Systems supported by the Atlas

Systems supported by the Atlas

As well, the Atlas is developing a Field Data Capture Toolkit.

Updating software

Two software applications have been updated by the Atlas to ensure their ongoing viability and compatibility with modern operating systems:

  • BioLink—BioLink software is used for collection, maintenance, analysis, application and dissemination of taxonomic, biodiversity and environmental information. Originally developed by CSIRO Entomology in the 1990s, BioLink has been adopted by mostly insect collections both in Australia and internationally
  • DELTA—DELTA (DEscriptive Language for TAxonomy) software was developed by CSIRO between 1971 and 2000 and is a flexible tool for encoding taxonomic descriptions for machine processing. The ALA-supported version is known as ‘Open DELTA’

Both applications are available under Open Source licences.

Establishing Australian nodes

Australian nodes are being established for three data repositories:

  • Biodiversity Heritage Library (BHL)—BHL is a global consortium of museum, herbarium, university and research institute libraries whose aim is to provide free and open access to digitised biological literature. The Atlas is working with local organisations to digitise biodiversity literature for BHL. Most of the literature referred to in the Atlas is drawn from BHL
  • BOLD (Barcode of Life Database)—BOLD is a workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The Atlas is working with the BOLD development team at the University of Guelph in Canada to integrate BOLD data into the Atlas and establish an Australian node
  • Morphbank—Morphbank is an Open Source web application and repository for storing and sharing specimen‐based images, principally for scientific use. As well as establishing the Australian node (morphbank.ala.org.au), the Atlas is working with the US Morphbank development team to develop the next version of the software. Several Atlas partners intend to establish their own instance of Morphbank for in-house management of images. Images in Morphbank will be used in the Atlas where appropriate

Providing development resources

Several information systems are being actively supported by the Atlas, primarily through funding development activities:

  • Bowerbird— is a collaborative website connecting users with experts to assist in identifying species
  • IdentifyLife— is a global, collaborative web application  providing tools to identify and manage descriptive data (identification keys) for organisms
  • National Species Lists—authoritative lists of species are central to biodiversity science accessible via web services. The Atlas is working with the Australian National Botanic Gardens, the Australian Biological Resources Study, the Council of Heads of Australasian Herbaria (CHAH) and taxonomists to compile a more complete list of Australian species. Part of this endeavour is the provision of web services to access the lists of fauna Australian Faunal Directory and flora Australian Plant Census
  • Species Interactions of Australia Database (SIAD)—SAID is an Open Source information system enabling users to gather and share information on species interactions and associations. It is at an early stage of development (late 2011)
  • TRIN Wiki— is an Open Source suite of tools providing contributors with simple online interfaces for creating, collating and compiling well‐structured biodiversity knowledge. It is organised around specific projects which vary in their maturity and target audience. Some contain information put together for public consumption. Others are moderated or closed spaces in which taxonomic projects collaborate on their own business prior to it being published. The project is also building a meta-taxon profile (Wallace Core), a single expansive framework capable of describing many arbitrary taxon profiles along with the means to use it to describe individual/given taxon profiles

Wallace Core mappings for TRIN Wiki. Photo courtesy of Garry Jolley-Rogers.

Information from all these systems will be included in the Atlas.

See also FAQ Identification keys

Providing software licences

The Atlas, in association with the Council of Heads of Australian Collections of Microorganisms (CHACM), provided, and assisted in implementing, BioloMICS software to manage collections of microorganisms. Assistance included helping migrate existing data, setting up the means to share data through the Atlas, training personnel, ensuring adequate technical support and developing a microorganism data schema to be used when sharing data.

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Providing information

Specify 6 is Open Source software designed to manage natural history collections. The Atlas has been actively exploring with those institutions in need of new or better collection management software how best to help—including determining whether Specify 6 would be suitable for their collections. Several institutions have decided to adopt Specify 6.