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1
22/10/14, Andrew Tokmakoff
AusPlots Rangelands field data
collection and publication
Infrastructure for Ecological Monit...
2
Objectives
✤ To cover:
✤ what AusPlots is, and why it exists
✤ how AusPlots data is collected, handled and
published
✤ t...
What is AusPlots Rangelands?
✤ AusPlots is based at Adelaide University and is one of 12
Terrestrial Ecosystem Research Ne...
So, what do Australian
Rangelands look like?
4
5
Collecting field data in a
prescribed methodology
✤ Prescribes a survey methodology for
collecting plot-based vegetation a...
What is collected? General
✤ High accuracy (DGPS) location
data for the plot’s corners, centre
and transect start/end poin...
What is collected? Vegetation
✤ Vouchering
✤ Vouchered vegetation
species (barcoded) over
the plot; later sent for
Herbari...
What is collected? Vegetation
✤ Point Intercept
✤ consists of 1010 points,
where each point records:
✤ the substrate;
✤ an...
✤ Basal Area
✤ recordings in each of the 9 segments of the plot, each consisting
of:
✤ a set of vegetation species under o...
What is collected? Vegetation
✤ PhotoPoints
✤ stitched from 3 sets of 360 degree high resolution images taken
from 3 point...
Trunk Identification and
Basal Area Calculation
12
Ben Sparrow and Ben Ward
What is collected? Vegetation
✤ Leaf Area Index (LAI)
✤ Site Structural Summary
✤ recording the three most dominant specie...
What is collected? Soils
✤ Characterisation of soils (barcoded)
✤ 1 metre deep pit, in 10cm increments (ec, ph, texture an...
What is collected? Soils
✤ 3 bulk density measurements, which quantify soil fine earth and
gravel.
15
Where are the plots?
16
Australian Transect Network
17
2
The AusPlots Approach: tooling
18
Some requirements..
✤ Core function: support data collection according to the protocol
✤ Minimise data double-handling
✤ M...
System
Architecture
20
cron
Internet
Data
Upload
Apach
e/PHP
Field App
Web-based Admin Interface
(Cloud) SWARM Server
2
AusPlots Rangelands
Field Data Collection App
21
Field App: Plot Creation
22
Field App: Site Description
23
Field App: Veg. Vouchering
24
Field App: Point Intercept
25
Field App: Basal Wedge
26
Field App: Structural Summary
27
Field App: Plot Upload
28
AusPlots Rangelands
Data management
29
Data Management
30
ingestion
✤ Two databases that are synchronised through regular and
automated ingestion of newly upload...
Data Management: CouchDB
✤ CouchDB acts as a ‘landing-spot’ for Field App
Data.
✤ 24/7 availability
of upload service
✤ Da...
Data Management: PostgreSQL
✤ PostgreSQL acts as the ‘permanent’ AusPlots data repository
(Vault).
✤ Data uploaded by
the ...
Data Management: Curation
33
Field App
Web-based Admin Interface
cron
REST/
JSON
Apach
e/PHP
(Cloud) SWARM Server
✤ Apache...
2
Publishing curated data
34
✤ Soils 2 Satellites offers visualisation
✤ (e.g. for land managers, consultants)
✤ Aekos offers raw data access,
data enr...
ÆKOS data warehouse and portal
36
Motivation: data entropy
37
Motivation: overcoming
barriers to ecological data re-
use
Identify
problem
Draft
approac
h
Search
for data
Acquire
data
A...
39
40
2
Soils to Satellites
41
42
image of 2s2 map page
43
44
45
2
Reflecting..
✤Benefits:
✤ Integrity of data
✤ Speed of data availability
✤Challenges:
✤ getting the UI right; resistance...
2
Looking ahead…
✤ New Woodlands module w/ protocols (Forests not)
✤ Veg Condition, Fauna and Soils are likely to be first...
Summary
✤ The AusPlots field data collection App generates clean data that is
readily curated and easy to publish.
✤ The s...
Any Questions?
andrew.tokmakoff@adelaide.ed
u.au
Andrew Tokmakoff
49
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A presentation detailing the AusPlots data collection process

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  1. 1. 1 22/10/14, Andrew Tokmakoff AusPlots Rangelands field data collection and publication Infrastructure for Ecological Monitoring
  2. 2. 2 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
  3. 3. 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. 3
  4. 4. So, what do Australian Rangelands look like? 4
  5. 5. 5
  6. 6. Collecting field data in a prescribed methodology ✤ Prescribes a survey methodology for collecting plot-based vegetation and soils data ✤ consistency of both data and collection method ✤ allows analysis of consistent data over time, by future researchers 6
  7. 7. 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, lithologies and landform pattern/element. 7
  8. 8. What is collected? Vegetation ✤ Vouchering ✤ Vouchered vegetation species (barcoded) over the plot; later sent for Herbarium Determinations. ✤ Genetic vouchering (barcoded) of species and extra sampling of dominant species (up to 4 samples). 8
  9. 9. 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 9
  10. 10. ✤ 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 10
  11. 11. 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) 11
  12. 12. Trunk Identification and Basal Area Calculation 12 Ben Sparrow and Ben Ward
  13. 13. 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). 13
  14. 14. 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 14
  15. 15. What is collected? Soils ✤ 3 bulk density measurements, which quantify soil fine earth and gravel. 15
  16. 16. Where are the plots? 16
  17. 17. Australian Transect Network 17
  18. 18. 2 The AusPlots Approach: tooling 18
  19. 19. 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 19
  20. 20. System Architecture 20 cron Internet Data Upload Apach e/PHP Field App Web-based Admin Interface (Cloud) SWARM Server
  21. 21. 2 AusPlots Rangelands Field Data Collection App 21
  22. 22. Field App: Plot Creation 22
  23. 23. Field App: Site Description 23
  24. 24. Field App: Veg. Vouchering 24
  25. 25. Field App: Point Intercept 25
  26. 26. Field App: Basal Wedge 26
  27. 27. Field App: Structural Summary 27
  28. 28. Field App: Plot Upload 28
  29. 29. AusPlots Rangelands Data management 29
  30. 30. Data Management 30 ingestion ✤ Two databases that are synchronised through regular and automated ingestion of newly uploaded plot data (from Field App). (Cloud) SWARM Server
  31. 31. Data Management: CouchDB ✤ CouchDB acts as a ‘landing-spot’ for Field App Data. ✤ 24/7 availability of upload service ✤ Data uploaded via internet (WiFi or 3G) 31 ingestion (Cloud) SWARM Server
  32. 32. 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. 32 ingestion (Cloud) SWARM Server
  33. 33. Data Management: Curation 33 Field App Web-based Admin Interface cron REST/ JSON Apach e/PHP (Cloud) SWARM Server ✤ Apache/PHP web “site” provides a User Interface for data curation. ✤ Allows “cleaning” of data and entry of new items such as herbarium determinations.
  34. 34. 2 Publishing curated data 34
  35. 35. ✤ 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 35 Field App cron REST/ JSON (Cloud) SWARM Server
  36. 36. ÆKOS data warehouse and portal 36
  37. 37. Motivation: data entropy 37
  38. 38. Motivation: overcoming barriers to ecological data re- use Identify problem Draft approac h 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 38
  39. 39. 39
  40. 40. 40
  41. 41. 2 Soils to Satellites 41
  42. 42. 42 image of 2s2 map page
  43. 43. 43
  44. 44. 44
  45. 45. 45
  46. 46. 2 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. 46
  47. 47. 2 Looking ahead… ✤ New Woodlands module w/ protocols (Forests not) ✤ Veg Condition, Fauna and Soils are likely to be first ✤ iOS support 47
  48. 48. 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. 48
  49. 49. Any Questions? andrew.tokmakoff@adelaide.ed u.au Andrew Tokmakoff 49

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