Unlocking Australia’s biodiversity, one dataset at a time

Illustration by CSIRO

Australia’s unique and highly endemic flora and fauna are threatened by rapid losses in biodiversity and ecosystem health, caused by human influence and environmental challenges. To monitor and respond to these trends, scientists and policy-makers need reliable data.

Biodiversity researchers and managers often don’t have the necessary information, or access to it, to tackle some of the greatest environmental challenges facing society, such as biodiversity loss or climate change. Data can be a powerful tool for the development of science and decision-making, which is where the Atlas of Living Australia (ALA) comes in.

ALA – Australia’s national biodiversity database – uses cutting-edge digital tools which enable  people to share, access and analyse data about local plants, animals and fungi. It brings together millions of sightings as well as environmental data like rainfall and temperature in one place to be searched and analysed. All data are made publicly available – ALA was established in line with open-access principles and uses an open-source code base.

The impressive set of databases on Australia’s biodiversity includes information on species occurrence, animal tracking, specimens, biodiversity projects, and Australia’s Natural History Collections. The ALA also manages a wide range of other data, including information on spatial layers, indigenous ecological knowledge, taxonomic profiles and biodiversity literature. Together with its partner tools, the ALA has radically enhanced ease of access to biodiversity data. A forum paper recently published with the open-access, peer-reviewed Biodiversity Data Journal details its history, current state and future directions.

Established in 2010 under the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS) to support the research sector with trusted biodiversity data, it now delivers data and related services to more than 80,000 users every year, helping scientists, policy makers, environmental planners, industry, and the general public to work more efficiently. It also supports the international community as the Australian node of the Global Biodiversity Information Facility and the code base for the successful international Living Atlases community.

With thousands of records being added daily, the ALA currently contains nearly 95 million occurrence records of over 111,000 species, the earliest of them being from the late 1600s. Among them, 1.7 million are observation records harvested by computer algorithms, and the trend is that their share will keep growing.

An ALA staff member. Photo by CSIRO

Recognising the potential of citizen science for contributing valuable information to Australia’s biodiversity, the ALA became a member of the iNaturalist Network in 2019 and established an Australian iNaturalist node to encourage people to submit their species observations. Projects like DigiVol and BioCollect were also born from ALA’s interest in empowering citizen science.

The ALA BioCollect platform supports biodiversity-related projects by capturing both descriptive metadata and raw primary field data. BioCollect has a strong citizen science emphasis, with 524 citizen science projects that are open to involvement by anyone. The platform also provides information on projects related to ecoscience and natural resource management activities.

Hosted by the Australian Museum, DigiVol is a volunteer portal where over 6,000 public volunteers have transcribed over 800,000 specimen labels and 124,000 pages of field notes. Harnessing the power and passion of volunteers, the tool makes more information available to science by digitising specimens, images, field notes and archives from collections all over the world.

Built on a decade of partnerships with biodiversity data partners, government departments, community and citizen science organisations, the ALA provides a robust suite of services, including a range of data systems and software applications that support both the research sector and decision makers. Well regarded both domestically and internationally, it has built a national community that is working to improve the availability and accessibility of biodiversity data.

Original source:

Belbin L, Wallis E, Hobern D, Zerger A (2021) The Atlas of Living Australia: History, current state and future directions. Biodiversity Data Journal 9: e65023. https://doi.org/10.3897/BDJ.9.e65023

How to import occurrence records into manuscripts from GBIF, BOLD, iDigBio and PlutoF

On October 20, 2015, we published a blog post about the novel functionalities in ARPHA that allows streamlined import of specimen or occurrence records into taxonomic manuscripts.

Recently, this process was reflected in the “Tips and Tricks” section of the ARPHA authoring tool. Here, we’ll list the individual workflows:

Based on our earlier post, we will now go through our latest updates and highlight the new features that have been added since then.

Repositories and data indexing platforms, such as GBIF, BOLD systems, iDigBio, or PlutoF, hold, among other types of data, specimen or occurrence records. It is now possible to directly import specimen or occurrence records into ARPHA taxonomic manuscripts from these platforms [see Fig. 1]. We’ll refer to specimen or occurrence records as simply occurrence records for the rest of this post.

Import_specimen_workflow_
[Fig. 1] Workflow for directly importing occurrence records into a taxonomic manuscript.
Until now, when users of the ARPHA writing tool wanted to include occurrence records as materials in a manuscript, they would have had to format the occurrences as an Excel sheet that is uploaded to the Biodiversity Data Journal, or enter the data manually. While the “upload from Excel” approach significantly simplifies the process of importing materials, it still requires a transposition step – the data which is stored in a database needs to be reformatted to the specific Excel format. With the introduction of the new import feature, occurrence data that is stored at GBIF, BOLD systems, iDigBio, or PlutoF, can be directly inserted into the manuscript by simply entering a relevant record identifier.

The functionality shows up when one creates a new “Taxon treatment” in a taxonomic manuscript in the ARPHA Writing Tool. To import records, the author needs to:

  1. Locate an occurrence record or records in one of the supported data portals;
  2. Note the ID(s) of the records that ought to be imported into the manuscript (see Tips and Tricks for screenshots);
  3. Enter the ID(s) of the occurrence record(s) in a form that is to be seen in the “Materials” section of the species treatment;
  4. Select a particular database from a list, and then simply clicks ‘Add’ to import the occurrence directly into the manuscript.

In the case of BOLD Systems, the author may also select a given Barcode Identification Number (BIN; for a treatment of BIN’s read below), which then pulls all occurrences in the corresponding BIN.

We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. We have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found on iDigBio. What we need to do is to locate the ID of the occurrence record in the iDigBio webpage. In the case of iDigBio, the ARPHA system supports import via a Universally Unique Identifier (UUID). We have already created a treatment for S. capillifolium and clicked on the pencil to edit materials [Fig. 2].

Figure-61-01
[Fig. 2] Edit materials
In this example, type or paste the UUID (b9ff7774-4a5d-47af-a2ea-bdf3ecc78885), select the iDigBio source and click ‘Add’. This will pull the occurrence record for S. capillifolium from iDigBio and insert it as a material in the current paper [Fig. 3].

taxon-treatments- 3
[Fig. 3] Materials after they have been imported
This workflow can be used for a number of purposes. An interesting future application is the rapid re-description of species, but even more exciting is the description of new species from BIN’s. BIN’s (Barcode Identification Numbers) delimit Operational Taxonomic Units (OTU’s), created algorithmically at BOLD Systems. If a taxonomist decides that an OTU is indeed a new species, then he/she can import all the type information associated with that OTU for the purposes of describing it as a new species.

Not having to retype or copy/paste species occurrence records, the authors save a lot of efforts. Moreover, they automatically import them in a structured Darwin Core format, which can easily be downloaded from the article text into structured data by anyone who needs the data for reuse.

Another important aspect of the workflow is that it will serve as a platform for peer-review, publication and curation of raw data, that is of unpublished individual data records coming from collections or observations stored at GBIF, BOLD, iDigBio and PlutoF. Taxonomists are used to publish only records of specimens they or their co-authors have personally studied. In a sense, the workflow will serve as a “cleaning filter” for portions of data that are passed through the publishing process. Thereafter, the published records can be used to curate raw data at collections, e.g. put correct identifications, assign newly described species names to specimens belonging to the respective BIN and so on.

 

Additional Information:

The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 642241.