Biodiversity Data Journal 9: e65023 OO)
doi: 10.3897/BDJ.9.e65023 open access

The Atlas of Living Australia: History, current
state and future directions

Lee Belbin?, Elycia Wallis’, Donald Hobern*, Andre Zerger*

$ Atlas of Living Australia, CSIRO, Canberra, Australia
§ Atlas of Living Australia, CSIRO, Melbourne, Australia

Corresponding author: Andre Zerger (andre.zerger@csiro.au)
Academic editor: Lyubomir Penev
Received: 25 Feb 2021 | Accepted: 29 Mar 2021 | Published: 21 Apr 2021

Citation: 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

Abstract

The Atlas of Living Australia (ALA) is Australia’s national biodiversity database, delivering
data and related services to more than 80,000 Australian and international users annually.
Established under the Australian Government's National Collaborative Research
Infrastructure Strategy to provide trusted biodiversity data to support the research sector,
its utility now extends to government, higher education, non-government organisations and
community groups. These partners provide data to the ALA and leverage its data and
related services. The ALA has also played an important leadership role internationally in
the biodiversity informatics and infrastructure space, both through its partnership with the
Global Biodiversity Information Facility and through support for the international Living
Atlases programmes which has now delivered 24 instances of ALA software to deliver
sovereign biodiversity data capability around the world. This paper begins with a historical
overview of the genesis of the ALA from the collections, museums and herbaria community
in Australia. It details the biodiversity and related data and services delivered to users with
a primary focus on species occurrence records which represent the ALA's primary data
type. Finally, the paper explores the ALA's future directions by referencing results from a
recently completed national consultation process.

© Belbin L et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY
4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are
credited.

2 Belbin L et al

Keywords

Atlas of Living Australia, biodiversity, research data infrastructure, informatics

Introduction

The Atlas of Living Australia (ALA) was established in 2010 by the Australian Government's
National Collaborative Infrastructure Strategy (NCRIS) to support the needs of the
Australian and international research community for comprehensive and timely access to
Australian biodiversity data. The ALA is now delivering data and related services to more
over 80,000 users a year across research, industry, governments and the public. It
supports programmes in taxonomy, biodiversity, genomics and ecosystem science,
contributes to major natural resource management programmes and supports the
international community as the Australian node of the Global Biodiversity Information
Facility (GBIF) and the code base for the successful international Living Atlases
community. The ALA was established on open-access principles, with data publishers by
default using Creative Commons licences and with an open-source code base. This
approach has encouraged re-use and maximised the value of data, especially for data that
have been funded, produced or collected by public institutions in Australia.

As of February 2021, the ALA holds almost 95 million records associated with more than
111,000 species, predominantly from the Australian region. As a complement to its species
data, the ALA also manages a wide range of other categories of data, including information
on natural historical collections themselves, spatial layers, indigenous ecological
knowledge, taxonomic profiles, biodiversity literature, data on biodiversity projects and
animal tracking data. Investment in the ALA and in its partner capabilities (including GBIF
and the Living Atlases) has radically enhanced ease of access to biodiversity data.

Fundamental to ALA's business has also been the development of tools and platforms to
enable different stakeholders to collect, manage and deliver open biodiversity data.
Examples include BioCollect for field-based data collection and management, DigiVol to
engage volunteers in the digitisation of analogue data, the Australian node of the
Biodiversity Heritage Library, ALA's spatial portal and species lists tools. Most recently, the
ALA has partnered with the global iNaturalist platform to support citizen scientists in the
acquisition and identification of biodiversity observations. Collectively, this portfolio of
capability has been fundamental in improving how ALA captures and utilises biodiversity
data.

This paper provides a history of the ALA including its origins and key drivers, a description
of the data and services it delivers and concludes with a summary of the findings from
recent stakeholder consultations that will provide information for the ALA's future directions.
Although these consultations focused on the ALA, the results offer insights of importance to
other national and international biodiversity data infrastructures regarding future trends,
stakeholder expectations and limitations around current approaches to delivering
biodiversity data and services.

The Atlas of Living Australia: History, current state and future directions 3

Biodiversity in Australia

As a result of its isolation for around 100 million years and its distinctive environment,
Australia's fauna and flora are rich and unique, exhibiting high degrees of endemism.
Human influence has led to significant loss and/or transformation of this biodiversity
(Woinarski et al. 2019). Environmental challenges and human consumption place
unprecedented and increasing stresses on the environment and species. At the global
scale, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem
Services (IPBES 2019) reports rapid losses in biodiversity and ecosystem health, and
states that insufficient information exists to monitor and respond to these trends.
Biodiversity researchers and managers commonly face the challenge of delivering and
interpreting disparate information to answer the greatest environmental questions facing
society. For example:

° Signs point to massive losses in insect numbers and diversity, but what is the
actual scale of these losses and the implications for ecosystem health? (Braby
2018)

° Australia is home to a number of global biodiversity hotspots, which have preserved
unique evolutionary lines through many climatic changes. How are current and
expected pressures on these ecosystems likely to modify these areas?

° How can we design effective ecosystem restoration programmes and respond to
ecological changes in response to major disturbances, such as the 2019-2020
bushfire season?

The Australian Government’s recent Independent Review of the Environmental Protection
and Biodiversity Conservation Act Interim Report (Samuel 2020) identified that a ‘quantum
shift in the quality of information, accessible data and information available to decision-
makers’ is necessary to support future regulatory environmental management
programmes. The ALA has an important role to play in supporting these emerging
regulatory policy needs of government.

Historical information on species distributions and population abundances is central to
ecology, conservation and to all areas of environmental planning and sustainability. The
ALA is highly regarded for the progress it has made over the last 10 years in significantly
improving open access to integrated information about species from previously diverse and
isolated sources. This impact has been valued by both national and global research
communities.

Establishment of the ALA

Australian herbaria and museums have a long history tackling the issues of data sharing,
standards and collaboration for natural history specimens. Standards development for this
work in Australia took place in an international context through involvement of Australian
biologists and data scientists in Biodiversity Information Standards (known by the acronym
TDWG) from its inception in the mid-1980s (http://old.tdwg.org/about-tdwa/history/). The

4 Belbin L et al

botanical community first published the HISPID data standard for herbarium specimens in
1989 (http:/AWwww.anbg.gov.au/projects/hispid/hispid3.html). In the late 1990s, the peak
body for herbaria in the region, the Council of Heads of Australasian Herbaria, formed a
consortium with the Australian Biological Resources Study (ABRS, hittps://www.
environment.gov.au/science/abrs), which held responsibility for coordination of taxonomic
research. This consortium sought funding to digitise herbarium specimens in all the state
and federal herbarium collections and received AUD$10 million for this purpose from the
Australian Government, states and territories and private sources. Its focus was on the
capture of herbarium specimen data into electronic databases, with the eventual goal of
producing an online resource. The result was Australia’s Virtual Herbarium (now
Australasian Virtual Herbarium, AVH, established in 2001). AVH currently provides access
to eight million records for specimens of plants, bryophytes and fungi across Australia and
New Zealand, both directly and through its connections to the ALA (https://avh.ala.org.au).

Internationally, interest in establishment of biodiversity data infrastructures had been
growing for more than a decade before the ALA was established. The Biodiversity in World
Science Report, published by UNESCO in 1996, identified biodiversity as ‘our most
precious “unknown” and made the case for developing better understanding of genes,
species and ecosystems (di Castri 1996). In Australia, the Environmental Resources
Information Network (ERIN, https:/Awww.environment.gov.au/about-us/environmental-
information-data/erin) was launched in 1992 through the former Australian Government
Department of the Environment with the first national remit to draw together, supplement
and make publicly available biodiversity data from the environmental departments from
Australian states and territories.

By 1999, the OECD had developed a focus on research infrastructure and emphasised the
need for international collaboration. One result was the recommendation by the OECD
Megascience Forum Working Group on Biological Informatics in 1999 (OECD
Megascience Forum 1999) to establish the Global Biodiversity Information Facility (GBIF, h
ttos://gbif.org) to make biodiversity data and information accessible worldwide. GBIF was
conceived as an online network funded by membership fees from participating countries,
who would contribute data to GBIF through their national ‘nodes’. The Working Group’s
recommendations were shaped by the experiences of a handful of key countries in
developing systems, based especially on digitised botanical specimens, including Australia
through ERIN.

In the early 2000s, the zoological community in Australian museums formed a peak body
called the Council of Heads of Australian Faunal Collections (CHAFC). This group was also
interested in sharing data through a public website. The zoological community had to
engage in extensive discussions to overcome philosophical hurdles around open data
sharing. In particular, the community was concerned that providing precise locality data for
threatened and rare species would encourage poaching and illegal collecting. There were
also concerns about protecting the privacy of collectors and donors. Technology fixes were
proposed for data sensitivity issues, including denaturing locality data through gridding and
excluding some data elements from sharing arrangements. The result was OZCAM -— the
Online Zoological Collections of Australian Museums, now a portal in the ALA

The Atlas of Living Australia: History, current state and future directions 5

(https://ozcam.ala.org.au). The establishment of the ALA owes much to the prior existence
of AVH and OZCAM.

The Australian Government commissioned a review of national research infrastructure with
the intention of funding new initiatives. The resulting National Collaborative Research
Infrastructure Strategy Roadmap in 2006 (Department of Education 2006) outlined 16
areas of priority infrastructure, including Integrated Biological Systems. The Government
sought a proposal from the collections community to continue their existing efforts to
database animal, plant and microbial collections and aggregate the results into a single
online platform. A group of approximately 25 representatives from Australia’s biological
collections, with representatives from ABRS, AVH and OZCAM, met at the Australian
Museum in Sydney in May 2006. This meeting identified many benefits from an aggregated
database, based on existing standards and settled on the concept of the ‘Atlas of Living
Australia’. The collections developed a strong case that the data held by collecting
institutions should be considered as significant research infrastructure. A submission from
the major museums and herbaria was successful and CSIRO was appointed as the
contracting agency.

The original scope of the ALA

The ALA was approved for Australian Commonwealth funding as part of the NCRIS
programme starting in 2007. NCRIS established a new generation of Australian national
research infrastructures (NRIs) to promote and support world-class research across
multiple domains. The rationale for the ALA funding was to enhance access to Australia’s
biological collections as an ‘important supporting infrastructure for research relating to
models of disease, biosecurity and biodiversity, and supporting quarantine, environmental
remediation and management.’ Accordingly, the ALA was established as a partnership
between CSIRO (which curates national collections for multiple taxonomic groups), major
state and territory museums and herbaria (and the associated national Councils), key
university collections, the Australian Biological Resources Study (ABRS, responsible for
the national species lists and funding for taxonomic projects) and the pest collections of the
Department of Agriculture, Forestry and Fisheries and the Victoria Department of Primary
Industries.

The announcement in 2007 also created two other NRIs with relevance to biodiversity and
the wider work of the ALA: The Integrated Marine Observing System (IMOS:
http://imos.org.au/) and the Terrestrial Ecosystem Research Network (TERN: https://www.
tern.org.au/). IMOS and TERN were established to support environmental research and
data management in the marine and terrestrial spaces. In both cases, the scope included
data collection and processing activities that relate to biodiversity composition across
space and time. The original NCRIS strategy did not specify how linkages would be formed
between ecological datasets and the largely collection-based data of the ALA.

The ALA itself was positioned in an Integrated Biological Systems cluster with the
Australian Plant Phenomics Facility (APPF: https:/Avwww.plantphenomics.org.au/) and the

6 Belbin L et al

Australian Phenomics Network (APN: http://australianphenomics.org.au/). This association
was based on all three NRIs delivering integrated data related to target species, and the
ALA was initially given responsibility to provide informatics support for APPF and APN. The
Australian Biosecurity Intelligence Network (ABIN) was also funded as an NRI to address
requirements around all aspects of biosecurity and overlapped with the ALA in the area of
observations and collections of pest species. Other investments with scope relevant to the
ALA included Bioplatforms Australia (BPA: https://bioplatforms.com/) for "-omics"
technologies and the Australian Urban Research Infrastructure Network AURIN:
https://aurin.org.au/) which addresses issues around urban environments.

Simultaneously with the establishment of these NRIs, a set of cross-domain research data
and computing infrastructures were created as the NCRIS Platforms for Collaboration
cluster. These included the Australian National Data Service (ANDS) to address issues
around data management and storage, and the Australian Research Collaboration Service
(ARCS) to support collaborative activities. These two facilities have now merged and
evolved into the Australian Research Data Commons (ARDC: https://ardc.edu.au/).

All NRIs, apart from ABIN, are still active and have developed in parallel with the ALA. The
Australian Government’s approach through NCRIS has been transformational in
encouraging collaborative effort throughout the Australian research sector and in delivering
a wide range of datasets and tools for use by researchers and the wider community.

Some downsides resulted from the simultaneous establishment of all NCRIS
infrastructures. The ALA needed to solve many issues in research data management long
before Platforms for Collaboration could offer stable and standardised models. This forced
the ALA to develop its own approaches to metadata standards, vocabulary services,
repository services and GIS functionality. Some of these elements are currently addressed
in more standardised ways by ARDC and other infrastructure partners. Similarly, the ALA,
TERN and IMOS all had to address their own needs around biodiversity data management
before reaching the necessary maturity to interconnect services. The overlap in
responsibilities between the ALA and ABIN limited opportunities for the ALA to fully address
the issues associated with biosecurity collections. Linkages with APPF and APN absorbed
some ALA resources at an early stage, but the three infrastructures shared no use cases
and these relationships have weakened over time. If these initiatives had been in a more
mature state when the ALA was brought into existence, it would have significantly affected
how decisions were made about priorities and investments.

NCRIS funding (AUD$8.5 million over the period 2006-2011) gave the ALA the stability to
address the following initial scope, using digital content from the partner institutions:

° names and nomenclatural data

° specimen and observational data
° descriptions and descriptive data
° DNA and genetic data

° multimedia

The Atlas of Living Australia: History, current state and future directions 7

The role of the ALA, as established under NCRIS, was to build the data integration
infrastructure required to support research use of the natural history collections and
associated digital assets. It was not funded for the generation of new digital content.

In May 2009, as part of a national response to the Global Financial Crisis, the Australian
Government announced the Super Science Initiative, a $989 million initiative to build and
create research infrastructure, funded through the Education Investment Fund (EIF). As
part of the Super Science Initiative, the ALA received an additional AUD$30M to build on
and enhance its work through the period 2009-2011. The scale of the funding and the
short time period justified a significant expansion of the scope of the ALA's work across five
major areas:

° Collection Data Management — tools and services to optimise the data supply chain
through Australia’s natural history collections, from field collection through
accession, digitisation and web publication. This included support to reinforce tools
around key national collection platforms, including AVH and OZCAM.

° Rich Data Stores — shared infrastructure to manage and maintain biodiversity
datasets on behalf of Australian institutions and projects, including mirrors or local
nodes for the Biodiversity Heritage Library (BHL: https:/Awww.biodiversitylibrary.
org/), Morphbank (htips:/Awww.morphbank.net/) and the Barcode of Life Database
(BOLD: http:/Awww.boldsystems.org/) and upgrades to the DELTA software for
taxonomic identification keys (https:/Awww.delta-intkey.com/).

° Australian National Species Lists — tools, services and expert curation to bring
together and complete the Australian National Species Lists, including the
Australian Plant Name Index (APNI: https:/www.anbg.gov.au/apni/), the Australian
Plant Census (APC: https:/Avww.anbg.gov.au/chah/apc/index.html) and _ the
Australian Faunal Directory (AFD: https://biodiversity.org.au/afd/nome), together
forming the taxonomic framework for Australian biodiversity data.

° Spatial Data Management — shared models, tools and services to ensure
interoperability of all spatial data accessed through the ALA and compatibility with
data shared through related NCRIS capabilities (particularly TERN and IMOS). This
activity led to the development of the ALA’s Spatial Portal (Belbin 2011,
https://spatial.ala.org.au).

° Data Dissemination — web portals and applications to improve delivery of
biodiversity data to end-user communities, including conservation and biosecurity
stakeholders and citizen scientists.

Some of these areas had limited long-term impact, but the EIF funding established the
scope still delivered by current ALA data and services. Most significantly, the work on the
Australian National Species Lists represented a recognition within NCRIS that core
datasets such as these can themselves be regarded as significant national infrastructure.
This recognition allowed funding to be directed to taxonomists for contributions to expand
the coverage or quality of sections of the national species lists.

8 Belbin L et al

The ALA was conscious from its inception of the significant role that citizen science could
play in contributing valuable information to Australia’s biodiversity. This undertaking has
evolved into ALA projects and capabilities, such as DigiVol and BioCollect, covered below.

ALA data and services

As of January 2021, the ALA contains nearly 95 million occurrence records of over 111,000
species from a total of over 195,000 species listed in the Australian National Species Lists
(https:/Awww.rbg.vic.gov.au/science/projects/taxonomy/atlas-of-living-australia-national-
species-lists-project). A total of 84.4% of the records are terrestrial and relate to areas of
Australian jurisdiction, 8.8% are marine, while the remaining 6.8% of the records are
spread across 270 other countries and dependencies. The ALA contains data from
observations of Australian species outside the Australian region and also data on
introduced species that can be found in the Australian region. Of the total records, around
72 million are field observations (categorised as human observations in the Darwin Core
standard: Wieczorek et al. 2012) and 13.5 million are of preserved specimens. There are
1.7 million machine observation records and we anticipate these will rise as a proportion of
total records. The earliest Australian record is from the late 1600s and, on average,
thousands of occurrence records are being added daily. Fig. 1 provides an overview of
summary metrics describing the various dimensions of the ALA.

27 countries

around the world
using ALA inf

1,880,920
data

taset downloads

a

|

Os 61 eo Mp

371,890 :

pag
lileratu ed for the
diver ie Librar

1,184,255
re tralian Magpie 99% of data
G cen), the most in the Creative

en), th

919,919

ed by

he ALA have

es in the ALA Commons licen

Figure 1. EES]

Summary metrics describing dimensions of the ALA. Real-time data regarding selected
metrics is also available at https://dashboard.ala.org.au/.

Field observations of species range from single ad hoc sighting records to hundreds of
data collections from over 500 institutions that provide data to the ALA. The largest single
data provider is Birdlife Australia (https://birdlife.org.au/) with over 15 million records. As
noted elsewhere in this paper, the ALA also manages bio-related terrestrial and marine
environmental layers, species lists, images, sounds, ecological related projects and over
500,000 location definitions in its gazetteer.

The Atlas of Living Australia: History, current state and future directions FS)

Over 800,000 specimen labels and 124,000 pages of field notes have been transcribed by
over 6000 public volunteers using the ALA’s DigiVol volunteer portal, hosted by the
Australian Museum (http://digivol.ala.org.au/). Collecting institutions around the world have
an incredible backlog of specimens, images, field notes and archives that are inaccessible
because they have not yet been digitised. DigiVol provides a way to harness the power and
passion of volunteers to help in the digitisation effort to make more information available to
science. Recently, an additional area that can benefit from volunteer input is around
automated camera trap data where the task is to identify and tag animals in photographs
taken by cameras mounted in the environment. Along with its success at attracting
volunteers, DigiVol is an excellent example of making infrastructure meet many different
objectives.

The wide range of data types requires the ALA to maintain an equally wide range of
services to accept, process and expose the data to meet the needs of diverse
communities. The landing page of the ALA (Fig. 2, htips://ala.org.au/) provides a simple
search for species, datasets and most of the information in the ALA. It is possible to
explore species-level information and drill down to any of the occurrence records. A suite of
application programming interfaces (APIs) are provided, as well as CSV downloads and an
ALA4R environment to support further research using data from the ALA, but outside of the
ALA website. The ALA also maintains a suite of portals that support specific communities
or specialised data and services, each with a web address of the form
<portalname>.ala.org.au. Examples include hitps://dashboard.ala.org.au/ -— a data

dashboard listing dimensions of ALA data holdings and usage; https://biocollect.ala.org.au/
for ecological project management and data collection; https://spatial.ala.org.au/ — a map-
and analysis-focused portal for the research community; and htips://lists.ala.org.au/ for lists
that group species for any purpose, including threat categories, presence in defined areas
or common traits. A more complete list of portals and services can be found at

https://www.ala.org.au/sites-and-services/.

Atlas of Living Australia

—— _——~
\3
i

Open access to Australia’s biodiversitydata ——

90,935,517 = 8,466
th palace Feat

Explore & contribute Tools M format

@ meysten fag aera a terrenewctes
earch relat All sites, services & tool
the ALA by cat
rm lity Project
sas $ BloCollect

& Search datasets eas

Figure 2. EES

ALA landing page at htips://ala.org.au/

10 Belbin L et al

The ALA's Biocache (https://biocache.ala.org.au) is a tool that provides an organised view
combining and linking specimen data, genetic information, field observations, sampling
events, animal tracking data and media collected by diverse stakeholders and arranges
these data for search, access, analyses and download through a standardised record
structure. The Biocache includes records from museum and herbarium specimens, citizen
science observations, field surveys, eDNA studies, literature, remote sensing, electronic
tags and machine observations and any other biological research activity that records the
occurrence of species in time and space.

The ALA is active across three of the tiers for biodiversity informatics identified in the
Global Biodiversity Informatics Outlook (GBIO, Hobern et al. 2012), promoting common
and consistent approaches around FAIR (findable, accessible, interoperable and reusable)
and open access to biodiversity data (Culture tier), supporting biodiversity stakeholders in
turning their assets, observations and measurements into digital formats (Data tier) and
developing the integrated views required by users to make use of these data (Evidence
tier). The ALA supports work in the fourth tier (Understanding tier) by making all these
views and services accessible for researchers and decision-makers to apply in their work.
FAIR data and software code underpin all ALA products and services.

The following sections provide a summary of ALA activities by data type. Each section
provides an outline of the nature of the data, how it is processed and how the data are
exposed publicly through various portals and tools. Fig. 3 provides a schematic overview of
the relationship between data partners, data systems and applications to support ALA
users and Table 1 provides URLs for key data described under Sections 4.2 to 4.8.

a)

Biodiversity data Data ingests from data providers Ko))

5 Species Dataset metadata . _— _
aro Universities “@® occurrence and data quality (JSON, XML, Species ji Download \ Species
and herbaria Ra records assertions WMS, CSV) ay profiles | data , list tool

@ National @ Species
checklists & Aust
Sctence Information Date = ©
taxonomies (NSL) t Nav 4
O— Osx. CB) rw FE) et) ae
Wa pages
Environmental Images, sounds, pag os he
NGOs and Ciuzen layers videos
ommuni science apps We), Search ALA: species information
groups Spatial BioCollect x and cocurrences
classifications project date
Indigeno:
eotry knowledg
holders Services
Occur { Spatial Expl f Expk
Biodiversity National Sensitive di (i) yes A beaten ) wo
Herttag checklists & service download
Ubrary taxonomie:
(NSL)
image Laye
service pr aie’)
Use Digital Object as —, on ,
management identifier (DO!) ‘ |] ashe © alacrgou
a te
The ALA is ma: ibl
1¢ ALA is made poss ble by eal Aggregated BioCollect Mobile apps Digivol FF:
contributions from its partners,is sengeteiee. taxonomic and Oashboord
supported by NCRIS, hosted by nr .
AM DO is th stralic m ye Ys, x .
CSIRO and is the Australia node Application Date prove ZoaTrack 5 hp WNaturaties i Helpdesk
of GBIF support 7 ZV > ie

metrics
* <a
yee & A€ GBIF Databases

Atlas of Living The Atlas of Living Australia uses open source

Australi lia software solutions to provide open access to

jla.org.au Australia’s biodiversity data.

Overview of the Atlas of wit Australia data, systems and applications.
Not all components are listed, for a full list visit ala.org.au

Figure 3. -

Overview of ALA data partners, data systems and user applications.

The Atlas of Living Australia: History, current state and future directions 11

Table 1.
Major ALA data types and URLs for public access.

Data URL

Species occurrence data https://biocache.ala.org.au

Animal tracking data httos://zoatrack.org/

Specimen data https://specimens.ala.org.au/

Natural history collections https://collections.ala.org.au/

Biodiversity literature https:/Awww.biodiversitylibrary.org/collection/bhlau
Species lists https://lists.ala.org.au

Biodiversity projects https://biocollect.ala.org.au

Environmental layers https://spatial.ala.org.au/layers

Descriptive species information https://bie.ala.org.au/

Taxonomic framework

The most fundamental axes for organising biodiversity data are taxonomy (species
identifications), space (coordinates) and time (dates and timestamps). The taxonomic
dimension is the most complex and difficult to standardise of these three and normally
relies on the accuracy and precision of scientific names supplied within data. Scientific
names are applied to occurrence records, species lists, species information and most other
data types within the ALA. The ALA handles these names through an _ integrated
Classification with accepted names and synonyms for each species and uses this to index
all data with a taxonomic name component.

The ALA does not assume authority for determining what native and non-native species
occur within the Australian region or what names should be preferred for these species. It
relies instead on the canonical sources of taxonomic name lists for Australian species (and
New Zealand species, given the Australasian focus of many users), including those
managed as the Australian National Species Lists:

° the Australian Faunal Directory for all animal groups (https:/Awww.environment.gov.
au/science/abrs/online-resources/fauna)

° the Australian Plant Names Index and the Australian Plant Census for vascular
plants (https://biodiversity.org.au/nsl/services/)

° AusFungi for fungi (see https:/Awww.rbg.vic.gov.au/science/projects/mycology/
cataloque-of-australian-fungi)

° AusMoss for mosses (https://moss.biodiversity.org.au/nsl/services/AusMoss)

° the New Zealand Organisms Register for all New Zealand organisms
(http :/Awww.nzor.org.nz/)

° the Catalogue of Life (http:/Awww.cataloqueoflife.org/) for cases where no match
can be found to the name supplied or where the occurrence record is for a species
not found in Australia

12 Belbin L et al

° the World Register of Marine Species (htip://www.marinespecies.org/), which is not
currently used by the ALA, but will be integrated in the future.

Where possible, the ALA links from species pages to literature in the Biodiversity Heritage
Library and also in the National Library of Australia’s Trove (https://trove.nla.gov.au/). The
ALA taxonomic framework includes a number of services that are heavily used across the
ALA infrastructure and also exposed for use by external users. The primary function is
name-matching to determine how to interpret scientific name strings. When an occurrence
record is ingested into the ALA, it may include a currently accepted scientific name or a
synonym that is no longer in use or depends on an alternative classification. A particularly
important case is where a name may no longer be accepted in the light of current
taxonomic knowledge, but has been written into legislation, for example, to refer to
threatened species. Such uses must be interpreted correctly.

The ALA name-matching service seeks to determine which taxon is intended by each
name included in a data record. When the name is included in an authoritative checklist
source, either as an accepted name or as a known synonym for a recognised taxon,
processing is simple. Synonyms can be mapped as references to an accepted taxon,
allowing the occurrence record or other information to be correctly handled in the context of
current taxonomic understanding. Processing may be more complex in the case of names
that have historically been misapplied or have been used to refer to a broad species
concept that is currently treated as several accepted species (pro-parte synonyms).

The service must also resolve taxonomic names even if there is no exact match in the
index, possibly as a result of spelling errors. In such cases, the ALA uses a fuzzy-matching
algorithm to seek a ‘closest’ match, but this process may return false positives.
Alternatively, the ALA can handle difficult cases by ‘upmatching’ the name to a higher-
ranked taxon — for example, mapping an occurrence record that was supplied as a species
record with a binomial scientific name to the genus or family level or even higher. Mesibov
(Mesibov 2013, Mesibov 2018) provides an analysis of the name-matching process,
reporting that up to one in five supplied names may be changed, a process that he
concludes, in some cases, loses or confuses data. When the ALA matches a name, it
stores both the provided name and the name selected as the best match. This ensures that
the original data are preserved and users can freely re-interpret them.

The name matching service not only attempts algorithmically to find the best match for any
scientific name, but also fills out the higher classification and flags possible data issues.
This process relies on the quality of the canonical sources available to the ALA and on
algorithms developed to apply the information they contain. Since the process is
automated, errors may occur particularly for names not recorded in these sources or for
names that are misspelled or malformed. The code and documentation for the ALA name
matching process is available from GitHub:

° the name-matching algorithm: https://github.com/AtlasOfLivingAustralia/ala-name-
matching/blob/master/doc/matching-algorithm-v2.md

The Atlas of Living Australia: History, current state and future directions 13

° the Biocache-store processing code: hittps://github.com/AtlasOfLivingAustralia/
biocache-store/blob/master/src/main/scala/au/org/ala/biocache/processor/
ClassificationProcessor.scala

° descriptive information about the conventions used to assemble the names index:

https://github.com/AtlasOfLivingAustralia/bie-index/blob/master/doc/nameology/
index.md.

Species occurrence data
Most data shared with the ALA are treated as occurrence records, broken down as follows:

° Over 80% of occurrence records are from field observations collected either as
individual observations (for example, by citizen scientist naturalists) or during
systematic surveys of geographic areas or organisms. A proportion of these records
are supported by images, video or sounds, but many are not directly associated
with any evidence that can be revisited to confirm the observation. Over time, the
proportion of unevidenced records is expected to decline as the ALA partners with
iNaturalist and other citizen science platforms that encourage and facilitate easy
sharing of images or sound recordings.

° Approximately 15% of occurrence records are for preserved specimens held by
museums, herbaria and other institutional collections. The evidence to support the
data for these records is the specimen on the shelves within the collections.

° Currently approximately 1.7% of occurrence records come from ‘genetic’ studies —
including sequence data, tissue data and environmental DNA. This figure is
destined to rise quickly in the future.

° A currently small proportion of records derives from animal tracking datasets.

Data quality is one of the most significant aspects to understand when using aggregated
occurrence records. ‘Data quality’ is, however, a complex term that will mean different
things to different users (see Belbin et al. 2013). In some cases, data are considered poor
in quality because they contain errors — for example, mistakes in species identification or
metadata. In an aggregation of over 90 million records from diverse sources, it is inevitable
that there will be errors. Even records with such failings may be valuable for some use
cases. From a user perspective, data quality may be judged in terms of ‘fitness for use’
(see Chapman et al. 2020). The concept is that a record that is unsuitable for one
application may be suitable for another. The ALA performs around 100 standard data
quality tests on all occurrence records belonging to any of the categories listed above.
These tests are designed to flag errors or unlikely values in the data and are largely
independent of the nature of any evidence associated with the record. These are stored as
assertions that the data provider may review and may be able to fix. Flagging potential
issues assists downstream users in reviewing data for their applications. The data quality
tests are automatic. Owing to the volume of data entering the ALA and the shortage of
taxonomic specialist expertise, there is no manual check of the records or the results of the
testing.

14 Belbin L et al

The ALA has long recognised the importance of data quality and commenced a project in
2020, both to help data providers detect issues that can be fixed and to help users
evaluate data fitness for use. User evaluation of occurrence records relies on the use of
filters. Users typically begin by searching for taxa of interest and then accessing the
occurrence records relating to that taxon. They may then derive a subset of the records
using filters that narrow selection using supplied values for Darwin Core terms, processed
values that had been applied to the record, assertions from the ALA tests, various options,
based on descriptions or status of a species (Sensitive, endangered, invasive etc.) and
location-based additions derived by intersecting the location of the occurrence records
(where they have a dwc:decimalLatitude and dwc:decimalLongitude) with all environmental
data layers held in the ALA (see below). One of the ALA tests checks to see if the record is
an outlier on one or more of five selected terrestrial environmental layers, as compared
with all records of that taxon. This is a typical example of a test that will ‘flag’ a warning for
the record but that, without additional information (which may not exist), does not
guarantee that the record is invalid. The record may, for example, be a species that is
adapting to climate change by extending its range south. The ALA, GBIF and iDigBio have
agreed to implement the work of Biodiversity Information Standards Task Group on a core

set of ‘Tests and Assertions’ (https://github.com/tdwg/bdq/tree/master/tg2).

While useful automated tests can be written to assess the location and time aspects of an
occurrence record, this is not feasible for the identification (species name). For observation
records, particularly ad hoc records, the ALA and similar projects rely increasingly heavily
on peer or community review. Capabilities such as iNaturalist (https://www.inaturalist.org/
places/australia) engage a volunteer pool of international expertise to validate the
identification of species observations. Before 2019, the ALA had several mobile
applications that offered no peer review, as well as BowerBird, an observation platform
hosted by Museum Victoria, that did provide peer review. In 2019, the ALA became a
member of the iNaturalist Network and established an Australian iNaturalist node to
encourage observers to submit their species observations using a tool that would provide
an improved level of validation. Records were transferred from BowerBird to iNaturalist
with the assistance of the BowerBird community.

The ALA preserves raw data as supplied for occurrence records. The general principle
adopted in the ALA is that no original data should be overwritten — a concept that is also
captured in the ‘verbatim’ terms of Darwin Core, for example, ‘dwc:verbatimCoordinates’
and ‘dwc:verbatimeventDate’. No data are overwritten without documenting the actions and
justification. There is, however, no current standard that captures everything that may
happen between the raw data submission and a final processed data product. The ALA
encourages any registered user to annotate potential issues associated with an occurrence
record.

All species occurrence records can be accessed through the ALA’s home page and several
other ALA portals. From the home page, the primary search returns matching species and
higher taxa, common names and other data resources, such as spatial layers, datasets
and collections. Each taxon overview page displays images, a map of the spatial
distribution (with links to the Spatial Portal), a link to a list of records, any conservation

The Atlas of Living Australia: History, current state and future directions 15

status, a description and references (See Species Information below). From a listing of
records, any number of filters can be applied. Records can be summarised by charts and
downloaded with any combination of selected terms and ‘value-added’ terms in CSV
format.

The ALA also provides over 100 Application Programming Interface (API) endpoints to
access species occurrence data and services (https://api.ala.org.au). These functions
enable URLs to be used from a browser or programming language to return results tuned
to user requirements. The API is grouped into functions for occurrences, species level
information, lists, datasets, species names, volunteer portal, environmental layers, data
dashboard and regions. API responses may be returned in multiple formats, including web
pages, images, ZIP files, shapefiles, and CSV, JSON, RDF, KML, WKT and EML files. The
ALA website and other front-end systems also utilise these APIs. ALA4R (https://
github.com/AtlasOfLivingAustralia/ALA4R) is an alternative programmatic access route to
ALA data and services for those who prefer to use the R environment (https:/Awww.r-
project.org/) for data analyses.

The Spatial Portal (Fig. 4) is the ALA’s primary portal to service the research community,
environmental managers, environmental consultants and enthusiastic citizen scientists. As
its name suggests, the portal has a spatial emphasis and includes a cross-section of
analytical tools. Users can enter the portal, search for species or an existing species list
(see below: https://lists.ala.org.au), use an advanced filtering tool, visualise and analyse
records. An alternative strategy available in the Biocache and Spatial Portal is to identify
occurrence records based on any combination of occurrence record terms and ALA-added
terms. For example, it is possible to list records of bird species that have associated
images, a CCO licence and coordinates that do not match the supplied state or territory.

Atlas of Living Australia

Facet Class

llr

Figure 4. EES]

The Spatial Portal. Distribution of genus Exocarpos in the family Santalaceae (sandalwoods)
with mean annual evaporation as a background. To reproduce: https://spatial.ala.org.au?
$s=1601846523658.

16 Belbin L et al

The ALA also permits area-oriented searches for occurrence records. Users can explore
biodiversity within user-defined areas using the Explore Your Area __ tool

(https://www.ala.org.au/explore-by-location/) or within pre-defined regions and areas using

the Region tool (https://regions.ala.org.au) or the Spatial Portal (hitos://spatial.ala.org.au).
The Spatial Portal provides 16 options for how areas can be defined and selected, from

clicking on the map, searching the gazetteer, importing or using an environmental
envelope. This area-centric approach enables users to answer a basic question: ‘What
biodiversity-related things (species, projects, literature etc.) occur in this area?’ The Spatial
Portal’s area reports provide a breakdown of species and records by life form, conservation
or invasive status, and allow a user to list and download the resulting species lists or
occurrence records.

Specimen data and genetic materials

Data related to preserved specimens are provided by museums, herbaria, national
collections and universities (Figure 4). Preserved specimens are a primary source of high-
value data since specimens can be examined repeatedly, yielding new data each time. The
ALA receives a subset of the data held by collection institutions, extracted from their
institutional collection management systems and mapped to Darwin Core terms. Coverage
is from most Australian collections and (via GBIF) from selected international collections.

Museums and herbaria use a range of commercial, open-source or in-house collection
management systems: Specify, EMu by Axiell, and Vernon Systems are in use in Australian
institutions. The ALA receives collections data in a variety of ways — commonly by having
the data packaged as Darwin Core Archives and less commonly by harvesting directly from
these systems. The ALA is looking to implement the GBIF Integrated Publishing Toolkit
more widely to help streamline repeated data provision from collections.

Emerging data types based on specimens include 3D images, using techniques such as
CT scanning, photogrammetry and stacked microscope imagery. A challenge for the ALA
will be to allow these new image types to be linked to the occurrence records and viewed
(University of Cincinnati 2019).

Specimens from collecting institutions provide fewer records, but cover a greater breadth of
species, than field observation records. Researchers working in the collections sector
include many taxonomists, whose professional skills are in describing the diversity of the
natural world. Collections also extend back several hundred years and include species that
are now threatened or extinct. Taxonomists and collections specialists also deliberately
collect organisms from every environment to document diversity. ALA records for deep-sea
marine invertebrates, cave-dwelling stygofauna, algae and other ‘non-charismatic’
organisms have, for the most part, been supplied from specimens in collections.
Interestingly, records for some exceedingly common species also mainly come from
collecting institutions — for example, for abundant but very small or cryptic insects and for
grasses. The ALA only has 980 occurrence records for the common mosquito, Aedes
notoscriptus, 770 of which are from preserved specimens. The relative paucity of
observations of house flies (Musca domestica), pigeons (Columba livia domestica) or

The Atlas of Living Australia: History, current state and future directions 17

dandelions (Taraxacum officinale) is likely to be both because of their ubiquity in the
environment and because observers under-record introduced and pest species.

Genetic data and genomics research are increasingly important in the study of biodiversity.
Advances in genetic techniques mean that DNA can now be extracted even from very old
museum specimens and this supports new research into evolution and phylogeny. The
ALA has not yet found an ideal way to incorporate genetics data into its systems. So far,
collecting institutions have started to supply data associated with tissues (e.g. muscle,
heart, skin) that have been specifically preserved at the time of collection to permit future
genetics work to be conducted. The ALA holds approximately 180,000 tissue records, with
data structured according to a relatively new standard, the Global Genome Biodiversity
Network (https://terms.tdwg.org/wiki/GGBN Data Standard). An even newer type of data
that ALA and GBIF alike are now needing to consider are data derived from environmental
DNA (eDNA). Following a project that tested how eDNA could be ingested as occurrence
records, there are now 1.17 million such records in the ALA.

Field observation data

A field observation of a species is documented through, but far from limited to, three
primary dimensions: a name (at species or high taxon level), a location and a date/time.
With these three components, many questions can be answered. For example, ‘Where has
Eucalyptus gunnii been observed?’, ‘Were there any observations of Alaba vibex after
1960?’ and ‘What reptile species have been observed in the Kimberley region between the
years 1950 and 2000?’ The precision and confidence associated with each of these three
elements varies. An organism may only have been identified to genus, or may be
attributable to a local variety. The location may have been measured with high precision
(e.g. one metre resolution) or derived from a general text description. Some observations
will be timestamped to a day, while others may only indicate a year. No minimum
information standard is imposed for these properties, since imprecise data may remain
valuable for users interested in other aspects of the record. In all cases, the values
included for each element may be incorrect or imprecise as a result of human or machine
error during observation, identification, data entry and data processing. Field observations
of species do not have a specimen that can be referred to, but they may contain links to
images, audio or video that provides evidence of name, location and date.

Each species observation in the ALA has a dual purpose. First, it indicates that evidence
exists for the recorded occurrence of the given species at the given location within a
specified time period. Second, where applicable, observation records can include
identifiers to make explicit that multiple records derive from a single standardised sample
(vegetation plot survey, bird count, eDNA sample etc.) or relate to a single individual of the
species (animal tracking). Field observation records are a fundamental unit for considering
past and present species distributions, spatial occupancy, community composition,
ecosystem health etc. Many of the Essential Biodiversity Variables (EBVs, Pereira et al.
2013, Kissling et al. 2018, Hardisty et al. 2018, Hardisty et al. 2019) can be constructed
using such records. Each field observation record also serves as a pointer to the varied

18 Belbin L et al

and potentially much richer information that may be associated with a field study (methods
and protocols, community composition, associated environmental measurements etc.), a
citizen science record (images, sound recordings, notes), eDNA (Sequences, community
composition), animal tracking (time series of locations for the same individual) or any other
suitable source of evidence.

Sampling event data are currently only handled as a source of occurrence records,
although Darwin Core elements, such as eventID and samplingProtocol, are retained with
each record, allowing users of the data to make use of the associated information. At
present, relatively few datasets are published to the ALA using the Darwin Core standard
event class (https://dwc.tdwg.org/terms/#event), and the ALA currently handles these data
only as a source of occurrence records. It would be relatively simple, however, for holders
of survey and monitoring data (e.g. vegetation plot data, standardised bird and frog counts,
pitfall and Malaise sample data, environmental DNA sequencing) to share their data in this
form. All such data can continue to contribute to the ALA occurrence record index — the
Biocache — but can also contribute to future data products that enable researchers to
locate and compare sites across space and time. The greater standardisation associated
with these data may also assist with validation and calibration of other ALA data.

Animal tracking data

With increasing miniaturisation and lowering costs, tracking devices are more commonly
being attached to animals to monitor their movements. The data these devices supply offer
rich insights into the habits of the organisms and their use of the landscape. For migratory
species, they are a key tool to identify key resources along their routes. A ping from an
electronic tag on an animal is, in Darwin Core terms, a ‘machine observation’. Tracking
data for a single animal may be very detailed, organised as a series of coordinates and
timestamps.

The ALA inherited an animal tracking software that was originally called OzTrack (Dwyer et
al. 2015) and is now called ZoaTrack (Newman et al. 2020, https://zoatrack.org/). This is a
portal that covers import of track data, storage, visualisation, analysis and export.
Supported spatial analysis methods with ZoaTrack include the minimum convex polygon,
kernel utilisation distribution, Kernel Brownian bridge, alpha hull, local convex hull, heat
map (point intensity), heat map (line intensity) and Kalman filter. Movement metrics include
the total number of locations for that animal, the mean number of detections per day, the
maximum number of detections per day, the distance moved along the track using great
circles (km), the mean step length (km) and the mean step speed (km/h). The results can
be exported as KML files or shapefiles.

Animal tracking data are imported from ZoaTrack into the Biocache in a minimal form. The
Biodiversity Information Standards Interest Group on Machine Observations
(https:/www.tdwg.org/community/mobs/) has been working on two standards for these
data, one for encoding the tag data directly and one that exposes these data using the
Darwin Core standard. Currently, tracks are imported as occurrence records in what are
best described as master records: one record per track. The convex hull of the track is

The Atlas of Living Australia: History, current state and future directions 19

calculated and added to the Darwin Core term dwe:footprintWKT, and other information,
such as dwc:scientificName, dwc: eventDate (as a range) and, in effect, metadata, is
added to the relevant Darwin Core terms. This method was used to enable tracks to be
used with any other records of the species, to be displayed as a convex hull and detected
as intersecting an area of interest in the Spatial Portal’s area reports. This strategy has
minimal performance impact on the ALA occurrence record store, the Biocache, and still
provides direct access from the master record to all associated data in ZoaTrack.

Collections and data resources

Information about Australia’s curated natural history collections can be explored in the ALA
through the Natural History Collections page (https://collections.ala.org.au/) (Fig. 5). There
are 209 collections (at October 2020) and several collections may be associated with a
single institution (often organised around taxonomic groups). Museums, herbaria,
university collections and CSIRO’s national collections usually provide the Darwin Core
elements dwc:institutionCode and dwc:collectionCode as a part of their specimen data
records, reinforcing the linkage between specimen data and collection information.

Atlas of Living Australia

Australia's natural history collections

Atlas of Living Australia y
Upload your observations
Sales Identity specs :

Figure 5. EES

Australia’s natural history collections. This page provides a way for users to investigate data
from museums, herbaria and collections in universities (https://collections.ala.org.au/).

Data within the ALA are also organised according to Data Resource (or dataset) and Data
Partner. There are 8160 Data Resources in the ALA (htips://collections.ala.org.au/public/
datasets) and these are grouped under Data Partners. Australia’s major museums and
CSIRO national collections, for example, all contain the phrase ‘provider for OZCAM’ in
their data resource name. This reflects ALA history, where the original datasets that formed
the basis of the data in the ALA came from the museums data aggregator as the Data
Partner — the Online Zoological Collections of Australian Museums (OZCAM). Similarly,
herbaria have ‘AVH’ in their data resource name, reflecting the data aggregator for the
herbaria — the Australasian Virtual Herbarium (AVH).

20 Belbin L et al

Biodiversity literature

The Biodiversity Heritage Library (BHL) is a global consortium of natural history, botanical
and research libraries based in museums, herbaria and universities, plus national and state
libraries. The mission of the BHL is to digitise literature related to biodiversity and natural
history and to make it freely and openly accessible. The secretariat for the consortium is
based at the Smithsonian Libraries in Washington, D.C. and the global website is managed
through that body. More than 58 million pages of scientific literature, with content ranging
from the 15° century to the present day, can be searched through the website

(https:/Awww.biodiversitylibrary.org/).

In partnership with the ALA, the Biodiversity Heritage Library project in Australia was
started in 2010. It was originally established to provide a literature service to support
taxonomic names within ALA. Within the ALA website, access to the content in BHL is
available from the Literature tab on species pages.

The project is based at Museums Victoria in Melbourne, where the digitisation equipment is
held. A small team of paid staff work collaboratively with Museums Victoria librarians to
nominate, locate and make available rare books, monographs and serials for scanning.
Since the project first started, much of the digitisation and post-processing has been done
by an active and extremely committed team of volunteers, some of whom have been with
the project since its inception. This small team has digitised more than 350,000 pages of
literature over the course of the last decade, and has focused more recently on literature
published in Australia.

In recent years, the BHL Australia project has invited participation from museums, herbaria,
learned societies, field naturalist groups and other organisations that produce publications,
but that may not have the means to digitise their content. Thirty organisations have so far
contributed publications to BHL via the Australian project § (https://www.biodiver
sitylibrary.org/collection/bhlau). The Australian team have also worked with project leaders
in New Zealand to initiate a similar project there.

Future possibilities exist to use the published literature as a source of taxonomic names
and of occurrence records. This may be developed further in the next few years.
Species lists

Within the ALA, lists of species names can be used to link multiple taxa into a group with a
common characteristic. The types of lists that are supported include:

° taxonomic checklists that include names and classifications for all species within a
group (either at the global scale or for a defined region)

° local occurrence checklists that list all species recorded from an area (e.g. a
national park)
° lists of species with a common conservation status

° lists of species with a common introduced or invasive status

The Atlas of Living Australia: History, current state and future directions 21

° lists that summarise diagnostic, morphological, ecological or distribution information
for each listed species (a simple form of species profile data).

At the most basic level, lists in the ALA are defined as a set of two or more taxon names (at
any taxonomic level), usually supplied as a CSV-formatted file or cut/pasted into the Lists
portal (https://lists.ala.org.au). As with most information in the ALA, lists can be created by
ALA-registered users and, if not designated as ‘private’, are publicly discoverable and
usable. More than 5000 lists have been created by research scientists, taxonomists, citizen
scientists, area managers, environmental consultants and members of the public. During
2020, there were more than 5000 users of the Lists tool.

Several tags can be associated with each list:

° authoritative (created by acknowledged responsible agency, committee or expert)

° included in species pages (referenced on the species summary pages)

° private (only visible to the user who uploaded the list)

° invasive species (species with any invasive status anywhere in the Australian
region)

° member of Sensitive Data Service (species have authoritative sensitivities)
° region provided (a formal area for the list has been defined)
° threatened species list (species with any conservation status in Australia).

Species character lists provide for any number of traits or attributes to be associated with
each name in the list. This information is currently unconstrained, meaning that trait labels
are local to each list, rather than being consistently interpreted across lists. Traits can take
any text or numeric value. Future developments could use accepted vocabularies, thesauri
and ontologies to constrain trait labels and states or expected value ranges. A simpler
version of this is done for the ALA Sandbox portal (https://sandbox.ala.org.au), which
attempts to match occurrence record header terms against the Darwin Core standard. This
strategy would provide a practical impetus for an evolution to international standards and
would enable the Lists portal to detect trait types and values, and to flag exceptions.

Authoritative lists are those for which a recognised expert, institution or committee has
formal responsibility. For example, the Environment Protection and _ Biodiversity
Conservation Act, managed by the Australian Department of Agriculture, Water and the
Environment (https:/www.environment.gov.au/epbc/about), lists species that are ‘extinct,
extinct in the wild, critically endangered, endangered, vulnerable or conservation
dependent’. The ‘Authoritative’ tag is applied only by the list administrators after
consultation with the authority.

Biodiversity projects

The ALA accommodates information on biodiversity projects — for example, from
government-funded on-ground interventions, such as weed management and riparian re-
vegetation activities, or from projects conducted by research and citizen science sectors. In
both cases, the ALA facilitates project documentation. MERIT (https://fieldcapture.

22 Belbin L et al

ala.org.au) is a platform for government-mandated planning and reporting. The ALA
BioCollect platform (https://biocollect.ala.org.au) supports biodiversity-related projects by
capturing both descriptive metadata for each project and raw primary field data. BioCollect
has a strong citizen science emphasis.

The ALA provides these capabilities for the collection of observational data as they
complement data from other sources and focus on data collection from systematic surveys.
For example, projects dealing with the management of alien invasive species may be
added to the ALA's list of records and, as with all occurrence records, are then available for
viewing, analyses and downloading. The intent is to facilitate the discovery of relevant on-
ground projects when examining area reports from MERIT, BioCollect and the ALA’s
Spatial Portal.

Projects registered into these ALA systems fall into three categories. At present, these
categories are not used as filters elsewhere in the ALA:

° ecological science (1600-plus projects at httos://www.ala.org.au/biocollect-for-
ecosciences/)
° natural resource management activities (15 projects at httops:/Avww.ala.org.au/

biocollect-for-natural-resource-management/)
° citizen science (524 projects at https://www.ala.org.au/biocollect-for-citizen-
science/)

Ecoscience projects (https://biocollect.ala.org.au/ecoscience) are generally not open for
public participation and focus on environmental assessment and monitoring surveys.
These are often, but not exclusively, established by scientists collecting data for their own
research projects or by ecologists and natural resource management practitioners
undertaking surveys for planning-related development applications and long-term site
monitoring projects.

Natural resource management (NRM) projects support environmental NGOs, NRM
organisations, community groups and local governments to create, manage and record
data and communicate project outputs and outcomes to their communities (see
https:/www.ala.org.au/biocollect-for-natural-resource-management/). These projects
record the sequence of activities which are undertaken to restore, re-vegetate and
rehabilitate environmental areas over a period. Many of these activities include
observation, collection, monitoring and establishment of plants and/or animals. In addition
to any occurrence records shared this way, the associated project, survey and activity
information can also be extremely useful to the broader scientific community in providing
context and descriptive information to interpret records. For example, information about re-
vegetation, site restoration, seed collection, weed and pest management are fundamental
to understanding ecological processes in an area or region.

Citizen science projects (https:/Awww.ala.org.au/biocollect-for-citizen-science/) are open to
involvement by anyone and BioCollect contributes to community outreach for project

support. Most of the citizen science projects relate to environmental observations but, as

The Atlas of Living Australia: History, current state and future directions 23

BioCollect is a platform that supports international citizen science projects and is closely
aligned with the Australian Citizen Science Association (ACSA, https://citizen
science.org.au/), projects can be of any nature. These citizen science projects can also be
accessed via the ACSA website (https://citizenscience.org.au/ala-project-finder/) or through
global access to their metadata (PPSR Core metadata, https://github.com/CitSciAssoc/
DMWG-PPSR-Core/wiki/About-the-PPSR-Core).

Environmental layers

Experiences in managing the ALA environmental data have largely been captured by
Belbin and Williams (Belbin and Williams 2015), so this paper provides a brief summary of
data, services and the lessons learnt. A recent review of environmental layers across four
Australian biodiversity infrastructures can also be viewed at hittps://support.ecocloud.

org.au/support/solutions/articles/6000237060-key-environmental-data-layers-across-
ecoscience-facilities.

When the ALA received expanded funding in 2009, it recruited an analytical ecologist to
support ecological and related research. A cross-section of experienced ecological
scientists were invited to two workshops. The first of these (Flemons et al. 2009) evaluated
potential tools and methods that the ALA could support, and the second (Flemons and
Belbin 2010) identified what data were required to support those tools. It was readily
apparent that the ALA needed to integrate a wide range of environmental data if it were to
support ecological research. The ALA references these datasets as ‘environmental layers’
to distinguish them from the point-based species occurrence data that form most of the
ALA's data holdings.

When the ALA was established, no other Australian agency held more than 10% of the
layers necessary to support research and environmental management. The environmental
layers currently held by the ALA can be viewed at https://spatial.ala.org.au/layers. A three-
level classification scheme was developed to help discovery of relevant layers in the ALA.
Layers may be gridded datasets with continuous values representing variables, such as
mean annual temperature or soil pH. These layers have been selected based on the
potential of the measured variables to influence the spatial distribution of species. The ALA
also includes datasets identified as ‘contextual layers’. These generally have a polygonal
structure and belonged to defined classes, such as states and territories or bioregions.
Environmental layers provide context for understanding the management of Australian
species. They are classified into major categories: area management, biodiversity, climate,
distances, fire, hydrology, land management, marine, political, sensitive data, social,
substrate, topography and vegetation. Each month, four global coverage internally
generated layers are created from all occurrence records: species occurrence density,
species richness, endemicity and Shannon Diversity (H).

Contextual layers are also cross-tabulated with all the ALA’s occurrence records. For
example, cross-tabulating the Australian states and territories layer with the terrestrial
CAPAD (parks and reserves) layer reports the area in square kilometres, the number of
taxa and the number of occurrence records in each of the areas defined by the spatial

24 Belbin L et al

intersection of the two layers. As the occurrence records are added to on an ad hoc basis,
the cross-tabulations for species and occurrences need to be updated regularly for all pairs
of contextual layers. This process imposes a significant load on ALA computers, but
enriches the data available to users.

The ALA's interest in these environmental layers is secondary to its primary purpose of
documenting species. They are, however, a valuable source of environmental properties
that the ALA uses to enrich all occurrence data, and they contribute to visualisation and
analysis tools in the Spatial Portal and other ALA portals.

Descriptive species information

The ALA Biodiversity Information Explorer or BIE (https://bie.ala.org.au) offers species
pages that serve as a standard entry-point for those exploring occurrence records. The
home page search links users to the BIE species pages.

Species pages in the ALA provide access to aggregated descriptive information about
species. Common to all pages is an overview, containing:

° descriptive text, which may have been obtained through third-party APIs

° threatened species or conservation status, derived from state, territory and federal
threatened species lists

° images, aggregated from media uploaded along with occurrence data

° taxonomic names and synonyms, brought in from the source names list

° classification hierarchy, also brought in from the source names lists

° relevant literature, sourced by sending queries on the species name to the
Biodiversity Heritage Library and to Trove, run by the National Library of Australia

° Links to genetic data using the GenBank API

° a list of Data Resources (and Data Partners if relevant) that have supplied
occurrence records

Several recent projects have broadened the authored informative content in the ALA. A
noteworthy example is the Indigenous Ecological Knowledge project. In this project, senior
knowledge holders from several Aboriginal communities have worked with non-Aboriginal
scientists and linguists to document local names for plants and animals. The ALA website
includes names from the Kamilaroi/Gamilaroi and Yuwaalawaay/Yuwaalayaay languages
for over 250 species. The Indigenous Ecological Knowledge project continues to work
actively with senior knowledge holders in various communities around Australia. Common
to all Indigenous Ecological Knowledge projects is the aim to bridge the gap between
traditional and non-Aboriginal science knowledge by working on country with communities
who want to share traditional knowledge in a culturally safe way. The next phase of the
Indigenous Ecological Knowledge project will use the species descriptive authoring tool
(Profiles: hittos://profiles.ala.org.au) to record information about the descriptions and
concepts embodied in the names. The Profiles platform is used for the Flora of Australia
project (https://profiles.ala.org.au/opus/foa). This project contains authored content that

The Atlas of Living Australia: History, current state and future directions 25

describes plants using technical language and is mainly used by botanists to aid in
descriptions and identifications.

Gaps in data and services

As new features are added, the complexity of the ALA increases. While improved
functionality is often valued by the users, the downside is increased computational and
human data-processing overheads. In contrast to some biodiversity data infrastructures,
the data types accepted by the ALA are wide-ranging, and the tools provided in the ALA
support an unusually wide range of services and users. A positive outcome of this is that
the ALA supports a diverse range of communities. The challenges, however, include the
number of applications requiring ALA technical support, a lack of consistency in user
interfaces and code base, challenges associated with generating consistent and
comprehensive documentation, and the complexity associated with integrating and linking
data.

One of the more significant gaps is the need for more comprehensive standards and better
attention by data providers to compliance with those standards already in use. Darwin Core
(https://dwc.tdwg.org/) is a fundamental standard used by the ALA and related
infrastructures. It provides the elements needed to allow any observation of a species or
occurrence record for a specimen to be aligned into an occurrence database. This, in turn,
enables records of species to be searched by, or filtered for, indexed Darwin Core terms,
such as species name, location or date of observation. Darwin Core has been developed
as a very flexible standard that can support the widest possible range of data sources
sharing spatiotemporal data on species occurrence, but this flexibility is achieved by
placing only minimal semantic constraints on published data. Different data publishers may
adopt different strategies for mapping data from otherwise comparable specimens or field
surveys into Darwin Core and this may lead to inconsistencies in how the data are
subsequently interpreted or used. Data in the ALA, moreover, could be improved. An
example is in the low use of dwc:samplingProtocol. Approximately 98.5% of the occurrence
records in the ALA have a dwc:occurrenceStatus of ‘present’, while the remainder are listed
as ‘absent’ or ‘unknown’. This would be typical of most infrastructures. What is hidden,
however, is the many absences or ‘unknowns’ that could be determined from another
Darwin Core element: dwc:samplingProtocol. Unfortunately, dwc:samplingProtocol has
been provided for only 0.4% of the ALA’s records, even though we know that a far larger
proportion of records could have this element filled, as they are the result of systematic
sampling but are not recorded as such. This includes most of the records from Birdlife
Australia and eBird.

While most biodiversity data infrastructures have adopted the Darwin Core standard, a
recent study on the production of Essential Biodiversity Variable (Hardisty et al. 2019)
highlighted the challenge of trying to merge GBIF and ALA records of three species.
Records in GBIF and the ALA are processed differently, resulting in inconsistent use of
terms derived from the raw or verbatim data. The study also showed that there were
Australian records in GBIF that were not in the ALA and vice versa. A current project has

26 Belbin L et al

begun to align GBIF and ALA occurrence record processing infrastructure to achieve
greater alignment and efficiencies.

The ALA has several other data streams for which necessary standards are not well
established to structure the data. Examples include trait data, annotations on occurrence
records, occurrence record tests and bioenvironmental data classification. This lack of
standards is not unique to the ALA, but it does present significant barriers to efficient
development for the acquisition, processing and sharing of biodiversity-related data and
services. The development of standards is complex and time-consuming and there is no
guarantee that, once work is complete, proposed standards will be adopted. The ALA,
however, does invest considerable time to contribute to internationals standards
development. It does this through its involvement over many years in the Biodiversity
Information Standards (TDWG) organisation. The ALA is committed to continuing to invest
in efforts to develop biodiversity data standards given how critical they are in supporting
data integration, nationally and internationally.

Major international activities

The ALA's role in hosting the Australian node of the Global Biodiversity Information Facility
(GBIF) is one of its most important partnerships. Since its inception, the ALA has worked
closely with GBIF to ensure occurrence records in the Australian region and beyond are
supplied to GBIF. Occurrence records relevant to the Australian region and published to
GBIF are also imported into the ALA.

GBIF catalyses a great deal of international activity around biodiversity data mobilisation,
standardisation and use, and actively promotes associated training and capacity
enhancement efforts around the world. This has included the development of the Global
Biodiversity Informatics Outlook (Hobern et al. 2012) and the alliance for biodiversity
knowledge (Hobern et al. 2019). The alliance is a consortium-based approach to
increasing the cooperation and synergy between biodiversity information producers,
managers and users to maximise benefit for all. The ALA's various contributions to
international biodiversity fit well into this approach, with multiple innovations and tools now
widely used in national and regional portals around the world.

Biodiversity Information Standards (TDWG) provides one of the most significant
foundations for ALA activities. The ALA’s dependence on biodiversity informatics standards
provides a strong case for the practical support of TDWG. This is done through ALA staff
contributing time to current standards developments such as Data Quality, Audubon Core,
Citizen Science metadata and others.

Over the past seven years, a community of national atlases, based on the ALA's open-
source code and supported by GBIF, has also been developed (see _hitips://living-
atlases.gbif.org/). Since 2013, the Living Atlases community has organised technical
workshops to present ALA modules to other institutions, to improve already existing
national data portals and to learn from each other’s achievements. As at March 2021, 27

The Atlas of Living Australia: History, current state and future directions

27

Living Atlas sites are online, three are under development and seven more are being
explored, highlighting the global impact of the ALA and NCRIS programmes.

ALA future directions

As the ALA entered its 10th year in production in 2020, it undertook a Future Directions
National Consultation process to provide information for its forward strategy. Consultation
began in early June 2019 with the design of the interview approach and development of a
stakeholder engagement plan framed around five key user domains: research,
government, industry, community and international. Stakeholders were partitioned into

three types:

° data contributors

° ALA users

° those with an institutional interest in the operation of the ALA.

The process adopted a semi-structured interview approach framed around a strengths,
weaknesses, opportunities and threats (SWOT) framework (Table 2). It captured feedback
from more than 100 Australian and international stakeholders and 35 organisations.

Table 2.

Summary of ALA Future Directions National Consultation against a strengths, weakness,
opportunities and threats framework.

Strengths

Weaknesses

Software team of high calibre and critical mass that solves the complex data
interoperability issues to harmonise biodiversity data.

Impressive amount of Australia's biodiversity data, particularly plant and bird data which
are of good quality and can be accessed for free.

User-friendly interface and good IT products that have underpinned and improved
national and global awareness of, and access to, Australia's biodiversity holdings/
collections.

Well networked and well regarded domestically and internationally and has built a
national community that is working to improve provision of biodiversity data.

Strong institutional support from CSIRO that has helped the ALA to weather funding
uncertainty and to retain its quality staff.

Lack of clear strategy and priorities for developing the work programme and lack of
consultation about this in the past.

Too many disconnected products and services because the work programme is driven by
project funding and opportunity rather than by a focused strategy.

Data quality or fitness for purpose can be hard to assess and poor in some cases,
including reliability of taxonomic names, lack of absence data or information about the
quality of species identifications.

Data types are not comprehensive; for example, the ALA lacks genomics data and
longitudinal (i.e. survey) data at scale or from a national perspective.

Data are not targeted to key national biodiversity questions or assessments, but rather
may reflect historical inconsistency of past sampling strategies, given the initial focus on
collections and museum data.

28

Belbin L et al

Opportunities

Threats

° Provide national leadership and coordination with respect to standards, biodiversity
informatics, data quality and future system development.

° Deliver a more integrated national data capability and suite of services through
partnerships with related NCRIS facilities.

° Become a data repository for monitoring surveys and environmental assessments
collected by government and industry.

° Collect and digitise data that address key biodiversity-related research questions.

° Provide analytics that can support decision-making or research insights, including in new

areas, such as biosecurity.

° Lack of ongoing resources because of dependence on government funding.

° Reputational risk through poor data quality or failure to engage more with subject matter
experts in taxonomy and ecological sciences.

° Unclear mandate undermined by competitors who can better deliver specialised portals
at lower cost.

° Failure to deal with new data streams in ecology and genomics, including the variety,
volume and velocity of data flow that will be difficult to integrate.

° Owners of data not willing to share data openly and nationally due to the constraints they
work in.

Results highlighted that the ALA has pioneered a step-change in the way that Australia’s
biodiversity data are utilised through its approach to open data access, by providing
innovative products and services and mobilising the national biodiversity community. The
ALA’s global impact received recognition through both its technical and strategic
contribution to the Global Biodiversity Information Facility (GBIF) and its technical
leadership of the global Living Atlases initiative. In this regard, the ALA was acknowledged

as one

of the world’s foremost national biodiversity data infrastructures. The consultation

also highlighted that the expectations of the ALA’s stakeholders are rapidly evolving, and
that the ALA has not always adapted as well as it might have. Notable concerns to address
if the ALA is to realise its full potential as an operational data infrastructure include:

data quality - this is critical for reliable decision-making and quality research
outputs. It is also important if the ALA seeks to move, not only to aggregate data,
but also to have a custodial role in curating data.

data diversity - this is needed to ensure that the ALA can effectively deliver to major
national biodiversity reporting, assessment and monitoring programmes and help to
address the ‘big questions’ in biodiversity research. It requires datasets that are
more diverse, representative or comprehensive in terms of geography, time and
taxonomy. The ALA will also need to assist partners to prioritise data collection and
digitisation efforts to align with national needs.

With respect to opportunities, stakeholders encouraged the ALA to:

include more industry data as, in some jurisdictions, this can represent more than
85% of the current biodiversity survey effort and would provide a_ useful
complement to the data already harmonised or potentially available from museums,
collections and state biodiversity data programmes

The Atlas of Living Australia: History, current state and future directions 29

° focus the ALA's product and services portfolio to reduce some confusion about the
mission and scope of the ALA and to provide ongoing support for priority operations

° support national capability to provide standard, interoperable biodiversity data by
assisting state and territory biodiversity data systems to align their approaches with
respect to standards and with hard and soft data infrastructure.

The ask from stakeholders from a_ national biodiversity infrastructure was _ clear.
Stakeholders want:

° data of high quality that have been corrected for obvious errors and include
metadata that indicate fitness for purpose, including suitability for research

° relevant data from a range of users that address key biodiversity questions,
including longitudinal data, data of comprehensive geographic and wide taxonomic
spread and monitoring data from government programmes, consultants and
industry

° integration of new data streams beyond occurrence records, such as images,
genomics, sound recordings and environmental assessment data

° tools and standards to assist in the collection, integration, analysis and synthesis of
these data.

It was also clear that stakeholders saw a key role for the ALA in ‘soft diplomacy’ — to be a
catalyst, to offer leadership by facilitating cooperation and collaboration between
institutions. The ALA has an ongoing role in identifying gaps in the national capability and
working with others to ensure that these are filled, even if not by the ALA itself. The ALA’s
relationships with other NCRIS facilities and international bodies were also seen to be an
important way of fulfilling this part of its role. The ALA is well positioned to shape a future
role that continues to be critical in the delivery of national biodiversity data. The recently
released ALA Strategy 2020-2025 further articulates these strategic priorities
(https://www.ala.org.au/publications/, last accessed 13 October 2020).

In response to these findings, the ALA has recently embarked on a number of
transformative projects through its annual work planning process. This includes the ALA
data quality project which culminated in the recent release of the data profiles functionality
(https://www.ala.org.au/data-quality-project/) and a core infrastructure upgrade project that
is being delivered in close partnership with GBIF and will improve alignment between ALA
and GBIF systems and data. Work in 2020-2021 includes investment in an ALA complex
data project to support richer data types than can currently be captured as Darwin Core
occurrence records and the beginnings of an industry engagement programme to identify
the ability of this sector to contribute data to the ALA. The ALA will also be working more
closely with partners in the Integrated Marine Observing System, Terrestrial Ecosystem
Research Network and the Australian Research Data Commons to develop cross-facility
data assets to support national environmental reporting (https://ardc.edu.au/project/
ecoassets/). This is in response to recommendations that the ALA should expand its
partnerships with related facilities to deliver greater collective benefit to users. Further
detail of ALA's plans may be found in the ALA Strategy 2020-2025 and the ALA Annual

30 Belbin L et al

Work Plan 2020-2021. These plans, along with future annual work plans as they are
published, may be accessed online at https://www.ala.org.au/publications/.

Conclusion

It has been 10 years since Australia’s museums and herbaria were the key force in
encouraging the establishment of the Atlas of Living Australia under Australia’s National
Collaborative Research Infrastructure Strategy (NCRIS). In that decade, more than 90
million occurrence records of 110,000 species, 5000 species lists, 2000 biodiversity-related
projects, 500 environmental layers, scores of portals and the underlying code have been
made openly available. Further, the establishment of 24 national Living Atlases based on
the ALA architecture attest to its success in delivering biodiversity data and related
services. In turn, these services and capabilities support research excellence in fields such
as biodiversity, genetics and ecosystem science; they support major government and
community-led natural resource management programmes; and, through the ALA's close
relationship with the Global Biodiversity Information Facility, Australian biodiversity data are
made available to the world. These achievements have been enabled by strong
partnerships and contributions from multiple stakeholders in Australia to build what remains
one of the world's foremost biodiversity data infrastructures.

Glossary

° ABCD: Access to Biological Collections Data, a TDWG standard

° ABRS: Australian Biological Resources Study, part of the Australian Department of
Agriculture, Water and the Environment

° ALA: Atlas of Living Australia, an NCRIS facility

° ALA4R: The ALA's R-based library of functions

° API: Application Programming Interface

° APNI: Australian Plant Name Index

° ARCS: Australian Research Collaboration Service, the original name for the ARDC

° ARDC: Australian Research Data Common, an NCRIS facility

° AURIN: Australian Urban Research Infrastructure Network, an NCRIS facility

° AVH: Australian Virtual Herbarium

° BHL: Biodiversity Heritage Library

° BIE: Biodiversity Information Explorer

° Biocache: The ALA's occurrence database

° BioCollect: The ALA's project-based portal

° BPA: BioPlatforms Australia, an NCRIS facility for genomics, proteomics,
metabolomics and bioinformatics

° CAPAD: Collaborative Australian Protected Area Database, a database listing all
Australian biologically-related parks and reserves collated by the Australian
Department of Agriculture, Water and the Environment

° CHAH: Commonwealth Heads of Herbaria

The Atlas of Living Australia: History, current state and future directions 31

CHAFC: Commonwealth Heads of Faunal Collections

CSIRO: Commonwealth Scientific and Industrial Research Organisation

DigiVol: The ALA's citizen science volunteer portal

Diversity: In the context of this paper, the number of different species

DNA: Deoxyribonucleic acid, a self-replicating material which is present in nearly all
living organisms as the main constituent of chromosomes. It is the carrier of genetic
information.

eDNA: Environmental DNA, DNA found within samples of the environment (e.g. in
soil or water)

Endemism: A taxon that is localised to a location — it does not occur outside that
location

ERIN: Environmental Resources Information Network (a previous project with the
Australian Department of Agriculture, Water and the Environment)

GBIF: The Global Biodiversity Information Facility

GBIO: Global Biodiversity Information Outlook

HISPID: Herbarium Information Standards and Protocols for Interchange of Data, a
TDWG standard

IDigBio: Integrated Digitized Biocollections, the USA facility for digitisation of
biodiversity collections, funded by the National Science Foundation

IMOS: Integrating Marine Observing System, an NCRIS facility

IPBES: The Intergovernmental Science-Policy Platform on Biodiversity and
Ecosystem Services

MERIT: Online reporting tool for projects supported by the Department of
Agriculture, Water and the Environment

NCRIS: National Collaborative Research Infrastructure Strategy

NSL: National Species List

Occurrences: Observations of species or specimen records that generally use the
Darwin Core standard

OZCAM: Online Zoological Collections of Australian Museums

Specimen: A physical instance of a species

Synonym: An alternative name for a taxon

Taxon/taxa: A group of one or more populations of an organism or organisms, seen
by taxonomists to form a unit

Taxonomy: A branch of science that encompasses the description, identification,
nomenclature and classification of organisms

TCS: Taxonomic Concept Schema, a TDWG standard

TDWG: Taxonomic Database Working Group, now better described as Biodiversity
Information Standards

TERN: Terrestrial Ecosystem Research Network, an NCRIS facility

Trait: An attribute of a specimen, species or group of species

UNESCO: The United Nations Educational, Scientific and Cultural Organization
Zoalrack: The ALA portal for import, analyses and export of animal track data
(formerly OzTrack)

32 Belbin L et al

Acknowledgements

The authors wish to acknowledge the fundamental contribution Dr John LaSalle made to
the formation and operation of the ALA during his tenure as Director.

We thank the following people for their contribution to this paper. From the ALA, Peter
Brenton (reviewed projects section), David Martin (reviewed draft manuscript), Peggy
Newman (reviewed Zoalack/track data section), Nick Dos Remedios (reviewed draft
manuscript), Corinna Paeper, Rita Chen and Matilda Stevenson (developed ALA metrics),
Martin Westgate (reviewed draft manuscript). Joanne Daly, Cameron Slatyer, Penny
Berents, John Hooper, Brett Summerell, Kevin Thiele, Tony Rothnie and Ken Walker were
instrumental in providing insights into the history of the ALA.

We acknowledge the work of Piers Higgs in setting the early agenda for the ALA's citizen
science work and Paul Flemons for creating and promoting further volunteer involvement
through DigiVol. Volunteers have also been instrumental in the success of the Biodiversity
Heritage Library Australia project and we thank them for their commitment. We also thank
BHL Australia manager Nicole Kearney and staff team. We also acknowledge the
enthusiasm and tremendous work of Ken Walker for support of the BowerBird community
and for their work in transferring data from BowerBird to the Australian iNaturalist platform.

Ultimately, the success of the ALA has been built on the leadership, goodwill and
contribution of individuals and organisations too numerous to list here. The authors
acknowledge this work and the ongoing support provided by our data partners, institutional
partners and those organisations that continue to support and promote the importance of a
national biodiversity data infrastructure. We are particularly grateful to our colleagues in the
Department of Education, Skills and Employment who continue to champion and so
effectively manage Australia’s portfolio of national research infrastructure.

We thank Gil Nelson (iDigBio) and Tim Robertson (GBIF) for review comments that have
improved this paper.

Funding program

National Collaborative Research Infrastructure Strategy

Grant title

Atlas of Living Australia

Hosting institution

Commonwealth Scientific and Industrial Research Organisation

The Atlas of Living Australia: History, current state and future directions 33

Author contributions

The paper was a genuinely shared undertaking with all authors contributing to, and editing
all sections. Primary responsibility for drafting each section were as follows. Lee Belbin led
the Introduction (1); Species occurrence data (5.2); Species lists (5.5); Biodiversity projects
(5.6); Environmental layers (5.7); Gaps in data and services (6) and the Glossary (10).
Donald Hobern led the Original scope of the ALA (4). Ely Wallis led Reasons for
establishing the ALA (3); Taxonomic framework (5.1); Biodiversity literature (5.4) and
Descriptive species information (5.8). Andre Zerger led Biodiversity in Australia (2) and ALA
future directions (8).

References

° Belbin L (2011) The Atlas of Livings Australia’s spatial portal. In: Jones MB, Gries C
(Eds) Proceedings of the Environmental Information Management Conference 2011
(EIM 2011).

° Belbin L, Daly J, Hirsch T, Hobern D, LaSalle J (2013) A specialist's audit of aggregated
occurrence records: An ‘aggregator’s’ perspective. ZooKeys 305: 67-76. https://doi.org/
10.3897/zookeys.305.5438

° Belbin L, Williams KJ (2015) Towards a national bio-environmental data facility:
experiences from the Atlas of Living Australia. International Journal of Geographical
Information Science 30 (1): 108-125. https://doi.org/10.1080/13658816.2015.1077962

° Braby MF (2018) Threatened species conservation of invertebrates in Australia: an
overview. Austral Entomology 57 (2): 173-181. https://doi.org/10.1111/aen.12324

° Chapman AD, Belbin L, Zermoglio PF, Wieczorek J, Morris PJ, Nicholls M, Rees ER,
Veiga AK, Thompson A, Saraiva AM, James SA, Gendreau C, Benson A, Schigel D
(2020) Developing standards for improved data quality and for selecting fit for use
biodiversity data. Biodiversity Information Science and Standards 4: e50889.
https://doi.org/10.3897/biss.4.50889

° Department of Education (2006) National collaborative research infrastructure strategy
Strategic Roadmap 2006. URL: https://docs.education.gov.au/documents/national-
collaborative-research-infrastructure-strategy-strategic-roadmap-2006-0

° di Castri F (1996) Biodiversity in World Science Report 1996. UNESCO, Paris. URL:
https://unesdoc.unesco.org/ark:/48223/pf0000102819

° Dwyer RG, Brooking C, Brimblecombe WV, et al. (2015) An open web-based system for
the analysis and sharing of animal tracking data. Animal Biotelemetry 3: 1.
https://doi.org/10.1186/s4031 7-014-0021-8

° Flemons P, Raymond P, Brenton P, Belbin L (2009) Atlas of Living Australia Report on
the Spatial Analysis Tools Workshop 3rd & 4th December 2009. Atlas of Living Australia.
URL: http:/Awww.ala.org.au/wp-content/uploads/2010/09/Lee ALA-Spatial-Ananysis-

Tools-Workshop-Report-V3.pdf
° Flemons P, Belbin L (2010) Report on the Environmental Data Library Workshop April

22-23, 2010. Atlas of Living Australia. URL: htto:/Awww.ala.org.au/wp-content/uploads/
2010/08/Lee-NEDL_Workshop-Report-Final.pdf

34

Belbin L et al

Hardisty AR, Michener WK, Agosti D, Enrique AG, Bastin L, Belbin L, Bowser A,
Buttigieg PL, Canhos DA, Egloff W, De Giovanni R, Figueira R, Groom Q, Guralnick RP,
Hobern D, Hugo W, Koureas D, Ligiang J, Los W, Manuel J, Manset D, Poelen J,
Saarenmaa H, Schigel H, Uhlir PF, Kissling WD (2018) The Bari Manifesto: An
interoperability framework for essential biodiversity variables. Ecological Informatics 49:
22-31. https://doi.org/10.1016/j.ecoinf.2018.11.003

Hardisty AR, Belbin L, Hobern D, McGeoch M, Pirzl R, Williams KJ, Kissling WWD (2019)
Research infrastructure challenges in preparing essential biodiversity variables data
products for alien invasive species. Environmental Research Letters 14: 025005.
https://doi.org/10.1088/1748-9326/aaf5db

Hobern D, Apostolico A, Arnaud E, Bello JC, Canhos D, Dubois G, Field D, Alonso
Garcia E, Hardisty A, Harrison J, Heidorn B, Krishtalka L, Mata E, Page R, Parr C, Price
J, Willoughby S (2012) Global Biodiversity Informatics Outlook: Delivering biodiversity
knowledge in the information age. Global Biodiversity Information Facility https://doi.org/
10.15468/6jxa-yb44

Hobern D, Baptiste B, Copas K, Guralnick R, Hahn A, van Huis E, Kim E, McGeoch M,
Naicker |, Navarro L, Noesgaard D, Price M, Rodrigues A, Schigel D, Sheffield C,
Wieczorek J (2019) Connecting data and expertise: a new alliance for biodiversity
knowledge. Biodiversity Data Journal 7: €33679. https://doi.org/10.3897/bdj.7.e33679
IPBES (2019) Summary for policymakers of the global assessment report on
biodiversity and ecosystem services. Zenodo https://doi.org/10.5281/zenodo0.3553458
Kissling WD, Ahumada JA, Bowser A, Fernandez M, Garcia EA, et al. (2018) Building
essential biodiversity variables (EBVs) of species distribution and abundance at a global
scale. Biological Reviews 93: 600-625. https://doi.org/10.1111/brv.12359

Mesibov R (2013) A specialist’s audit of aggregated occurrence records. ZooKeys 293:
1-18. https://doi.org/10.3897/zookeys.293.5111

Mesibov R (2018) An audit of some filtering effects in aggregated occurrence records.
ZooKeys 751: 129-146. https://doi.org/10.3897/zookeys.751.24791

Newman P, Dwyer R, Belbin L, Campbell H (2020) ZoaTrack - an online tool to analyse
and share animal location data: User engagement and future perspectives. Australian
Zoologist 41 (1): 12-18. https://doi.org/10.7882/az.2019.031

OECD Megascience Forum (1999) Final Report of the OECD Megascience Forum
Working Group on Biological Informatics. URL: http:/Awww.oecd.org/sti/inno/
2105199.pdf

Pereira HM, Ferrier S, Walters M, Geller GN, Jongman RH, Scholes RJ, Bruford MW,
Brummitt N, Butchart SH, Cardoso AC, Coops NC, Dulloo E, Faith DP, Freyhof J,
Gregory RD, et al. (2013) Essential biodiversity variables. Science 339: 277-278.
https://doi.org/10.1126/science.1229931

Samuel G (2020) Independent review of the EPBC Act — Interim Report. Department of
Agriculture, Water and the Environment. Canberra, June 2020.

University of Cincinnati (2019) Museums put ancient DNA to work for wildlife: Old
museum specimens are giving researchers fresh insights into endangered species.
https:/Awww.sciencedaily.com/releases/2019/10/191017132229.htm.

Accessed on: 2019-10-17.

Wieczorek J, Bloom D, Guralnick R, Blum S, Déring M, Giovanni R, et al. (2012) Darwin
Core: An evolving community-developed biodiversity data standard. PLOS One 7 (1):

e29715. https://doi.org/10.1371/journal.pone.0029715

The Atlas of Living Australia: History, current state and future directions

Woinarski JC, Braby MF, Burbridge AA, et al. (2019) Reading the black book: The
number, timing, distribution and causes of listed extinctions in Australia. Biological
Conservation 239: 108261. https://doi.org/10.1016/j.biocon.2019.108261

35