Post on 16-Dec-2015
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