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22/10/14, Andrew Tokmakoff

AusPlots Rangelands field data collection and publicationInfrastructure for Ecological Monitoring

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Objectives

✤ To cover:

✤ what AusPlots is, and why it exists

✤ how AusPlots data is collected, handled and published

✤ the AusPlots system architecture, its key functions and the technical path we’ve have taken

✤ For you to consider what our work might mean for you

What is AusPlots Rangelands?✤ AusPlots is based at Adelaide University and is one of 12

Terrestrial Ecosystem Research Network (TERN) facilities

✤ AusPlots identifies, prioritises, and fills data gaps in environmental monitoring of Australian rangelands bioregions (81% of the continent)

✤ AusPlots has defined a standardised survey methodology and undertakes surveys over a national network of permanent 1 hectare plots, collecting baseline vegetation and soils ecological data.

✤ This work facilitates ongoing evidence-based decision making at local, regional, national and international levels.

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So, what do Australian Rangelands look like?

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Collecting field data in a prescribed methodology

✤ Prescribes a survey methodology forcollecting plot-based vegetation and soils data

✤ consistency of both data and collection method

✤ allows analysis of consistent dataover time, by future researchers

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What is collected? General

✤ High accuracy (DGPS) location data for the plot’s corners, centre and transect start/end points

✤ Site observations in regard to condition, erosion, drainage, micro-relief, lithologiesand landform pattern/element.

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What is collected? Vegetation✤ Vouchering

✤ Vouchered vegetationspecies (barcoded) over the plot; later sent for Herbarium Determinations.

✤ Genetic vouchering (barcoded) of species and extra sampling of dominant species (up to 4 samples).

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What is collected? Vegetation✤ Point Intercept

✤ consists of 1010 points, where each point records:

✤ the substrate;

✤ any vegetation intercept(s), indicating the species and intercept height

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✤ Basal Area

✤ recordings in each of the 9 segments of the plot, each consisting of:

✤ a set of vegetation species under observation, the associated wedge factor and the number of ‘hits’

What is collected? Vegetation

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What is collected? Vegetation

✤ PhotoPoints

✤ stitched from 3 sets of 360 degree high resolution images taken from 3 points at the plot centre

✤ used to automatically calculate basal area using computer vision (experimental)

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Trunk Identification and Basal Area Calculation

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Ben Sparrow and Ben Ward

What is collected? Vegetation

✤ Leaf Area Index (LAI)

✤ Site Structural Summary

✤ recording the three most dominant species in the Upper, Middle and Lower strata, (with floristics comments).

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What is collected? Soils✤ Characterisation of soils (barcoded)

✤ 1 metre deep pit, in 10cm increments (ec, ph, texture and colour)

✤ 9 subsite samples:

✤ barcoded meta-genomics surface soil samples and soil samples in 10cm increments to 30cm depth

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What is collected? Soils

✤ 3 bulk density measurements, which quantify soil fine earth and gravel.

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Where are the plots?

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Australian Transect Network

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The AusPlots Approach: tooling

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Some requirements..

✤ Core function: support data collection according to the protocol

✤ Minimise data double-handling

✤ Maximise integrity of data (e.g. transcription errors)

✤ Use ‘off-the-shelf’ where appropriate (rapid development)

✤ Be able to function without a network (remote locations)

✤ Offer efficiency gains vs. traditional data collection methods

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SystemArchitecture

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cronInternet

DataUpload

Apache/PHP

Field App

Web-based Admin Interface

(Cloud) SWARM Server

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AusPlots RangelandsField Data Collection App

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Field App: Plot Creation

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Field App: Site Description

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Field App: Veg. Vouchering

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Field App: Point Intercept

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Field App: Basal Wedge

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Field App: Structural Summary

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Field App: Plot Upload

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AusPlots RangelandsData management

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Data Management

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ingestion

✤ Two databases that are synchronised through regular and automated ingestion of newly uploaded plot data (from Field App).

(Cloud) SWARM Server

Data Management: CouchDB✤ CouchDB acts as a ‘landing-spot’ for Field

App Data.

✤ 24/7 availability of upload service

✤ Data uploaded viainternet(WiFi or 3G)

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ingestion

(Cloud) SWARM Server

Data Management: PostgreSQL

✤ PostgreSQL acts as the ‘permanent’ AusPlots data repository (Vault).

✤ Data uploaded by the Field App into CouchDB is periodically “ingested”

✤ Relational DB

✤ 24/7 availability, scheduled backups.

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ingestion

(Cloud) SWARM Server

Data Management: Curation

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Field App

Web-based Admin Interface

cronREST/JSON

Apache/PHP

(Cloud) SWARM Server

✤ Apache/PHP web “site”provides a User Interfacefor data curation.

✤ Allows “cleaning” of data and entry of new items such as herbarium determinations.

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Publishing curated data

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✤ Soils 2 Satellites offers visualisation

✤ (e.g. for land managers, consultants)

✤ Aekos offers raw data access,data enrichment and search

✤ (e.g. for ecological scientists)

Publishing to external services

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Field App

cronREST/JSON

(Cloud) SWARM Server

ÆKOS data warehouse and portal

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Motivation: data entropy

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Motivation: overcoming barriers to ecological data re-use

Identify problem

Draft approach

Search for data

Acquire data

Assess suitability

Modify approach

Prepare data

Conduct analysis

Interpret results

Dispersed: Data is stored in many storage locations and formats

Source:Forestcheck: www.dec.wa.gov.au

Complex: Data usually needs explanation and context before it can be accurately used

www.nswrail.net

Diverse and fragmented: Ecological data covers a wide range of topics and there are many different ways of measuring, observing and expressing different concepts* Rapidly evolving with few measurement standards

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Soils to Satellites

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image of 2s2 map page

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Reflecting..

✤Benefits:✤ Integrity of data ✤ Speed of data availability

✤Challenges:✤ getting the UI right; resistance when it is slower than

“recording audio” (with subsequent data entry later on).✤ dealing with legacy data at the same time as introducing

new tools.

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Looking ahead…

✤ New Woodlands module w/ protocols (Forests not)

✤ Veg Condition, Fauna and Soils are likely to be first

✤ iOS support

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Summary

✤ The AusPlots field data collection App generates clean data that is readily curated and easy to publish.

✤ The solution was developed iteratively, based upon experience from field use and adopted a component-based design for fast results.

✤ Complexity of the data collected led to a custom solution.

✤ ÆKOS provides a publishing platform for AusPlots.

✤ Together, we have a field-to-web solution that makes data accessible for use in long-term studies and facilitates informed ecological decision-making.

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Any Questions?

andrew.tokmakoff@adelaide.edu.au

Andrew Tokmakoff

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