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.