The National Species List (NSL) team has released the source code underpinning parts of the NSL interim service layer. This interim service layer is currently serving data from the Australian Faunal Directory (AFD) and the Australian Plant Names Index (APNI) at biodiversity.org.au, but is built to accommodate delivering arbitrary XML.

The code release encompasses an integrated implementation of a Life Sciences Identifier (LSID) resolver, Linked Data service, and Open Archives Initiative – Protocol for Metadata harvesting (OAI-PMH) endpoint.

With this software, data loaded into the underlying “eXist” open-source XML database (exist.sourceforge.net) can be accessed by these three above protocols, and transformed into a variety of formats as required by content negotiation. The software supports conversion of the data into CSV, JSON, as well as transformation into arbitrary XML (and thus RDF/XML formats).

Key benefits are:

  • The system is a stand-alone web server.
  • The system implements an LSID resolution service out-of-the-box.
  • The system exposes the data to the “Semantic Web” out-of-the-box.
  • The system imposes few restrictions on the form of the XML loaded into it.
  • Supports 3 million records (currently) at biodiversity.org.au
  • Extensible with XSLT and XSQL

The code (and a sample data set) is available at:

and by SVN at:

For more information

Contact: Atlas Support »

The ALA’s spatial portal and mapping tools have been greatly enhanced and are now available at http://spatial.ala.org.au. This has been a major re-work of the portal, simplifying the user interface and adding a lot more flexibility to the manipulation of species, areas and layers. A list of available ‘layers’ is at http://spatial.ala.org.au/layers. As well as mapping species distributions and customising the map view in the spatial portal, Atlas users can:

  • incorporate a selection of over 350 map layers in species modelling and environmental classification. Layers include land-use, social and political boundaries, climate, hydrology, substrate, topography, fire and vegetation.
  • download species records including values from map layers at each location.
  • visualise species records in their environmental context through scatterplots based on any pair of environmental variables.
  • upload their own files of species records for analysis in the spatial portal.

Registrations are open for the International Botanical Congress in Melbourne, Australia, from 23 – 30 July 2011. The IBC already has 1806 delegates registered to attend, with more expected to register within the coming weeks and on site. Read more

Please note the following when using the entire world as the active area.

The projection used does not permit the use of a bounding box > 85 degrees north and south of the equator. We have therefore estimated the reduced area of the bounding box to be ~510,000,000 square kilometres.

ALA Article from Australian Geographic site. Accessed 10 June 2011.

Just one click to identify Australian species
By Natalie Muller (edit ALA)

Australian wildlife enthusiasts are putting our native species on the map, all with the click of a mouse.


DONALD HOBERN REMEMBERS
spending much of his childhood looking at beetles and moths without knowing how to identify what he was looking at. What he needed was a good book – one with pictures, descriptions and species distribution maps.

Now a trained computer programmer, Donald is using his information technology skills to further his interest in natural history. He is leading a project that aims to make Australian biology collections available to the public via the web. Donald is the inaugural director of the Atlas of Living Australia, an online treasure trove of data about Australia’s native plants and animals. “The biggest problem most people have in understanding the wildlife around them is not knowing how to identify them,” he says.

Green-spotted Triangle Butterfly. Photo by CSIRO

The interactive encyclopaedia, which acts as both a Yellow Pages of Australian species and a social networking site for naturalists, is still a work in progress. But Donald hopes it will be a handy resource for experts and policy makers, as well as for kids, eco-tourists, educators, NRM managers and amateur naturalists.

So far the Atlas features downloadable distribution charts, identification tools, images, scientific literature and data sets that provide as complete a picture as possible about each species. Eventually, DNA barcoding data will also be added.

The Atlas was launched late last year and already contains more than 23 million records from museums and data collections around the country. But digitising Australia’s wildlife records is no small task.

That’s one of the reasons why the Atlas team is encouraging the public to upload their own field notes, sightings and photographs to the encyclopaedia’s citizen science portal.

Citizen science

For many years, dedicated community groups have played an important role in collecting field data in the name of science. By throwing online tools into the mix, data sharing between experts and enthusiastic volunteers has been revolutionised. ClimateWatch, Birds Australia, RabbitScan, Birdata, and FungiMap are just some examples of networks that are now using online applications to share their information via the Atlas’s portal.

Dr John Hooper, Head of the Biodiversity and Geosciences programs at the Queensland Museum, says the Atlas is a real benchmark for science.

“People these days are impatient, they’d much rather go to the web, so this offers them the option to go online and put these images up,” he says. “The idea is to pick up all the really keen people and nurture an interaction with them.”

Last month in Brisbane, John launched the Atlas’s latest citizen science web portal, Wild Backyards. He is hoping Queenslanders will get involved in documenting wildlife in their own suburbs.

“We’re trying to get people into life sciences,” he says. “We’re using the technology they love, but they’re doing something that can contribute to their appreciation and protection of the environment around them.”

In other parts of the world, particularly in the USA and Europe, the use of web portals and sophisticated applications for mobile devices, such as iPhones, has created burgeoning online communities of wildlife buffs who share information with each other.
 
”We don’t have those luxuries in Australia,” Donald says. “There are a lot of unknown species, but we want to change that.”

Mapping the species

Nearly 75 per cent of Australia’s estimated 570,000 native species are unknown, but the Atlas team is optimistic their encyclopaedia will help fill this huge gap in knowledge. As recently as 2005, the Queensland Museum found more than 300 new species in Brisbane’s urban bush. John hopes that with the help of Wild Backyards and an enthusiastic community, more will come to light.

“It’s a huge task,” he says. “That’s why the Atlas is so important, to find out what is known and what isn’t, and discover more about what isn’t known.”

Pinning down new species and building data about known species could also prove vital for conservation in a period of environmental and climate change. “The ability to predict [what will happen to native species] is going to be very important as we try and protect Australia’s biodiversity into the future,” Donald says. Detailed online records can allow researchers to track changes in species distribution over time to learn how changes in environment and climate affects wildlife.

The Atlas of Living Australia is a collaboration involving more than 60 biological collections from the CSIRO, Museums and Herbaria, Federal and State departments, universities and fungal and microbial collections.

Article

Fourth International Barcode of Life Conference

When: 28 November – 3 December 2011
Where: Adelaide, South Australia
Website: www.dnabarcodes2011.org

The Consortium for the Barcode of Life and the University of Adelaide invite you to join us in Adelaide, Australia from 28 November – 3 December 2011 for the Fourth International Barcode of Life Conference. This conference will be an exciting opportunity for participants to gain an insight into DNA barcoding and meet the community driving this rapidly advancing biodiversity research movement forward. The conference aims to bring together the international and national leaders in this area which will allow direction for the field to be set for the next 5 years.

Delegate and scientific abstract registration is now open at www.DNAbarcodes2011.org.

Sign up before it’s too late (abstract deadline 15th June).

Building on the momentum achieved at the 3rd International Barcode of Life Conference held in Mexico City, the conference expects to attract 350 delegates from more than 50 countries, and will bring together leaders in the field of this rapidly expanding area; so we hope you will join participants from around the world for the biggest barcoding event ever! The conference will also showcase the growing commercial applications and opportunities that are being created through barcoding.

The 2011 International Barcode of Life Conference will address a range of Barcoding applications and developments, including illegal wildlife and timber trade; pest and disease diagnostics; forensics; quarantine identifications; environmental monitoring and assessment; animal, plant and microbial systematics; and Beyond Barcoding.

More information about the Conference, including accommodation, is available at: www.dnabarcodes2011.org. Introduction to Barcoding by Prof Andy Lowe About Barcoding [PDF, 63Kb]

Initial conference program

The main scientific sections will be held on 30 November-3 December, with 28-29 November set aside for pre-conference workshops. An initial conference program is available at: http://www.dnabarcodes2011.org/conference/program/index.php

Important dates

  1. Call for Abstracts NOW OPEN. Deadline: 15 June 2011. Submit your abstract at: http://www.dnabarcodes2011.org/conference/program/abstract_submission/index.php
  2. Conference Registration and Accommodation Bookings NOW OPEN at: http://www.dnabarcodes2011.org/register/index.php
  3. Travel Bursary Applications NOW OPEN. Deadline: 15 June 2011. Submit your application for a travel bursary at: http://www.dnabarcodes2011.org/travel/travel_support/index.php Note: Travel bursaries will be awarded on a competitive basis to approximately 30 doctoral students and to participants from developing countries, contingent on the availability of funds. Applications will be judged according to the applicant’s past involvement in DNA barcoding and their plans for future involvement. Priority will be given to applicants whose abstracts have been accepted for presentation. Questions about travel bursaries should be posted on the Connect social network – see www.dnabarcodes2011.org
  4. Agenda with speakers available: 1 August 2011

Conference contact details

Website: www.dnabarcodes2011.org
Twitter: dnabarcodes2011
RSS: dnabarcodes2011.wordpress.com/feed

About the conference venue

Adelaide is the capital city of the state of South Australia in Australia. The Conference will be held at the University of AdelaideUniversity of Adelaide  sits in a world-class biodiversity precinct including the South Australian Museum, Botanic Gardens and State Herbarium, and Adelaide Zoo.

Historic Bonython Hall will host the social nerve centre of the conference, as this will be the site for sponsors and exhibitors displays as well the site for the consumption of morning and afternoon tea as well as lunch. Bonython Hall is one of the showcase buildings of Adelaide University, which is Australia’s third oldest University and will provide an outstanding focus point for these core conference activities.

As an information aggregator, it is of paramount importance to the Atlas that all the individuals, institutions and projects that contribute to the ALA are appropriately recognised as the source of the information. The Atlas documents and verifies attribution information when discussing data sharing with contributors and ensures that it is collected when contributions are made via electronic means.  The attribution information is then displayed as prominently as possible wherever information is displayed or downloaded.

The methods of contributions and attribution capture are listed below, followed by the mechanisms for display and access to the attributions.

Attribution capture for contributions

Information harvested from web sites

  • Citation information is determined in consultation with the website owner and is documented either in a Data Provider Agreement (DPA) or in writing (typically in an email).
  • If the website is clearly labelled as licensed for reuse (e.g. creative commons) the citation information is harvested along with the content.

Information contributed via “share” forms

  • Citation and license are selected on the web form when contributing the image, link or data set.

Information provided via other means (e.g. sent on a disk, FTP)

  • Citation information determined in consultation with the data set owner and is documented either in a DPA or in writing (typically in an email).

Visibility of and access to attribution information

Occurrence data

Occurrence data is available in the generation of static  maps, as record sets for view and download and for analysis in the spatial portal.

Species page

Mapped occurrence records

  • Currently no citation.

List of records

  • Indicates dataset for each record.

Single record

  • Indicates data provider and data set.
  • Data set page indicates citation text and rights for the data set.

Download

Archive file includes a citation file

  • Resource name
  • Citation
  • Rights
  • More information (link to collectory page)
  • Data generalisations
  • Information withheld.

Spatial portal

  • Select information for the layer lists data resources and a link to the collectory page for the data set (data set page indicates citation text and rights for the data set).
  • Download (sample) includes a citation.csv file
    • Resource name
    • Citation
    • Rights
    • More information (link to collectory page)
    • Data generalisations
    • Information withheld.

Profile information

Profile information, including links, multimedia and text, is displayed on species pages.

Overview tab

Text

Indicates source and links back to original source website or page.

Online Resources

Indicates content available and links back to the website or page.

Images

Search results

  • no citation.

On species page.

Overview tab

  • Photo by
  • Rights
  • Source.

On individual image view

  • Photo by
  • License
  • Rights
  • Source.

Gallery tab

  • Images – No citation
  • Videos (currently only contains links to videos hosted on the IBC)
  • Video By
  • License
  • Rights
  • Source.

Names Tab

  • Indicates source(s) and link to website

Records Tab

  • Indicates Data set.

Spatial layers

Spatial layers available in the Atlas spatial portal includes environmental and biodiversity surfaces as well as area layers from the gazetteer.

Info popup:

  • Metadata contact organisation
  • Resource constraints
  • License notes
  • More information (where this links to a comprehensive metadata record it will contain details rights and citation information.