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December 2008 newsletter summary

December 2008 – Atlas activities, articles and reports, media releases, conferences and workshops, biodiversity weblinks

Seasons Greetings from the ALA team

The Atlas team would like to thank all those who have expressed interest in the project during 2008. It has been a year of laying foundations and we look forward to delivering some results in 2009. Season’s Greetings.

Atlas user needs analysis

A team from the Australian Museum has recently completed a project to analyse user requirements for biodiversity information and to identify areas in which the Atlas can assist users. This user needs analysis document will be an essential tool in setting the direction for the work of the Atlas over the next few years. The main body of the report is available through the Atlas web site.

Priority setting for the Atlas

The Atlas now has several essential tools to guide us in our planning and help us to set priority goals for the project. These tools include:

We now need to take the next steps and identify specific projects, tools and services which should be the primary focus of attention for the Atlas up to June 2011. These projects should be selected to maximise the benefit to users of biodiversity data and to demonstrate the potential benefits which are to be expected from bringing all available information on all Australian species online in an integrated form.

The Atlas is therefore seeking input into defining the set of projects which will best meet these goals. Please take time to look at the documents and provide your comments.

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November 2008 newsletter summary

November 2008 – Atlas activities, articles and reports, media releases, conferences and workshops, biodiversity weblinks

Getting involved in the Atlas of Living Australia

The Atlas of Living Australia (ALA) team has been busy over the last few months starting work on systems to integrate Australian biodiversity data. We hope soon to be able to offer early versions of some tools and interfaces. The real value from a project like the Atlas will however come from the resources which data owners share through the system.

We would like therefore to ask for your involvement in any of the following ways:

Sharing specimen and observation data

The ALA aims to help researchers to understand the distribution of Australian plants and animals. We are therefore inviting everyone to let us know of data they hold on the occurrence of any Australian species. We will then explore the best ways to assist data owners in linking their information to the ALA.

Sharing images through Flickr

(Before the public release in November 2010. This group is still available and is harvested regularly into the Atlas. Alternatively see the Tools – Images Page for more details.

The Encyclopedia of Life (EOL) has set up a group on the Flickr photo-sharing site to allow photographers to share their images of any organism. The Atlas encourages Australian photographers to use this site make their images available to the ALA, EOL and other users of biodiversity information.

Sharing collection information through the Biodiversity Collections Index

The Biodiversity Collections Index (BCI) is an international initiative to build an online catalogue of all herbaria and natural history collections. The ALA will use the BCI as a key reference and would like to encourage Australian collection managers to make sure that their collections are registered and described in the system.

For more information, see Biodiversity Collections Index

Contributions to the ALA from Queensland Museum

The ALA is a collaboration between a large number of participant organisations and institutions. Their content will be the most significant part of what the Atlas has to offer. Over the coming months we plan to highlight what different ALA participants are doing to develop and share information as part of their contribution to the project.

This month we have an update from Queensland Museum on the new Vernon software system they have been implementing to manage information on more than 1.2 million specimens and other collection objects held by the museum. This has required significant effort on their part in cleansing data and ensuring that it makes consistent use of standard terms.

The Vernon software supports Darwin Core, one of the key data standards adopted by the ALA. This will allow Queensland Museum to share existing and future data from its biodiversity collections through the Atlas.

TDWG Conference in Fremantle

TDWG held its annual conference on biodiversity informatics in Fremantle, WA, 19-26 October 2008. This meeting was very well attended by delegates from across Australia and around the world and addressed many issues of relevance to the ALA.

Presentations from the conference were recorded and are available online as movie files. This includes ten presentations specifically addressing Australian biodiversity informatics and the work of the ALA.

For more information on the conference, see TDWG conference in Fremantle, October 2008 and Atlas’ presentations given at TDWG.

Other activity

Over the last two months work has continued on the following tasks:

  • Collaborating with the team from the Australian Museum producing the Atlas user needs analysis (due to be available in the next few weeks).
  • Participating in the TDWG Conference in Perth, a major opportunity to share ideas and learn from similar projects around the world.
  • Setting up and configuring a copy of the data portal software developed by GBIF (GBIF Data Portal) to index data on the occurrence of Australian organisms
  • Developing detailed specifications for the DIAS-B project (Metadata Repository and Data Annotation Services) and evaluating candidate technologies
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TDWG conference in Fremantle, October 2008

Taxonomic Database Working Group (TDWG) held its annual conference in Fremantle, WA, 19-26 October 2008. This was the largest TDWG meeting ever, with around 180 participants from all continents, including 60 from across Australia. Links are provided to the agenda, abstracts and presentations.

Taxonomic Database Working Group (TDWG) held its annual conference in Fremantle, WA, 19-26 October 2008. This was the largest TDWG meeting ever, with around 180 participants from all continents, including 60 from across Australia.

Over the five days of the main conference a large number of presentations were given on many aspects of biodiversity informatics. The programme from the conference is available online at http://www.tdwg.org/conference2008/program/ and includes links to the presentations, many of them with audio captured on the day. Abstracts for all presentations are included in the Proceedings of TDWG 2008 (also available as a PDF).

The Wednesday morning sessions were dedicated to an exploration of Australian biodiversity informatics and of the services under development as part of the Atlas of Living Australia.

On Wednesday afternoon participants joined workshops to explore user requirements for the Atlas and to consider approaches to addressing them. The results of these workshops will be incorporated into the Atlas user needs analysis report which will be issued shortly.

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September 2008 newsletter summary

September 2008 – Atlas activities, articles and reports, media releases, conferences and workshops, biodiversity weblinks

Bioinformatician positions advertised

Two positions have been advertised for bioinformaticians to work with the ALA to manage data captured by the Australian Phenomics Network (based in Canberra, closing date, 24 September 2008) and the Australian Plant Phenomics Facility (based in Adelaide, closing date 19 September 2008).

Memorandum of Cooperation with Earthwatch Australia

The ALA has signed a Memorandum of Cooperation with Earthwatch Australia to work together on developing tools for capturing observations of Australian organisms, particularly as part of Earthwatch’s ClimateWatch project to capture data on the timing of recurring natural phenomena such as flowering or nesting dates.

Sharing data with the ALA

Draft guidelines have been prepared to assist data providers with making data accessible through the ALA. Comments are welcomed on these guidelines and the ALA staff will be happy to talk to potential data providers to clarify any issues.

For more information on sharing data with the Atlas.

Data Integration and Annotation Services for Biodiversity

The Data Integration and Annotation Services for Biodiversity (DIAS-B) project (funded by the NCRIS National e-Research Architecture Taskforce, NeAT) has now developed its project plan. This project will develop the Atlas’ Metadata Repository and Data Annotation Services components. The kick-off meeting for the project team will take place in Canberra on 8th and 9th September 2008.

The DIAS-B NeAT Project Plan is online – PDF (136KB).

TDWG meeting in Perth, 19-24 October 2008

TDWG, the international organisation dedicated to developing standards and tools to support the integration of biodiversity information, is meeting this October in Perth. The agenda for the conference is almost finalised and includes a whole day devoted to the ALA (Wednesday, 22 October), as well as many other topics of relevance to those using or developing information on Australian organisms. We encourage anyone interested to come along and participate in the meeting. Note that conference fees are reduced for registrations received on or before 6 September 2008.

The TDWG conference agenda is online.

Other activity

Over the last seven weeks the ALA team has been working on the following tasks:

  • Finalising the ALA Business Plan 2008-2009 (Draft) – PDF (329KB)
  • Planning the implementation of the DIAS-B project (Metadata Repository and Data Annotation Services)
  • Starting work to port the GBIF Data Portal software for use as an Australian data portal
  • Continuing work on the Atlas’ user needs analysis
  • Meetings to explore possible collaborations with related organisations and projects, including contacts with representatives from Council of Australian Museum Directors, Australian Biosecurity Information Network, Canberra Ornithologists Group, Australian National Botanic Gardens, Australian National University, Landcare New Zealand, the e-Marine Information Infrastructure Facility, the DEWHA Genetic Resources Management Section and the Australian Partnership for Sustainable Repositories.
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Bioinformatician positions advertised

Two positions have been advertised for bioinformaticians to work with the ALA to manage data captured by the Australian Phenomics Network and the Australian Plant Phenomics Facility. These positions closed late September 2008.

APN Logo
APPF Logo

NCRIS has funded the ALA to work closely with two other major NCRIS capabilities, the Australian Phenomics Network (APN) and the Australian Plant Phenomics Facility (APPF).

The APN is a network of research centres providing Australian and international researchers with mouse models for the study of human and animal disease.

The APPF has two nodes exploiting recent advances in robotics, imaging and computing to enable sensitive, high throughput analyses to be made of plant growth and function.

The ALA is providing some of the core information infrastructure to enable these capabilities to organise large quantities of data and images on their study organisms and to make these resources accessible to researchers in Australia and overseas.

Two positions are being advertised for bioinformaticians to work with the APN and the APPF to explore their data management requirements and to work with the ALA to develop appropriate services to support these communities.

The APN is seeking a bioinformatician to be based at ANU in Canberra. See the advertisement and documentation. The closing date for applications is 24 September 2008.

The APPF is seeking a bioinformatician to be based at the University of Adelaide. See the advertisement and documentation. The closing date for applications is 19 September 2008.

These positions are now closed.

This is a DRAFT – please send us your comments and suggestions.

The Atlas of Living Australia will integrate a wide range of data resources which have already been shared online and which can be accessed without any additional work on the part of the data providers.

However many institutions and individual researchers are hindered from making biodiversity data available by the complexity of the existing tools. Some of these tools require significant understanding of database and web technologies. In all cases they require the data provider to have access to a web server and permission to run executable code on such a server. This is an insurmountable technical threshold for many research groups.

The Atlas will therefore invest resources during 2008-2009 and beyond in improving the usability of existing tools and in developing alternative means for data providers to share their data. The key elements in this activity will be:

  • Developing installable software bundles including web server and database components and all prerequisite software necessary to run standards-compliant wrapper software. (At present data providers are often obliged to download and even compile some of these prerequisite components.)
    The following features are desirable:

    1. A fully configured web server implementation (without providers being required to find prerequisite packages themselves) for Windows and Linux.
    2. A simple default database (e.g. MySQL) with a basic predefined structure into which data can easily be imported from spreadsheets, etc.
    3. Interfaces to import data into the default database.
    4. Preconfigured TAPIR (and any other required interfaces) offering Darwin Core and ABCD interfaces against the default database (developed in conjunction with AVH and OZCAM to ensure that they also support their needs).
    5. Wizard interfaces for mapping other databases and exposing their data using the same Darwin Core and ABCD interfaces.
    6. Basic HTML user interface for users to browse or search the data – with simple configuration to apply basic styling, logos, etc. (in other words to allow the installation to serve as part or all of a web site for the provider).
    7. Google Maps (or similar) map interface integrated into the HTML user interface (including clear instructions on getting the necessary key from Google to use their maps).
    8. MorphBank, Gallery (or similar, open source) image management integrated into database to make it easy to associate images with specimen data
    9. Documentation and tutorial materials for installing and using this software
  • Enhancing the Atlas’s Metadata Repository and Data Harvesting components to support harvesting of data directly from flat-file, spreadsheet formats (CSV dumps, Excel, etc.). This will allow data providers to share data simply by placing a file on a web server and registering associated metadata in the Atlas Metadata Repository.
  • Exploring collaborative opportunities for the Atlas and third-party organisations to develop online repositories to which data providers may upload biodiversity data. Such a repository should give users of all kinds (from lab researchers to amateur naturalists) to upload and view data (especially ecological and observational data sets) through a web browser interface. The interface should provide all of the features listed above for the installable software bundles and should give users control over the visibility and publication of data.

The Atlas will work with existing projects dedicated to integrating Australian biodiversity data. The Atlas will help to consolidate the work of these projects and provide infrastructure required to enable them to succeed. The following relationships will be particularly significant:

  • Australia’s Virtual Herbarium (AVH), Online Zoological Collections of Australian Museums (OZCAM), Australian Plant Protection Database (APPD) and Australian Microbial Research Information Network (AMRIN) – the Atlas will work with these existing network projects to ensure that Atlas software developments (especially Data Provision Services) are fully supportive of the needs of each project; Atlas activities should reinforce the development and identity of these networks, which will be key contributors of content to the Atlas.
  • Australian Biological Resources Study (ABRS) – the Atlas will work with ABRS to develop web delivery mechanisms (especially web services) for data sets produced through ABRS activities
  • Australian Biodiversity Information Facility (ABIF) – the Atlas will assume responsibility for the integration of Australian data resources with GBIF, and will work with the Australian GBIF delegation to ensure that mechanisms and processes are in place for making decisions on the content Australia should offer at this level.
  • Ocean Biogeographic Information System (OBIS) – many data sets of relevance to the Atlas also relate to OBIS; the Atlas will coordinate activity with OBIS to ensure compatibility and efficient use of resources; this relates in particular to Data Provision Services and the Metadata Repository, but linkages are likely for all the Atlas components identified below.

dont confuse us

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July 2008 newsletter summary

July 2008 – Atlas activities, articles and reports, media releases, conferences and workshops, biodiversity weblinks

Many thanks to all those who responded positively to the first Atlas newsletter and particularly to those who have already provided input to the Atlas’ user needs analysis. All information in these newsletters is included in the Atlas of Living Australia website at Atlas Updates.

To subscribe to this newsletter, you need to create a My Profile. For more information »

Atlas Business Plan 2008-2009

The Atlas has developed its Business Plan for the coming year and would value input from any interested parties on the approach taken and the developments planned. This plan describes the key components which have been identified as priorities for the Atlas.

For more information on the business plan, see ALA Business Plan 2008-2009 (Draft) – PDF (329KB).

The Atlas and other networks

The Atlas is fortunate to be able to build upon the work of existing biodiversity data networks, in particular the Australian Virtual Herbarium (AVH) and the Online Zoological Collections of Australian Museums (OZCAM). The AVH and OZCAM each bring together data from collections throughout Australia and offer public interfaces for searching these data. The ALA will work with these and with similar networks to develop compatible tools and data standards, e.g. with the Ocean Biogeographic Information System (OBIS), the Australian Microbial Resource Information Network (AMRIN), and the Australian Plant Pest Database (APPD). The Atlas aims to contribute to the further development of these networks and to assist them in delivering information products targeted to their specific audiences.

For more information on the Atlas’ plans to support data sharing networks, see Data Provision Services.

Atlas staff

The Atlas recently has recruited a few key staff to join the core team based in Canberra. Dr Lynette Woodburn has taken up the role of Metadata Curator and will be responsible for developing relationships with data providers around Australia and for managing the Atlas metadata repository. Dr Nick dos Remedios has started work as a Java Developer and will initially be focusing on tools to harvest geospatial data. A Technical Architect has also been appointed and will start work later in the year.

For more information on contacting the Atlas of Living Australia, see Contact Us.

Data Integration and Annotation Services for Biodiversity

Data Integration and Annotation Services for Biodiversity (DIAS-B) is a project funded by the NCRIS National e-Research Architecture Taskforce (NeAT). This project provides additional support for the ALA to develop its Metadata Repository and Data Annotation Services components. The project will enable the Atlas to recruit four developers to work on these components (two based at the CSIRO ICT Centre and two at the University of Queensland). Additional support for these activities has been committed from CSIRO’s Information Management and Technology group.

For more information on DIAS-B, see NeAT Business Plan Component Data Integration and Annotation Services in Biodiversity (DIAS-B) – PDF (299KB).

Other activity

Over the last month the Atlas team has been working on the following tasks:

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June 2008 newsletter summary

June 2008 – Atlas activities, articles and reports, media releases, conferences and workshops, biodiversity weblinks

Welcome to the Atlas of Living Australia Newsletter

The Atlas of Living Australia project is now making progress and we plan to produce a regular informational newsletter to keep stakeholders and friends aware of what is happening. We would appreciate it if you could pass this first newsletter on to interested colleagues.

Please send an email to (info@ala.org.au) if you wish to be added to the mailing list for this newsletter, or if you wish to be removed from the list.

The project

The Atlas of Living Australia (ALA) is a five-year project funded under the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS) and involving a wide range of Australian scientific institutions and organisations.

The goal of the project is to develop web-based tools to enable users to discover, access and use the widest possible range of information resources relating to Australia’s fauna and flora, including databases from natural history collections and ecological field work, images and other multimedia, text documents, identification tools and molecular data.

A presentation giving an overview of some of the planned project activities can be found in the Presentations section:
The ALA – Challenges and Opportunities for Managing Biodiversity Information (D Hobern, 15 May) – PPT (11.5MB) – PDF (2.3MB)

Atlas web site

The Atlas has launched its web site. At present it mostly comprises information about the project and its participant organisations, but the site will increasingly include information and discussions on the planning and implementation of the project. Ultimately it will become the Atlas portal for discovering information on all Australian species.

Atlas user needs analysis

What can you do for the Atlas today? We need your contacts in biodiversity – lots of them, and from as many different fields as you can identify. We want to ask them (and you) a few simple questions.

We have commissioned a small team to investigate how users access such information today and how they use it in their own studies and decision-making. Over the next few months, this team will be contacting many of you to learn more about your needs. Please give them your support – we want to understand how the ALA can become a useful tool for you in your work.

For more information on this process, see the planning for the User Needs Analysis.

TDWG 2008 conference to be held in Perth

Taxonomic Database Working Group (TDWG), the international biodiversity information standards organisation, will hold its annual conference at the Western Australian Maritime Museum, Perth, 19-25 October 2008. One day of the conference will be devoted specifically to the Atlas of Living Australia and will include workshops to explore ways for the project to meet the needs of Australian researchers.

For more information on the conference, see TDWG Annual Conference 2008.

ALA review of online and desktop tools

Paul Flemons and John Tann from the Australian Museum have carried out an extensive review of software components which could feed into the development of the Atlas or which could be of benefit to data providers or users. The results of this review are online at http://alatools.pbwiki.com/. Please take a look at this resource and suggest any additional tools which should be included.

For more information on this review, see the Tools Survey.

The Atlas and GBIF

We have started discussions with the Global Biodiversity Information Facility (GBIF) to ensure that the Atlas can act as the Australian node within GBIF. The Atlas expects to reuse code from the GBIF Data Portal to develop its own cache of Australian biodiversity records. This cache will then serve as an efficient way to integrate Australian data into GBIF’s global network. The Atlas has also begun discussions with GBIF New Zealand on possible ways to share resources and align activity.

Other activity

Over the last few months the Atlas team has been working on the following tasks:

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TDWG 2008 conference to be held in Perth

TDWG the international biodiversity information standards organisation, will hold its annual conference at the Western Australian Maritime Museum, Perth, 19-25 October 2008. A full day symposium on the Atlas of Living Australia will take place on Wednesday 22 October.

Taxonomic Database Working Group (TDWG), the international biodiversity information standards organisation, will hold its annual conference at the Western Australian Maritime Museum, Perth, 19-25 October 2008. This conference will bring together a wide range of biologists and informaticians with interest in managing biodiversity data for use across the web.

A full day symposium on the Atlas of Living Australia will take place on Wednesday 22 October. The morning will be devoted to presentations on current biodiversity informatics activity in Australia and to a set of presentations on the Atlas itself. The afternoon will be used for workshops to review some of the user needs that have been identified for the Atlas and to identify ways to bring the necessary data online and to develop the tools and interfaces to make it accessible. This will be an opportunity for those involved in the Atlas and in Australian institutions to benefit from TDWG’s international expertise.

Other sessions of interest include training in the use of TDWG tools and standards on the Tuesday afternoon and Thursday morning.

For more information, and the draft agenda, see the TDWG conference website. We encourage you to come along and learn more about global activity in biodiversity informatics.

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Tools survey

The Atlas of Living Australia has carried out an extensive review of software components which could feed into the development of the Atlas or which could be of benefit to data providers or users.

ALA Review of Online and Desktop Tools

Paul Flemons and John Tann from the Australian Museum have carried out an extensive review of software components which could feed into the development of the Atlas or which could be of benefit to data providers or users.

This impressive review has been made available as an online, editable website at http://alatools.pbwiki.com/. Please feel free to suggest additional tools which should be included – or, better still, take the time yourself to add information on such tools (send an email to John Tann, john.tann@austmus.gov.au, or Donald Hobern, Donald.Hobern@csiro.au to gain access). We hope that this will become an increasingly useful resource for a wide range of users.

The review can also be downloaded as a document including all information entered up to February 2008:
Review of online and desktop tools for the ALA, (J Tann & P Flemons, February 2008) – PDF (6.8MB).