Bioenvironmental Data as a Web Service

Mr Lee Belbin1

1Blatant Fabrications Pty Ltd, Carlton, Australia,

THE ATLAS OF LIVING AUSTRALIA [1]

The Atlas of Living Australia is an Australian government funded project established in 2010 and managed by CSIRO to collect and integrate information on observations and specimens of species in the Australian region. There was a recognition that the diverse and valuable data held by Australian herbaria and museums needed to be integrated and exposed publicly in a consistent form. The Atlas currently holds more than 90 million records of over 100 thousand terrestrial, marine and freshwater species and a broad range of species attributes (e.g., images) [2]. To June 2017, there have been 11.3 billion records downloaded from the Atlas.

The geographic focus of the Atlas of Living Australia is naturally enough, the Australian region but how do we even define this region? Notionally, this has been defined as the bounding box that contains Australia’s Economic Exclusion Zone and Australia’s External territories. There are however no fixed spatial limits to the biological and bioenvironmental data within the Atlas. For example, the Atlas currently contains observations of species in 254 countries.

THE SPATIAL PORTAL [3]

The Atlas has several web portals, one of which, the Spatial Portal, has been designed to support ecological research and environmental management. As its name suggests, the Spatial Portal provides a map focus but also adds around 500 ‘environmental layers’ [4] and range of analytical tools to demonstrate the utility of integrated biological and environment data. The spatial extent of the Spatial Portal’s environmental layers are predominantly within the Australian region as defined above, but global extent layers are included to support the analyses of invasive species in their home ranges.

Tools such as scatterplots enable users to evaluate how species are related to their environments. If the axes on the scatterplots are replaced by classes of an environmental layer, a cross-tabulation of species occurrences, species diversity and area can be calculated for each combination of classes. More advanced tools such as MaxEnt [5], a species distribution modelling algorithm based on maximum entropy, examines the relationship between species observations and the environment to predict where species could occur.

BIOENVIRONMENTAL [6]

While the Atlas wasn’t an obvious home for these bioenvironmental layers, no alternative currently exists. The ~500 layers were sourced from 64 different agencies/departments. Layers were added to the Spatial Portal if they were evaluated as showing a potential relationship to species distributions or provided a context for species occurrences. For example, species distributions are controlled in part by temperature and precipitation. Similarly, the distribution of species across for example parks and reserves may contribute to how areas are managed.

The exposure of these bioenvironmental layers is via key words and a three-level hierarchical classification; layer type, classification 1 and classification 2. The layer type is either environmental implying gridded continuous values such as temperature or precipitation, or polygonal contextual layers implying a class value such as soil type or state/territory.  Classification level 1 includes area management, biodiversity, climate, distance, fire, hydrology, marine, political, sensitive data, social, substrate, topography and vegetation. Level 2 classification terms include age, biodiversity, biology, boundaries, chemistry, classification, culture, energy, evaporation, exclusion zones, farming, fpar, habitat, humidity, moisture, phenology, phylogenetic diversity, physics, precipitation, region, status, temperature, topography, turbidity and wind.

The Atlas negotiated various forms of CC-BY [7] licenses for the biological data but the environmental data layers range from various creative commons licenses to “contact the creator”. Therefore, while biological data can be freely downloaded, for simplicity, the environmental data has been restricted to ‘sampling’: providing layer values at geographic points corresponding to biological observations in the Atlas or as uploaded by users.

Access to environmental layer values can either be through the Spatial Portal’s web interface, via an R-library (ALA4R: http://www.ala.org.au/faq/spatial-portal/spatial-portal-case-studies/ala4r/) or via the Atlas web services [8]. For example, to determine what state or territory an observation is in, the URL http://spatial.ala.org.au/ws/intersect/{id}/{latitude}/{longitude} can be used. The ‘id’ is a local identifier that is assigned to each layer and the latitude and longitude are to be supplied in decimal degrees. For example, http://spatial.ala.org.au/ws/intersect/cl22/-23.1/149.1 will show that the location with a latitude -23.1 and a longitude of 149.1 is, on layer cl22 (contextual layer 22), located in state of Queensland. Similarly, http://spatial.ala.org.au/ws/intersect/el761/-34.43/145.12 will return that the mean annual temperature – diurnal range at the latitude -34.43 and longitude 145.12 is 13.575c.

DISCUSSION

The 500+ bioenvironmental layers in the in the Atlas of Living Australia requires approximately one f/t position to maintain. New layers and associated metadata can take days to locate, download, check licensing, classify and process into a consistent form for efficient use within the Atlas environment. The availability of new layers is an ad hoc manual process, and new layers may either replace older versions (deprecate), or add to older versions.

Ideally, a Federally-funded national committee within NCRIS [9] should be established that will identify relevant bioenvironmental layers for the Australian region, and establish a standard protocol for their delivery nationally and globally. Fundamental to that service should be a basic web service that takes the form-

http://bioenvironment.au/ws/intersect/{layerID}/{latitude}/{longitude}

A batch version of the above service would be a useful addition. The responsibility for the delivery of the service would then reside at the data source, errors in processing greatly minimized, and currency assured. Such a service would also avoid costly duplication of effort, storage and computation. Professor Henry Nix proposed an “Australian Environmental GIS (AEGIS)” back in 1986. Hopefully, this simpler recommendation won’t take another 30 years to implement.

REFERENCES

  1. The Atlas of Living Australia, http://www.ala.org.au, accessed 27 Jun 2017.
  2. The Atlas dashboard, http://dashboard.ala.org.au, accessed 27 Jun 2017.
  3. Belbin, L., The Atlas of Livings Australia’s Spatial Portal, in, Proceedings of the Environmental Information Management Conference 2011 (EIM 2011), Jones, M., B. & Gries, C. (eds.), 39-43. Santa Barbara, USA. http://spatial.ala.org.au, accessed 27 Jun 2017.
  4. Environmental layers, http://spatial.ala.org.au/layers, accessed 27 Jun 2017.
  5. Phillips, S.J., Anderson, R.P. and Schapire, R.E. Maximum entropy modeling of species geographic distributions. Ecological Modelling 2006 190, p. 231-259.
  6. Creative Commons, https://creativecommons.org/licenses/by/2.0/au/, accessed 26 Jun 2017.
  7. The Atlas of Living Australia’s web services, http://api.ala.org.au, access 27 Jun 2017.
  8. Belbin, L., Williams, K.J., Towards a national bio-environmental data facility: experiences from the Atlas of Living Australia. International Journal of Geographical Information Science 2016 30(1), p. 108-125 http://dx.doi.org/10.1080/13658816.2015.1077962.
  9. The National Collaborative Research Infrastructure Strategy (NCRIS), https://www.education.gov.au/national-collaborative-research-infrastructure-strategy-ncris, accessed 27 Jun 2017.

Biography

I am a geoscience graduate and IT postgraduate who has evolved from exploration geology, teaching and research, analytical ecology to management, standards and policy development.  For the past 15 years, I have provided project management for, and advice to international and national information management projects. I have been referred to as a surfer with a work problem. ORCID: 0000-0001-8900-6203

About the conference

eResearch Australasia provides opportunities for delegates to engage, connect, and share their ideas and exemplars concerning new information centric research capabilities, and how information and communication technologies help researchers to collaborate, collect, manage, share, process, analyse, store, find, understand and re-use information.

Conference Managers

Please contact the team at Conference Design with any questions regarding the conference.

© 2016 - 2017 Conference Design Pty Ltd