Env-DATA - Movebank

The Environmental-Data Automated Track
Annotation (Env-DATA) System Tutorial
Somayeh Dodge
([email protected])
Dept. of Geography and Environmental Studies
University of Colorado at Colorado Springs
AMOVEE Symposium
May 2014
types,+there+are+also+many+important+commonalities+associated+with+the+analysis+of+any+movement+data+
irrespective+of+the+type+of+object.+++
GIScience(2014(Workshop(on!!
Analysis!of#Movement#Data!(AMD’14)!
This+workshop+aims+to+serve+as+a+platform+to+discuss+the+recent+trends+in+the+study+of+movement+and+
novel+methods+for+analyzing+and+contextualizing+movement+data.+The+workshop’s+focus+is+on,+but+not+
limited+to,+topics+concerning+analysis,+modeling,+and+representation+of+movement+patterns.+The+
workshop+will+cover+research+on+any+type+of+movement+data+from+different+domains+such+as+
transportation+(e.g.,+vehicles,+pedestrians),+movement+ecology+(e.g.+plants,+animals),+and+environmental+
Workshop(website:(http://blogs.utexas.edu/amd2014/.(
hazards+(e.g.+hurricanes,+wildfire,+oil+spills).+
http://blogs.utexas.edu/amd2014/
Workshop!Overview:!!
Workshop!Themes:!
Technological+advancements+in+global+positioning+systems+(GPS)+and+related+satellite+tracking+
technologies+have+resulted+in+significant+increases+in+the+availability+of+highly+accurate+data+on+moving+
The+focus+of+this+workshop+is+on+novel+methods+used+to+contextualize+and+analyze+movement+data.+We+
objects,+dramatically+outpacing+the+development+of+appropriate+methods+with+which+to+analyze+them.+In+
invite+submissions+of+short+papers+of+1500+words+that+describe+research+that+fits+the+general+theme+of+
addition+to+increased+spatial+accuracy+and+temporal+resolution+of+the+locational+information,+
movement+pattern+analysis,+with+particular+emphasis+on+novel+techniques+that+address+the+following+
improvements+are+being+made+to+accelerometers+and+‘biologgers’+that+enable+the+collection+of+ancillary+
examples+of+topics:+
behavioral+and+physiological+information+as+well.+Research+in+movement+pattern+analysis+(MPA)+extends+
• Analyzing+movement+patterns+using+external+influences+(e.g.+environment,+geographic+context)+
previous+work+in+timeIgeography+that+focused+primarily+on+representation+and+semantics,+therefore+the+
methodological+and+analytical+framework+associated+with+MPA+is+new+and+still+evolving.+Recent+
• Analyzing+interactions+between+moving+entities+
developments+on+MPA+involve+exploring+movement+patterns+within+specific+contexts,+in+the+interaction+
• Simulation+and+agentIbased+modeling+of+movement+
among+individuals,+and+across+different+geographical+and+temporal+scales.+MPA+applications+address+the+
• CrossIscale+movement+pattern+analysis+
movement+of+vehicles+(e.g.,+traffic,+fleet+management),+people+(e.g.,+pedestrians,+queues),+or+animals,+to+
• Entity+behavior+as+a+driver+for+patterns+of+movement+
name+but+a+few.+Although+there+are+obvious+and+fundamental+differences+among+these+application+
types,+there+are+also+many+important+commonalities+associated+with+the+analysis+of+any+movement+data+
irrespective+of+the+type+of+object.+++
Workshop!Format:!
This+full+day+workshop+will+consist+of+two+invited+keynote+talks,+as+well+as+presentations+of+research+
This+workshop+aims+to+serve+as+a+platform+to+discuss+the+recent+trends+in+the+study+of+movement+and+
novel+methods+for+analyzing+and+contextualizing+movement+data.+The+workshop’s+focus+is+on,+but+not+
based+on+the+short+paper+submissions.+In+order+to+stimulate+discussion,+a+breakIout+group+session+will+be+
limited+to,+topics+concerning+analysis,+modeling,+and+representation+of+movement+patterns.+The+
held+in+the+afternoon,+followed+by+a+plenary+synthesis+session.+
workshop+will+cover+research+on+any+type+of+movement+data+from+different+domains+such+as+
transportation+(e.g.,+vehicles,+pedestrians),+movement+ecology+(e.g.+plants,+animals),+and+environmental+
hazards+(e.g.+hurricanes,+wildfire,+oil+spills).+
Workshop!Themes:!
The+focus+of+this+workshop+is+on+novel+methods+used+to+contextualize+and+analyze+movement+data.+We+
Submissions+of+short+(1500+words)+discussion+papers+should+be+emailed+in+PDFIformat+to+Somayeh+
http://blogs.utexas.edu/amd2014/
Dodge+([email protected])+with+the+subject+header+GIScience*AMD*Submission.+A+template+for+paper+
submissions+is+provided+here:+https://drive.google.com/file/d/0B16vzI4vnUaGb3BHZGNpODRoVEE.+For+
more+information+please+see+workshop+website:+http://blogs.utexas.edu/amd2014/.+
Important!Dates:!
•
•
•
•
•
•
•
Deadline+for+workshop+submissions+(1500+words):+1+June+2014+
Decisions+to+authors:+22+June+2014+
Workshop:+23+September+2014+
Full+paper+submission+for+special+issue:+15+December+2014+
Initial+decision+on+full+papers:+15+February+2015+
Final+papers+due+for+special+issue:+30+April+2015+
Final+decisions+on+full+papers:+31+May+2015+
Workshop!Organizers:!
Sean%C.%Ahearn%–%Professor+and+Director,+Center+for+Advanced+Research+of+Spatial+Information+
(CARSI),+Hunter+College,+CUNY.%
Maike%Buchin%–%Junior+Professor+for+Computer+Science,+Department+of+Mathematics,+RuhrI
University+Bochum.%%
Somayeh%Dodge%–%Assistant+Professor+of+GIScience,+Department+of+Geography+and+Environmental+
Studies,+University+of+Colorado+at+Colorado+Springs.+%
Jennifer%A.%Miller%–%Associate+Professor+of+GIScience,+Department+of+Geography+and+the+
Environment,+University+of+Texas+at+Austin.++
Robert%Weibel%–%Professor+of+GIScience+and+Head,+Department+of+Geography,+University+of+Zurich.+
The Env-‐‑DATA System •  Goals:
o  to streamline the co-registration of animal tracking data
with a diverse range of environmental variables
o  to allow scientists to examine relationships between animal
movement and ambient atmospheric observations and
underlying landscape
Ref: Dodge et al., (2013). The Environmental-Data Automated Track Annotation (Env-DATA)
System: Linking Animal Tracks with Environmental Data, Movement Ecology.
A growing, global database!
www.movebank.org
Contributor : over 250!
Taxa: 335!
Tracks: over 41,170!
Events: over 61 million!
Locations of studies currently visible to the public
!
The Env-‐‑DATA System •  Automate the acquisition of data from open web resources of
remote sensing and weather data
o  50 large global datasets (>4000 variables)
o  NASA, NOAA, USGS, NCEP/NCAR and ECMWF weather
reanalysis datasets
o  Complete list: https://www.movebank.org/node/7471
Env-‐‑DATA System Architecture Env-DATA application cluster
Computing Center Garching, Germany Track Annotation
The OSU Supercomput
er Center Track Simulation
Knowledge Discovery
and Visualization
Ref: Dodge et al., (2013). Movement Ecology.
Movement Track Annotation
•  Attributing environmental data to each tracking
location in space and time
•  Interpolation in space and time:
o  IDW, nearest neighbor, bilinear interpolations
•  More info: https://www.movebank.org/node/6400
Demo
•  Track Annotation Service:
o  Find step-by-step instructions at:
https://www.movebank.org/node/6608
•  What do you need?
o  A Movebank account (sign up at www.movebank.org)
o  A study on Movebank
Start Annotation Request
Start Annotation Request
Select Annotation Variables
•  by type
•  by source
To get additional details about
individual data sources or variables,
click on ”i” and a popup will appear
with more information and links.
Select Annotation Variables
by type
Select Annotation Variables – By Type
Select Annotation Variables – By Type
Select Annotation Variables – By Type
Select Annotation Variables – By Source
Select Interpolation Method
Summary of Annotation Order
Summary of Annotation Order
Successful Annotation Submission
Annotation Request Submission
Annotation Request Submission
Check the Status of Request •  You can check on the status of your requests by
going to Env-DATA > Show my requests from the
Studies menu from any study
Download Annotated Data
•  When your annotated data file is ready, it will be
shown as available in the My requests table.
•  A download link will appear on the right side of the
table. Click on this to download your annotated
data file.
Annotation Results
•  All downloads come as a .zip file containing a .csv
with the annotated data along with a readme.txt
file with additional information.
Annotation Results
•  All data files contain the following attributes:
o  Event ID: unique identifier from your study in Movebank)
o  Location lat: latitude in decimal degrees, WGS84 reference
system
o  Location long: longitude in decimal degrees, WGS84
reference system
o  Timestamp: the time of the location estimates from your
study in Movebank, in UTC
o  Individual/Tag local identifier: animal and/or tag IDs from
your study in Movebank
•  Additional columns will contain the annotated
environmental data.
readme.txt
•  Details about annotated variables
o  units and resolution of the source datasets
•  Details about the data providers
o  a link to the source and the provider's terms of
use
Concluding Remarks
•  Source of environmental data
•  Spatial and temporal resolutions of environmental
data
•  Interpolation techniques
•  Send your questions to [email protected]
Concluding Remarks
•  Env-DATA (www.movebank.org)
o  Future extensions:
•  Development of open R , Python, JAVA libraries
•  Data mining and knowledge discovery approaches
•  Visual analytics
Galapagos Albatross (Phoebastria irrorata)
•  Study aim:
o  Investigate the effects of wind assistance on albatrosses’
movement patterns
•  Tracking data:
o  9 adult albatrosses
o  Breeding season (June to September, 2008)
o  Temporal resolution 90 minutes
Image courtesy of Sebastian Cruz
Flow Assistance (Wind Eﬀects)
Env-‐‑DATA Annotation Service
Wind speed and wind direction
o  NCEP Reanalysis 2
o  6-hour, 2.5°, U/V-wind
components
o  http://www.esrl.noaa.gov/
Image courtesy of Sebastian Cruz
Tail-‐‑wind support and side-‐‑wind
Computed using U and V wind components
Ground speed =
Wind speed =

w

a

Tail-wind (tw) = w •cosθ

Side-wind (sw)= w •sin θ
è movement
a

a
è
tw
θ
è
sw
è
W wind
Ref: Safi et al., (2013), Movement Ecology.
Flow Assistance (Wind Eﬀects)
Ref: Dodge et al., (2013), Movement Ecology.
Thank You!
•  The Ohio State University!
–  Gil Bohrer (Env-DATA Project PI) !
•  Max Planck Institute for Ornithology (Movebank)!
–  Rolf Weinzierl (system admin), Sarah Davidson (data curator) !
–  Matthias Berger, Martin Storhas (Developers)!
–  Martin Wikelski (Movebank PI), Sebastian Cruz (Albatross data)!
•  North Carolina Museum of Natural Sciences and NC State University!
–  Roland Kays (Movebank PI)!
•  U.S. Geological Survey, Alaska Science Center!
–  David Douglas!
•  Lafayette College!
–  David Brandes!
Contact Info:
Somayeh Dodge
Assistant Professor of GIScience
Director, GIS Lab
Dept. of Geography and Environmental Studies
University of Colorado at Colorado Springs
http://somayehdodge.wordpress.com/
[email protected]
1420 Austin Bluffs Parkway
Colorado Springs, CO 80918
(719) 255-4025

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