Global Biodiversity Information Facility.

• Atlas of Living Australia

Taxonomy Research & Information Network (CERF Project)

The CERF Taxonomy Research & Information Network aims to enhance and accelerate taxonomic research and delivery of information on Australia’s biodiversity, with broad goals to:

• Reinvigorate taxonomy within Australia
• Evaluate and road test new methodologies for research and delivery of taxonomic information for a wide range of end users
• Create and maintain a modern collaborative national electronic framework for taxonomic knowledge delivery.

Relevant websites:

• Taxonomy Research & Information Network (National website)
• Taxonomy Research & Information Network (CPBR project)
• Lantana (Weeds of National Significance)

2008 Report

Australia's Virtual Herbarium (AVH)

The Centre continued its role as a key contributor and developer of the AVH in terms of strategic direction, application and data contribution. In addition to the contribution of data to the AVH, CPBR and ANH staff have been involved in developing specifications for redevelopment of the AVH interface underlying data delivery protocols and in testing work done under contract at the University of Adelaide.
The new AVH will be released in October 2008. Work continues on standards to deliver other data types through the AVH including taxonomy and nomenclature (see APNI/APC below) and digital images of plant portraits, herbarium specimens and description protologues.
Planing is underway to deliver this data to the ALA when it is ready to accept it.

Herbarium Informaton Systems Committee (HISCOM)

CPBR and ANH staff are active contributors to HISCOM in strategic direction setting, and policy, standards and application development.
The Australia's Virtual Herbarium continues to be the the key project and focus of HISCOM. HISCOM is a key participant in the infrastructure development of the ALA and CPBR HISCOM participants have been working with zoological colleagues of the Fauna Collections Information Group (FCIG) on common approaches to engagement with the ALA.

Australian Biodiversity Information Facility (ABIF)

CPBR and ANH staff have been involved in contributing to the development of ABIF in terms of both design and content. During the year the decision was made to suspend active development of the site and redirect effort and support to the Atlas of Living Australia as the primary vehicle for Australia's data contribution to GBIF. This is now being managed as part of the overall ALA strategy and CPBR and ANH staff continue to be involved.

Global Biodiversity Information Facility (GBIF)

CPBR and ANH staff continue active engagement with the Global Biodiversity Information Facility and its technical working groups to ensure compatibility of data and applications. CPBR provides a vice chair of the Nodes committee and attended the GBIF governing board meeiting and symposium in Amsterdam.

Biodiversity Information Systems (TDWG)

CPBR and ANH staff continue active involvement in the Taxonomic Databases Working Group which provides the technical standards foundation for GBIF, contributing to a number of the working groups.
Standards endorsed by TDWG were implemented locally. Staff attended technical workshops in Denmark and the USA and have been actively involved in preparation for the annual TDWG conference to be held in Perth in October 2008.

International Plant Names Index (IPNI)

The CPBR and ANH are partners with Kew and Harvard in the International Plant Names Index. Application development is dependent on external resources and has slowed during the year. Data content through APNI if made available to IPNI. IPNI is a key component of the emerging 'Global Names Architecture' and projects such as the Catalogue of Life that form the nomenclatural and taxonomic backbone of global biodiversity projects such as GBIF and the Encyclopedia of Life.

Atlas of Living Australia (ALA)

The Atlas of Living Australia is a project of the Australian biological collections and taxonomy communities funded by the Australian Government's National Collaborative Research Infrastructure Strategy (NCRIS). New Director and program staff have been appointed and teh new website has been established. CPBR and ANH staff have been in regular with the ALA contact on standards and applications development and the ALA has funded a number of biodiversity informatics projects to be undertaken at the CPBR.

Taxonomy Research & Information Network (TRIN)

TRIN is a national project funded by the Commonwealth Environment Research Fund (CERF). Originally known as the CERF Taxonomy Hub, its name was changed to better reflect its distributed and national focus.
During the year information technology staff were appointed and established the hub website and wiki and research staff are bing trained in using this collaborative environment. A key technical project will be documenting the taxonomic process to see when technology might be engaged to improve efficiency; staff have been holding workshops with researchers to assess processes and business needs.

Miscellaneous

IdentifyLife: http://www.identifylife.org/ CPBR and ANH staff are participants in a global project to provide on-line identification tools and resources for all of the earth's organisms. Project design is taking place on the IdentifyLife wiki, http://wiki.identifylife.org/. The ALA, EoL and the University of Queensland are supporting partners.

APNI and the Australian Fauna Directory: APNI and the AFD have initiated a codevelopment partnership,rogramming pooling resources to improve productivity, develop and implement compatible standards and build on the commonality of plant and animal taxonomy to create a single integrated resource fot Australian plant and animal names.

Standards for biodiversity image storage and retrieval: CPBR and ANH staff have been working with colleagues in the USA attending a workshop in Florida in image storage, documentation and retrieval standards

Scientific and Technical Staf

PROJECT LEADERS

Whitbread, Greg #
Jim Croft #

STAFF, HONORARY ASSOCIATES & STUDENTS

Fuchs, Anne #
John Hook #
Whiting, Andrew