The Gulf of Maine Biogeographical Information System(GMBIS) Project

COD ConferenceBrussels, 25-27/11/2002

Vardis M. TsontosVardis M. TsontosDale A. KieferDale A. Kiefer

University of Southern CaliforniaUniversity of Southern California

tsontos@usc.edutsontos@usc.edu

A spatial data management framework in support of OBIS

AtlanticAtlanticReferenceReferenceCentreCentre

• 2 year project funded May 2000 by ONR via NOPP2 year project funded May 2000 by ONR via NOPP

• PartnersPartners - University of Southern California (USC)- University of Southern California (USC)

- DFO Bedford Institute of Oceanography (BIO)- DFO Bedford Institute of Oceanography (BIO)- Atlantic Reference Centre (ARC)- Atlantic Reference Centre (ARC)- System Science Applications (SSA)- System Science Applications (SSA)

• ObjectivesObjectives- develop framework & tools for integration, visualisation, dissemination- develop framework & tools for integration, visualisation, dissemination of biogeographic & oceanographic dataof biogeographic & oceanographic data

- demonstrate the viability of the assembled information system via a pilot- demonstrate the viability of the assembled information system via a pilot application for the Gulf of Maine:application for the Gulf of Maine:

• use extensive BIO & ARC survey databasesuse extensive BIO & ARC survey databases• thematic context: structured scientific storylinesthematic context: structured scientific storylines

The Gulf of Maine Biogeographic InformationThe Gulf of Maine Biogeographic InformationSystem Project (GMBIS)System Project (GMBIS)

• component of the Census of Marine Life / OBIS initiativecomponent of the Census of Marine Life / OBIS initiative - address critical issues of data management / integration- address critical issues of data management / integration

GMBIS Thematic ApproachGMBIS Thematic Approach

Part IPart I The SettingThe Setting

• Large-Scale Topography, Environment and Ecosystem: Scotian Shelf and Gulf of Large-Scale Topography, Environment and Ecosystem: Scotian Shelf and Gulf of MaineMaine• Climatological seasonal structure of the Gulf of Maine RegionClimatological seasonal structure of the Gulf of Maine Region• Biological Distributions in relation to GOM physical structure Biological Distributions in relation to GOM physical structure • Characterization of Species Diversity in the GOM by Aggregated Taxonomic Characterization of Species Diversity in the GOM by Aggregated Taxonomic CategoriesCategoriesPart IIPart II Temporal VariabilityTemporal Variability

• Past Examples of Marine Population Changes in relation to Variable Subpolar InfluencesPast Examples of Marine Population Changes in relation to Variable Subpolar Influences• Interannual Variability in Drift, Growth & Survival of Browns Bank Haddock Early Life Interannual Variability in Drift, Growth & Survival of Browns Bank Haddock Early Life StagesStages• Recent Interannual Variability in Plankton & Haddock larvae on Western/Central Scotian Recent Interannual Variability in Plankton & Haddock larvae on Western/Central Scotian ShelfShelf

““Distribution of marine populations in relation to environmental variability in the GoM”Distribution of marine populations in relation to environmental variability in the GoM”Subthemes: scales of variability (spatial, temporal, levels of biological organisation)Subthemes: scales of variability (spatial, temporal, levels of biological organisation)

• Show utility of system in addressing biogeographic Show utility of system in addressing biogeographic questionsquestions• Developed by DFO – longstanding research activities in GoM (eg. GLOBEC G.Bank)Developed by DFO – longstanding research activities in GoM (eg. GLOBEC G.Bank)

• Resulted in a form of synthesis (“Atlas” & data gaps)Resulted in a form of synthesis (“Atlas” & data gaps)

Summary of electronically archived data maintained by BIO & ARCSummary of electronically archived data maintained by BIO & ARC

• Diverse types of oceanographic & biogeographic dataDiverse types of oceanographic & biogeographic data

• GMBIS tapped a representative range of data and archival systemsGMBIS tapped a representative range of data and archival systems

DATABASE SURVEY TYPE PERIOD / FREQ. DATA DESCRIPTION

Groundfish Stratified random Research Trawl 1970-1999; 1-3/year 300 vertebrate and invertebrate species georeferenced catches (total numbers and weight) size-frequency distributions subsample length, weight, age, sex, maturity Temperature-salinity profiles or surface/bottom values

Larval SSIP/FEP egg and larval surveys 1976-1999 Georeferenced egg/larval abundances 487 species

Herring larval surveys 1972-1999 Georeferenced herring larval abundances Fisheries ICNAF/NAFO 1969-1999; monthly catch statistics for 151 species Canadian National Catch Statistics 1960-1999; monthly catch statistics for 158 species Fishing Vessel Logbooks 1991-1999 geo-referenced catch records for 158 species

Fishing Vessel Port Landings 1947-1999 Biological length/age samples for 37 species At-Sea Observer records 1977-1999

Genetic Population Genetics

1993-1999

cDNA and microsatellite gene probe data commercially harvested species NW Atlantic

Climate Hydrographic 1920-1999 temperature/salinity profiles SST

Remote Sensing Data JPL 18 km MCSST (sea surface temperature) SeaWifs Chlorophyll

ODI Ocean Data Inventory 1965-1999

Current meter and thermograph time series

BIOCHEM National marine biological and chemical database

1970-1999 1960-1999

BIO nutrient data Approximately 100 chemical parameters NW Atlantic Zooplankton samples Continuous Plankton Recorder data (lines E and Z)

ARC GOM/NW Atlantic taxonomic data 1900-1999 Ichthyoplankton Deep sea epibenthos Taxonomic reference collection

GMBIS Information System Design: Components & Information flowGMBIS Information System Design: components & information flow

GMBIS Web ServerWeb Site

ACON

DFO FTP/ DODS Servers

Archive for high volume datasets

Satellite Imagery (AVHRR/SeaWifs)Synthetic data products (Climatologies)

Online BiogeographicInformation Sources

eg. FishBase LarvalBase GenBank

Institutional Data Providers

GMBIS Data Server & Web Portal

OBIS Portal

Rutgersservernode

FishBaseCephBase

Fishnet

Museum specimen data &descriptive species information

DFO rDBMS

rDBMSservernode

Oracle BIOSt.Johns

Field survey datasetseg. Groundfish, BioChem, Climate

ARC rDBMS

SpecifyrDBMS

MS Access

Museums collections data

Protocols: FTP/DODS ODBC ODBCHTTP

http://netviewer.usc.edu/web

NETVIEWER

EASy GIS

External-usersscientists, managers, public

(Web-Browser)

GMBIS Client PCproject collaborators

(developer tools eg. EASy, Matlab etc)

XMLODBCSQLnet

BIO ARC

Sim

ulation control panel

AVHRR SST imagery for the Gulf of MaineAVHRR SST imagery for the Gulf of MaineSpecies richness relative to bathymetry, water density differentials & bottom temperatureSpecies richness relative to bathymetry, water density differentials & bottom temperature

(summer climatology)(summer climatology)

Environmental Analysis System (EASy GIS)Environmental Analysis System (EASy GIS)

• PC/WinNT/XP/00/98 systemPC/WinNT/XP/00/98 system • 4D (lat/lon/depth/time) internal data representation4D (lat/lon/depth/time) internal data representation

Tim

e S

erie

s pl

ots

Dep

th p

rofi

le p

lots

Transect vertical contourplots

Image B

rowse T

oolbarF

alse colour plotC

ontour plotB

ubble Plots

EASy Netviewer – GIS Web ServerEASy Netviewer – GIS Web Server

• Web-enabled EASy GIS applications with Netviewer plug-inWeb-enabled EASy GIS applications with Netviewer plug-in

• Clients access with Web-browser (MS I.Explorer)Clients access with Web-browser (MS I.Explorer)

PC ServerMS IIS

EASyNetviewer DLL

WEB

PAGE

Internet

Remote Clients

browser

• Deploy multiple GIS applications from single serverDeploy multiple GIS applications from single server

• Netconsole:Netconsole:- administration/monitoring tool- administration/monitoring tool

• Client-side Functionality:Client-side Functionality:- full data visualisationfull data visualisation- data export/downloaddata export/download- conferencingconferencing

Mean field Cod & Haddock abundance distributions - Summer Mean field Cod & Haddock abundance distributions - Summer

Diverse Imagery SupportedDiverse Imagery Supported

SAR Image, Santa Monica Bay Aerial photography, Malibu NOAA Nautical Charts

[CHL] SEAWIFS, Gulf of Maine SST AVHRR, Gulf of Maine Vector Imagery – LAESRI Shapefiles

• Automated imagery ingestion/georeferencing – FTP , DODS sourcesAutomated imagery ingestion/georeferencing – FTP , DODS sources

• Multiple types / formats (eg. HDF, NetCDF, Binary, DOQQ, Shp)Multiple types / formats (eg. HDF, NetCDF, Binary, DOQQ, Shp)

Virtual Database UtilityVirtual Database Utility

Dialog SequenceDialog Sequence- Select a data source- Select a data source- Choose data types to import- Choose data types to import- Map the data fields- Map the data fields- Save the configuration- Save the configuration

• Connectivity to any ODBC compliant data source (eg. Oracle, Excel, ASCII)Connectivity to any ODBC compliant data source (eg. Oracle, Excel, ASCII)

Meas Value

sample #meas type #

timedepth

value/image #

ImageFormatTable

SourcesTable

Image Format

InternetTable

Data Category

SystemTable

Meas Value(+1)

Image Format

ImageTable

Measure-ment Table

Measure-ment Type

Table

(Image #)

SampleTable

FormatTable

SensorTable

StationTable

VoyageTable

Image DataFile

Relationships

One-to-One (1:1)

Labels Link-Field name

One-to-Many (1:M)

EASy Project Database StructureEASy Project DatabaseEASy Project Database

Generic relational database

Import

• Maps variably structured relational DB to key fields required by EASyMaps variably structured relational DB to key fields required by EASy

• Save mapping configurations for reuse/automationSave mapping configurations for reuse/automation

• Maps columnar, flat-file data to critical EASy fieldsMaps columnar, flat-file data to critical EASy fields

Columnar ASCII/Excel flat-fileColumnar ASCII/Excel flat-file

Linking to Online Databases & WebpagesLinking to Online Databases & Webpages

• Interactively browse web pages with either static or dynamic contentInteractively browse web pages with either static or dynamic content

GoM Herring distributions and FishBase descriptive species informationGoM Herring distributions and FishBase descriptive species information

• Context sensitive querying of online biogeographic/species identification databases (eg. OBIS portal, Fishbase, GenBank)

• Assembled information system– precursor to a dynamic, electronic Atlas for the GoMAssembled information system– precursor to a dynamic, electronic Atlas for the GoM

ConclusionsConclusions

• Reusable software tools (EASy & ACON) for the assimilation, integration, visualizationReusable software tools (EASy & ACON) for the assimilation, integration, visualization & dissemination of the full range of likely CoML data types (biological & environmental)& dissemination of the full range of likely CoML data types (biological & environmental)

• Generic approach for biogeographic/oceanographic information systemGeneric approach for biogeographic/oceanographic information system design & implementationdesign & implementation

GMBIS – Methods for mapping species distribution patterns in the Gulf of MaineGMBIS – Methods for mapping species distribution patterns in the Gulf of Maine

GMBIS has produced a range of products of relevance to CoML/OBISGMBIS has produced a range of products of relevance to CoML/OBIS