Presentation on theme: "Technical developments at the Ocean Biogeographic Information System"— Presentation transcript:
1 Technical developments at the Ocean Biogeographic Information System Ei Fujioka1, Edward Vanden Berghe2, Ben Donnelly1, Jesse Cleary1, Julio Castillo31 Marine Geospatial Ecology Lab, Nicholas School, Duke University2 Institute of Marine and Coastal Sciences, Rutgers University3 Universidad Simón Bolívarcorrespondence:
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, 2010.CoML:OBIS:
3 Global Biodiversity of Ocean Life OBIS Mission:Document diversity, distribution and abundance of marine lifeProvide biodiversity data to global biodiversity researchesRelated oral presentation “The Ocean Biogeographic Information System: current state and future plans” by E. Vanden Berghe (Abstract No. 0328)Biodiversity researches using OBIS data e.g. Ardron et al, 2009 ; Tittensor et al, 2010.
4 International Partnership International collaboration in international projectfor international audiencesINCOISIndiaInfrastructureMirror siteiOBIS project PIDevelopment leadDatabase developmentDuke Univ. USARutgers Univ. USAUniv.Simón BolívarVebezuelaSearch Interface developmentHardware and Server infrastructureHost of OBIS-SEAMAPWeb site programming and contentTaxonomic expertise(Halpin et al, 2009)VLIZBelgiumInfrastructureTool developmentGeoServer upgrade & supportIOC & IODE
5 Renovated iOBIS Portal Bring in latest technologies tobetter serve biodiversity dataExample map: Cetacean species observations in LME region ‘Celtic-Biscay Shelf’(left); (right)
6 Infrastructural View Concept & Philosophy Internet Amazon Cloud Web siteSearch InterfaceAmazon CloudConcept & PhilosophyAn intuitive system to browse the biodiversity datastandards-compliantopen-sourceinteroperable and flexible for international developmentcodereplicationDatabasereplicationDatabasemanagementPortaldevelopment
8 Schema for Search Interface Data StructureSchema for Search InterfaceRaw data(DiGIR table)Normalized tablesCalculated point dataTaxon infoPositionsResourcesAdditional attributesDenormalized for better performanceOceanographic data using WOAKeys to external layers such as EEZTaxonomyBased on multiple taxon databaseWoRMSITISIRMNGCOLScriptedSummarized tablesCalculatedsummary dataPer speciesPer species and resourceGrids using CSquare5/1/0.5/0.1 degree(s)Denormalized for better performance5/1/0.5/0.1 degree(s)SupplementalEEZ etc.World Ocean AtlasCSquareSearch InterfaceGeoServer
9 Standards-compliant Mapping Engine Upgraded GeoServer provides OGC servicesSupports OGC standardsWMS / WFS / KMLUsed for the online map and data downloadsParametric views introducedOpenGeo upgraded GeoServer for this projectImplemented as vendor-specific parameters for OGC requestsallow to extract data based on user inputsExample parametric view definition:%param_name% is a placeholder which is replaced with an actual value of the user inputsOGC: Open Geospatial Consortium (
10 Biodiversity indices Making various biodiversity indices handy #speciesES 50Shannon IndexSimpson Index
11 Environmental Attributes (1) Association of observation points with oceanographyObservation data associated withBottom depthTemperatureSalinityNitrogen / OxygenPhosphate / SilicateVisualized through interactive graphsTime-series graphsHistogramsEnvironmental attributes from World Ocean AtlasWOA09,
12 Environmental Attributes (2) Explore oceanographic attributes with interactive graphsTime-series graphsAverage over timeZoom in/out on time scalesCenturies / DecadesYears / Year-months / DaysSeasons or months of the yearHistogramsZoom in/out on bin sizesBin sizes optimized for oceanographic variablesAverage temp.over yearsOne zoom level upAverage temp.over year-monthHistograms (left) and seasonal changes (right) also available
13 Environmental Attributes (3) Extract observations based on environmental conditionsExample 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
14 Data in Region of Interest (1) Extract observations in a region of interest (study area)Draw a region on the mapFixed size (CSquare cell)RectanglePolygonDefine a region by coordinatesCan edit / fine-tune the regionDrawing 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) Extract observations in commonly referred zonesZone selectionFrom listClick a zone on mapObs. locations are pre- referenced to zonesFast extraction onlineExample mapCetacean species observations in LME region ‘Celtic-Biscay Shelf’* Future plan
16 Multi-language Support Español (Spanish)by Eduardo Klein and Julio Castillo, Simón Bolívar日本語 (Japanese)by Ei Fujioka, Duke Univ.Русский (Russian)by Volodymyr VladymyrovNat’l Academy of Sciences of UkraineFrançais (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 resourcesChoice of OS and software versionsScaling of disk, processor, and RAMThrow-away development instances for learning and testingFreedom from:Server ownership and hardware maintenanceCampus network authentication and admin rulesEncouraged very systematic server configurationInstances could be built quicklyInstance setup can be scripted
18 Clone of tested new data disk previous data revision Cloud Computing (2)Novel approach to data managementTest new data on virtual disk of dev serverNew data disk image is attached to production serverDevelopmentdatabase serverProductionDatabase serverNew data loaded through system administration, rather than database administrationMinimal downtime as disk is mounted and database is restartedClone of tested new data diskNew dataVirtual diskOld disk discardedprevious data revision
19 Cloud Computing (3)Scaling for major media event, London Press ConferenceSporadic scaling-up possibleIn cases for expected high demands such as media eventsiOBIS application & on-the-fly data search isn’t cacheableChallenge of the media event coped wellTwo Quad Core, 15GB RAM servers: Database & PortalPeak day: 3,157 visitors averaging 3:28 minutes on the Data Search application11,000 total site visitorsMajor 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 AreasPresented in CBD COP10, Nagoya, Japan, 2010Areas of high biodiversityAreas of special importance for the life history of a speciesAreas of significant naturalnessAreas of uniqueness or rarityRelated 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 Improved web servicesSupport regional/thematic map instantiationImprove database performanceFacilitate collaboration among the International OBIS NetworkMirror sitesRegional nodesImproved biological data representationDiGIR schema upgradesNon-traditional data types (e.g. acoustic data, telemetry-tracked animals)Tackle emerging demands of OBIS dataMarine spatial planning
23 Census of Marine Life Collections published on PloS ONE: References (1)In WCMBRelated oral presentation: “The Ocean Biogeographic Information System: current state and future plans” by E. Vanden Berghe (Abstract No. 0328)Related digital object presentation: “Using Ocean Biogeographic Information System data in the CBD EBSA process” by E. Vanden Berghe et al. (Abstract No. 1123).Census of Marine Life Collections published on PloS ONE: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.
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: /oceanogRees, T '"C-Squares", a New Spatial Indexing System and its Applicability to the Description of Oceanographic Datasets', Oceanography 16 (1), ppTittensor, 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), ppVanden 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: /OceanObs09.cwp.91, Venice, Italy, September 2009.
25 AcknowledgmentsWe 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.