Download - Aus plots escience-brasil
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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
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