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Technical developments at the Ocean Biogeographic Information System Ei Fujioka 1, Edward Vanden Berghe 2, Ben Donnelly 1, Jesse Cleary 1, Julio Castillo.

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Presentation on theme: "Technical developments at the Ocean Biogeographic Information System Ei Fujioka 1, Edward Vanden Berghe 2, Ben Donnelly 1, Jesse Cleary 1, Julio Castillo."— Presentation transcript:

1 Technical developments at the Ocean Biogeographic Information System Ei Fujioka 1, Edward Vanden Berghe 2, Ben Donnelly 1, Jesse Cleary 1, Julio Castillo 3 1 Marine Geospatial Ecology Lab, Nicholas School, Duke University 2 Institute of Marine and Coastal Sciences, Rutgers University 3 Universidad Simón Bolívar correspondence:

2 Census of Marine Life & OBIS 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. Ausubel, 1999; Grassle, 2000; Vanden Berghe et al, CoML: OBIS:

3 Global Biodiversity of Ocean Life OBIS Mission: Document diversity, distribution and abundance of marine life Provide biodiversity data to global biodiversity researches Biodiversity researches using OBIS data e.g. Ardron et al, 2009 ; Tittensor et al, Related oral presentation The Ocean Biogeographic Information System: current state and future plans by E. Vanden Berghe (Abstract No. 0328)

4 International Partnership INCOIS India VLIZ Belgium IOC & IODE Rutgers Univ. USA International collaboration in international project for 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

5 Renovated iOBIS Portal Bring in latest technologies to better serve biodiversity data Example map: Cetacean species observations in LME region Celtic-Biscay Shelf (left); (right)http://iobis.org/maps/distribution

6 Infrastructural View Database replication 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 development Database management Portal development code replication

7 Application Architecture OpenLayers 2.9 EXTJS 3.1 Javascript PHP 5.3 Front Page Drupal 6 Search Interface Mapping Engine Database Apache 2 GeoServer 2.1 Tomcat 6 Ubuntu Extra Large Instance on Amazon Cloud PostGIS 1.5 PostgreSQL 8.4 Ubuntu Extra Large Instance on Amazon Cloud

8 Data Structure Raw data (DiGIR table) Raw data (DiGIR table) Normalized tables Taxon info Positions Resources Additional attributes Calculated point data Summarized 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) Taxonomy Based on multiple taxon database WoRMS ITIS IRMNG COL Supplemental EEZ etc. World Ocean Atlas CSquare Scripted Schema for Search Interface GeoServer Search Interface

9 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

10 Biodiversity indices Making various biodiversity indices handy #speciesES 50 Shannon IndexSimpson Index

11 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,

12 Environmental Attributes (2) Explore oceanographic attributes with interactive graphs Time-series graphs Average over time Zoom in/out on time scales o Centuries / Decades o 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 / Decades o 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

13 Environmental Attributes (3) Extract observations based on environmental conditions Example map #1 Cetacean species observations in LME regionCeltic-Biscay Shelf (no environmental conditions set) Example map #2 Cetacean species observations in LME regionCeltic-Biscay Shelf filtered by a temperature range of 13 to 15 degrees

14 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.

15 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 map Cetacean species observations in LME region Celtic-Biscay Shelf

16 Multi-language Support (Japanese) by Ei Fujioka, Duke Univ. Español (Spanish) by Eduardo Klein and Julio Castillo, Simón Bolívar Русский (Russian) by Volodymyr Vladymyrov Natl Academy of Sciences of Ukraine Français (French) by Bruno Danis, GBIF contractor; Mary Kennedy, Roberta Miller and Mathieu Ouellet, Fisheries and Oceans Canada

17 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

18 Cloud Computing (2) Novel approach to data management Test new data on virtual disk of dev server Development database server New data Virtual disk Clone of tested new data disk Production Database 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

19 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 isnt 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 isnt 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

20 OBIS Data in Products (1) National Geographic Wall Map

21 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, 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).

22 Future Plans More advanced mapping & visualization o Improved web services o Support regional/thematic map instantiation o Improve database performance Facilitate collaboration among the International OBIS Network o Mirror sites o Regional nodes Improved biological data representation o DiGIR schema upgrades o Non-traditional data types (e.g. acoustic data, telemetry-tracked animals) Tackle emerging demands of OBIS data o Marine spatial planning More advanced mapping & visualization o Improved web services o Support regional/thematic map instantiation o Improve database performance Facilitate collaboration among the International OBIS Network o Mirror sites o Regional nodes Improved biological data representation o DiGIR schema upgrades o Non-traditional data types (e.g. acoustic data, telemetry-tracked animals) Tackle emerging demands of OBIS data o Marine spatial planning

23 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 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: 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

24 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: /oceanog Rees, T '"C-Squares", a New Spatial Indexing System and its Applicability to the Description of Oceanographic Datasets', Oceanography 16 (1), pp Tittensor, DP, Mora, C, Jetz, W, Lotze, HK, Ricard, D, Vanden Berghe, E, Worm, B 'Global patterns and predictors of marine biodiversity across taxa', Nature, 466(7310), pp 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 OceanObs09: Sustained Ocean Observations and Information for Society (Vol. 2), ESA Publication WPP-306, doi: /OceanObs09.cwp.91, Venice, Italy, September 2009.

25 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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