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 code (and a sample data set) is available at:
and by SVN at:
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:
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)
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.
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.
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.
When: 28 November – 3 December 2011
Where: Adelaide, South Australia
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.
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
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.
Occurrence data is available in the generation of static maps, as record sets for view and download and for analysis in the spatial portal.
Archive file includes a citation file
Profile information, including links, multimedia and text, is displayed on species pages.
Indicates source and links back to original source website or page.
Indicates content available and links back to the website or page.
On species page.
On individual image view
Spatial layers available in the Atlas spatial portal includes environmental and biodiversity surfaces as well as area layers from the gazetteer.