What prompted me to focus on Data Science and Analytics in this week’s blog is the imminent publication of a paper I contributed to – ‘AusTraits – a curated plant trait database for the Australian flora’ (Falster D et al., 2021 – in press).  As the paper says:

“AusTraits synthesises data on 375 traits across 29230 taxa from field campaigns, published literature, taxonomic monographs, and individual taxa descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological parameters (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual-, species- and genus-level observations coupled to, where available, contextual information on-site properties. This data descriptor provides information on version 2.1.0 of AusTraits which contains data for 937243 trait-by-taxa combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data to increase our collective understanding of the Australian flora.”

I and other colleagues from the Western Australian Herbarium were invited to contribute our data from the Descriptive Catalogue initiative, which contributed a small number of observed traits for c. 12,000 WA plant taxa. To my mind, one key strategy for data science is that major datasets are developed and maintained in a manner that can contribute to even larger integrative projects such as AusTraits, for further data analysis, again as we outline in the paper:

“AusTraits version 2.1.0 was assembled from 351 distinct sources, including published papers, field campaigns, botanical collections, and taxonomic treatments. Initially, we identified a list of candidate traits of interest, then identified primary sources containing measurements for these traits. As the compilation grew, we expanded the list of traits considered to include any measurable quantity that had been quantified for a moderate number of taxa (n > 20). To harmonise each source into the common a format AusTraits applied a reproducible and transparent workflow – a custom workflow to clean and standardise taxonomic names using the latest and most comprehensive taxonomic resources for the Australian flora: the Australian Plant Census (APC) and the Australian Plant Names Index (APNI).”

The AusTraits project is hosted by the Australian Research Data Commons (ARDC) formed in July 2018. The ARDC is “a transformational initiative that aims to enable the Australian research community and provide industry access to nationally significant, leading-edge data-intensive eInfrastructure, platforms, skills and collections of high-quality data”.  This hosting contributes towards the maintenance aspect I mentioned above.

Full details on those processes will be available in the forthcoming publication, a link to which I’ll add when it becomes available.  Meanwhile, if you’d like to know more about this project, or about what we can offer in the Data Science and Analytics areas, please drop me a line at alex.chapman@gaiaresources.com.au, or connect with us on Twitter, LinkedIn or Facebook.

Alex

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Over 120 people attended over the 21st and 22nd June 2018, coming from as far afield as Kalgoorlie, Karratha and NSW and including representatives from the three levels of government, EIA practitioners, botanical (and zoological) consultants, universities, community groups and mining companies.

A full house (thanks to ECA for the image).

DAY 1
Session 1: a panel discussion by representatives from the Department of Water and Environmental Regulation (DWER), Environmental Protection Authority (EPA) Strategy and Guidance, Department of Mines, Industry Regulation and Safety (DMIRS) and the Federal Department of Energy and Environment (DoEE) discussing guidance materials, scope and quality of survey reports, indirect impacts, assessment time-frames and strong advice to consult with agencies early.

Session 2: community involvement in botanical EIA including how they are conducted on public lands, the responsibilities that consultant botanists have more broadly in EIA.

Session 3: legal frameworks that govern botanical EIA, including clearing regulation history and updates to the drafting new Biodiversity Conservation Act 2016 regulations (due to come into effect on the 1st January 2019).

Session 4: technical discussions with a specialist flora and vegetation consultant views on ensuring robust technical surveys, followed by EPA’s expectations of botanical survey reports and discussion with representatives from the WA Biodiversity Science Institute on leveraging aggregated biodiversity data.

DAY 2
Session 1: practitioners views on how flora and vegetation surveys operate within EIA process, including a NSW perspective from guest-speaker Dr John Hunter and an end-user perspective from WA consultant Kelli McCreery.

Session 2: national flora taxonomy initiatives by Dr Kevin Thiele including the Decadal Plan for Taxonomy, and case studies from Malcolm Trudgen and Geoff Cockerton illustrating how much more there is to know about our flora.

Session 3: challenges in classifying and describing our vegetation reliably and comparably, including the rationale behind plot-based surveys and the science of phytosociology that might underpin them. Greg Keighery elaborated on the (sometimes poor) definition of Threatened and Priority ecological communities (TECs and PECs).

Session 4: covered allied knowledge domains such as WA soil and geology, and the need for fungi to be included in surveys for EIA. The symposium was then wrapped up with a group discussion.

Some important issues that came up during the conference (from our perspective) included:

• environmental consultants and regulators rely on quality data/information to do their jobs well; this event was in part to help each understand the others’ data/info needs that could streamline approvals;
• consultants were trying to find out what causes delays in approvals, and where to find guidelines and standard practices;
• regulators were acknowledging being swamped and behind but stressed the importance of early dialogue and providing good quality data (eg. targeted data against the key flora/fauna objectives for that specific project area);
• understanding the ramifications of requirements for survey compliance and report submissions (eg. IBSA)
• reviewing the current data collection methods (pen/paper, tablets, phones etc.);
• the need for standardisation of data capture;
• solving the apparent lack of information defining WA’s TECs and PECs;
• lobbying for reliable ongoing taxonomic resources — for identification, names data, and the circumscription of new species, such as the work of the WA Herbarium and FloraBase, for a national maintained and comprehensive eFlora; or for the WA Biodiversity Science Institute.

If you’d like to know more about how we can help you with developing systems for capturing, managing or analysing environmental data, then please leave a comment below – or email us directly: alex.chapman@gaiaresources.com.au or Chris.Roach@gaiaresources.com.au.

Alex and Chris

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