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Technical developments at the Ocean Biogeographic Information System
Ei Fujioka1, Edward Vanden Berghe2, Ben Donnelly1, Jesse Cleary1, Julio Castillo3
1 Marine Geospatial Ecology Lab, Nicholas School, Duke University2 Institute of Marine and Coastal Sciences, Rutgers University3 Universidad Simón Bolívar
Email correspondence: efujioka@duke.edu
Census of Marine Life & OBIS
A 10-year international project to assess the diversity, distribution and abundance of marine life.
A 10-year international project to assess the diversity, distribution and abundance of marine life.
Ocean Biogeographic Information System (OBIS) is a data center for the Census.
Ocean Biogeographic Information System (OBIS) is a data center for the Census.
Ausubel, 1999; Grassle, 2000; Vanden Berghe et al, 2010.CoML: http://coml.orgOBIS: http://www.iobig.org
Global Biodiversity of Ocean Life
OBIS Mission: Document diversity, distribution and abundance of marine lifeProvide biodiversity data to global biodiversity researches
Biodiversity researches using OBIS data e.g. Ardron et al, 2009 ; Tittensor et al, 2010.
Related oral presentation “The Ocean Biogeographic Information System: current state and future plans” by E. Vanden Berghe (Abstract No. 0328)
International Partnership
INCOISIndia
VLIZBelgium
IOC & IODEIOC & IODE
Rutgers Univ. USA
International collaboration in international projectfor international audiences
•Search Interface development•Hardware and Server
infrastructure•Host of OBIS-SEAMAP
(Halpin et al, 2009)
•iOBIS project PI•Development lead•Database
development
• Web site programming and content
• Taxonomic expertise
• GeoServer upgrade & support
Univ.Simón Bolívar
Vebezuela
Duke Univ. USA
•Infrastructure•Mirror site
•Infrastructure•Tool
development
Renovated iOBIS Portal
Bring in latest technologies to better serve biodiversity data
Example map: Cetacean species observations in LME region ‘Celtic-Biscay Shelf’http://iobis.org/mapper (left); http://iobis.org/maps/distribution (right)
Infrastructural View
Databasereplication
Amazon Cloud
Search Interface
Internet
Web site
Concept & Philosophy An intuitive system to
browse the biodiversity data standards-compliant open-source interoperable and flexible for
international development
Concept & Philosophy An intuitive system to
browse the biodiversity data standards-compliant open-source interoperable and flexible for
international developmentDatabasemanagement
Portaldevelopment
codereplication
Application Architecture
OpenLayers 2.9
EXTJS 3.1JavascriptPHP 5.3
Front PageFront Page
Drupal 6
Search InterfaceSearch Interface Mapping EngineMapping Engine DatabaseDatabase
Apache 2Apache 2
GeoServer 2.1
Tomcat 6Tomcat 6
UbuntuUbuntu
Extra Large Instance on Amazon CloudExtra Large Instance on Amazon Cloud
PostGIS 1.5PostgreSQL
8.4
UbuntuUbuntu
Extra Large Instance on
Amazon Cloud
Extra Large Instance on
Amazon Cloud
Data Structure
Raw data(DiGIR table)
Raw data(DiGIR table)
Normalized tablesNormalized tables
Taxon info Positions Resources Additional
attributes
Calculated point dataCalculated point data
Summarized tablesSummarized tables
Per species Per species and
resource Grids using CSquare 5/1/0.5/0.1 degree(s)
Denormalized for better performance
Oceanographic data using WOA
Keys to external layers such as EEZ
Calculated summary data
Calculated summary data
Denormalized for better performance
5/1/0.5/0.1 degree(s)
TaxonomyTaxonomy
Based on multiple taxon database• WoRMS• ITIS• IRMNG• COL
SupplementalSupplemental
EEZ etc. World Ocean
Atlas CSquare
Scripted
Schema for Search Interface
GeoServerGeoServerSearch InterfaceSearch Interface
Standards-compliant Mapping Engine
Upgraded GeoServer provides OGC services
Supports OGC standards WMS / WFS / KML Used for the online map and data
downloads
Parametric views introduced OpenGeo upgraded GeoServer
for this project Implemented as vendor-specific
parameters for OGC requests allow to extract data based on
user inputs
Supports OGC standards WMS / WFS / KML Used for the online map and data
downloads
Parametric views introduced OpenGeo upgraded GeoServer
for this project Implemented as vendor-specific
parameters for OGC requests allow to extract data based on
user inputs
OGC: Open Geospatial Consortium (http://www.opengeospatial.org/)
Example parametric view definition:%param_name% is a placeholder which is replaced with an actual value of the user inputs
Biodiversity indices
Making various biodiversity indices handy
#species ES 50
Shannon Index Simpson Index
Environmental Attributes (1)
Association of observation points with oceanography
Observation data associated with Bottom depth Temperature Salinity Nitrogen / Oxygen Phosphate / Silicate
Visualized through interactive graphs Time-series graphs Histograms
Observation data associated with Bottom depth Temperature Salinity Nitrogen / Oxygen Phosphate / Silicate
Visualized through interactive graphs Time-series graphs Histograms
Environmental attributes from World Ocean Atlas
WOA09, http://www.nodc.noaa.gov/OC5/WOA09/pr_woa09.html
Environmental Attributes (2)
Explore oceanographic attributes with interactive graphs
Time-series graphs Average over time Zoom in/out on time scales
o Centuries / Decadeso Years / Year-months / Days
Seasons or months of the year
Histograms Zoom in/out on bin sizes Bin sizes optimized for
oceanographic variables
Time-series graphs Average over time Zoom in/out on time scales
o Centuries / Decadeso Years / Year-months / Days
Seasons or months of the year
Histograms Zoom in/out on bin sizes Bin sizes optimized for
oceanographic variables
Average temp. over years
Average temp.over year-month
One zoom
level up
Histograms (left) and seasonal changes (right) also available
Environmental Attributes (3)
Extract observations based on environmental conditions
Example map #1Cetacean species observations in LME region ‘Celtic-Biscay Shelf’(no environmental conditions set)
Example map #2Cetacean species observations in LME region ‘Celtic-Biscay Shelf’ filtered by a temperature range of 13 to 15 degrees
Data in Region of Interest (1)
Extract observations in a region of interest (study area)
Draw a region on the map Fixed size (CSquare cell) Rectangle Polygon
Define a region by coordinates Can edit / fine-tune the region
Draw a region on the map Fixed size (CSquare cell) Rectangle Polygon
Define a region by coordinates Can edit / fine-tune the region
Drawing tools allow you to draw a rectangular region (above) or a polygon of any shape (right) on the map. Can edit it with numeric coordinates.
Data in Region of Interest (2)
* Future plan
Extract observations in commonly referred zones
Zone selection From list Click a zone on map
Obs. locations are pre-referenced to zones
Fast extraction online
Zone selection From list Click a zone on map
Obs. locations are pre-referenced to zones
Fast extraction online
Example mapCetacean species observations in LME region ‘Celtic-Biscay Shelf’
Multi-language Support
日本語 (Japanese)by Ei Fujioka, Duke Univ.
Español (Spanish) by Eduardo Klein and Julio Castillo, Simón Bolívar
Русский (Russian) by Volodymyr VladymyrovNat’l Academy of Sciences of Ukraine
Français (French) by Bruno Danis, GBIF contractor;Mary Kennedy, Roberta Miller and Mathieu Ouellet, Fisheries and Oceans Canada
Cloud Computing (1)
Cloud computing from Amazon EC2
Provides most flexibility in the allocation of base level resources
Choice of OS and software versions Scaling of disk, processor, and RAM Throw-away development instances
for learning and testing
Freedom from: Server ownership and hardware
maintenance Campus network authentication and
admin rules
Encouraged very systematic server configuration
Instances could be built quickly Instance setup can be scripted
Provides most flexibility in the allocation of base level resources
Choice of OS and software versions Scaling of disk, processor, and RAM Throw-away development instances
for learning and testing
Freedom from: Server ownership and hardware
maintenance Campus network authentication and
admin rules
Encouraged very systematic server configuration
Instances could be built quickly Instance setup can be scripted
Cloud Computing (2)
Novel approach to data management
Test new data on virtual disk of dev server
Developmentdatabase server
New dataVirtual disk
Clone of tested new data disk
ProductionDatabase server
New data disk image is attached to production server
previous data
revision
Old disk discarded
New data loaded through system administration, rather than database administration
Minimal downtime as disk is mounted and database is restarted
New data loaded through system administration, rather than database administration
Minimal downtime as disk is mounted and database is restarted
Cloud Computing (3)
Scaling for major media event, London Press Conference
Sporadic scaling-up possible In cases for expected high demands
such as media events iOBIS application & on-the-fly data
search isn’t cacheable
Challenge of the media event coped well Two Quad Core, 15GB RAM
servers: Database & Portal Peak day: 3,157 visitors
averaging 3:28 minutes on the Data Search application
11,000 total site visitors
Sporadic scaling-up possible In cases for expected high demands
such as media events iOBIS application & on-the-fly data
search isn’t cacheable
Challenge of the media event coped well Two Quad Core, 15GB RAM
servers: Database & Portal Peak day: 3,157 visitors
averaging 3:28 minutes on the Data Search application
11,000 total site visitors
Major surge of accesses to the iOBIS Portal witnessed during the London Press Conference in October 2010
OBIS Data in Products (1)
National Geographic Wall Map
OBIS Data in Products (2)
CBD Ecologically or Biologically Significant Areas
Areas of high biodiversity
Areas of special importance for the life history of a species
Areas of significant naturalness
Areas of uniqueness or rarity
Presented in CBD COP10, Nagoya, Japan, 2010Presented in CBD COP10, Nagoya, Japan, 2010
Related presentation “Using Ocean Biogeographic Information System data in the CBD EBSA process” by E. Vanden Berghe et al. is available (Abstract No. 1123).
Future Plans
More advanced mapping & visualizationo Improved web serviceso Support regional/thematic map instantiationo Improve database performance
Facilitate collaboration among the International OBIS Networko Mirror siteso Regional nodes
Improved biological data representationo DiGIR schema upgradeso Non-traditional data types (e.g. acoustic data, telemetry-tracked animals)
Tackle emerging demands of OBIS datao Marine spatial planning
More advanced mapping & visualizationo Improved web serviceso Support regional/thematic map instantiationo Improve database performance
Facilitate collaboration among the International OBIS Networko Mirror siteso Regional nodes
Improved biological data representationo DiGIR schema upgradeso Non-traditional data types (e.g. acoustic data, telemetry-tracked animals)
Tackle emerging demands of OBIS datao Marine spatial planning
References (1)
Ardron, J, Dunn, DC, Corrigan, C, Gjerde, K, Halpin, PN, Rice, J, Vanden Berghe, E & Vierros, M 2009, 'Defining ecologically or biologically significant areas in the open oceans and deep seas: Analysis, tools, resources and illustrations', Report to the CBD Expert Workshop on scientific and technical guidance on the use of biogeographic classification systems and identification of marine areas beyond national jurisdiction in need of protection.
Ausubel, JH 1999, 'Toward a census of marine life'. Oceanography, 12(3), pp.4–5.
Grassle, JF 2000, 'The Ocean Biogeographic Information System (OBIS): an on-line, worldwide atlas for accessing, modeling and mapping marine biological data in a multidimensional geographic context', Oceanography. 13 (3), pp. 5-7.
Related oral presentation: “The Ocean Biogeographic Information System: current state and future plans” by E. Vanden Berghe (Abstract No. 0328)
Census of Marine Life Collections published on PloS ONE:http://www.ploscollections.org/static/comlCollections.action
Related digital object presentation: “Using Ocean Biogeographic Information System data in the CBD EBSA process” by E. Vanden Berghe et al. (Abstract No. 1123).
In WCMB
References (2)
Halpin, PN, Read, AJ, Fujioka, E, Best, BD, Donnelly, B, Hazen, LJ, Kot, C, Urian, K, LaBrecque, E, Dimatteo, A, Cleary, J, Good, C, Crowder, LB & Hyrenbach, KD 2009, 'OBIS-SEAMAP: The world data center for marine mammal, sea bird, and sea turtle distributions' Oceanography 22(2):104–115, doi:10.5670/oceanog.2009.42.
Rees, T 2003. '"C-Squares", a New Spatial Indexing System and its Applicability to the Description of Oceanographic Datasets', Oceanography 16 (1), pp. 11-19.
Tittensor, DP, Mora, C, Jetz, W, Lotze, HK, Ricard, D, Vanden Berghe, E, Worm, B 2010. 'Global patterns and predictors of marine biodiversity across taxa', Nature, 466(7310), pp.1098-1101.
Vanden Berghe, E, Halpin, P, Lang da Silveira, F, Stocks, K & Grassle, F 2010, 'Integrating Biological Data Into Ocean Observing Systems: The Future Role of OBIS' in Hall, J, Harrison, DE & Stammer, D (eds.), Proceedings of OceanObs’09: Sustained Ocean Observations and Information for Society (Vol. 2), ESA Publication WPP-306, doi:10.5270/OceanObs09.cwp.91, Venice, Italy, 21-25 September 2009.
Acknowledgments
We would like to thank Alfred P. Sloan Foundation for unprecedented efforts to make the Census project possible. We also would like to thank all contributors organizing OBIS regional and thematic nodes. Finally, we express deepest appreciation to data providers around the world; without them, the OBIS database would not be made possible.
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