Transcript Document

The Gulf of Maine Biogeographical Information System
(GMBIS) Project
A spatial data management framework in support of OBIS
Vardis M. Tsontos
Dale A. Kiefer
University of Southern California
[email protected]
Atlantic
Reference
Centre
COD Conference
Brussels, 25-27/11/2002
The Gulf of Maine Biogeographic Information
System Project (GMBIS)
• component of the Census of Marine Life / OBIS initiative
- address critical issues of data management / integration
• 2 year project funded May 2000 by ONR via NOPP
• Partners
- University of Southern California (USC)
- DFO Bedford Institute of Oceanography (BIO)
- Atlantic Reference Centre (ARC)
- System Science Applications (SSA)
• Objectives
- develop framework & tools for integration, visualisation, dissemination
of biogeographic & oceanographic data
- demonstrate the viability of the assembled information system via a pilot
application for the Gulf of Maine:
• use extensive BIO & ARC survey databases
• thematic context: structured scientific storylines
GMBIS Thematic Approach
• Show utility of system in addressing biogeographic questions
• Developed by DFO – longstanding research activities in GoM (eg. GLOBEC G.Bank)
• Resulted in a form of synthesis (“Atlas” & data gaps)
“Distribution of marine populations in relation to environmental variability in the GoM”
Subthemes: scales of variability (spatial, temporal, levels of biological organisation)
Part I
The Setting
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Large-Scale Topography, Environment and Ecosystem: Scotian Shelf and Gulf of Maine
Climatological seasonal structure of the Gulf of Maine Region
Biological Distributions in relation to GOM physical structure
Characterization of Species Diversity in the GOM by Aggregated Taxonomic Categories
Part II Temporal Variability
• Past Examples of Marine Population Changes in relation to Variable Subpolar Influences
• Interannual Variability in Drift, Growth & Survival of Browns Bank Haddock Early Life Stages
• Recent Interannual Variability in Plankton & Haddock larvae on Western/Central Scotian Shelf
Summary of electronically archived data maintained by BIO & ARC
• Diverse types of oceanographic & biogeographic data
• GMBIS tapped a representative range of data and archival systems
DATABASE SURVEY TYPE
PERIOD / FREQ.
Groundfish
Stratified random Research Trawl
1970-1999; 1-3/year
Larval
SSIP/FEP egg and larval surveys
1976-1999
Herring larval surveys
ICNAF/NAFO
Canadian National Catch Statistics
Fishing Vessel Logbooks
1972-1999
1969-1999; monthly
1960-1999; monthly
1991-1999
Fishing Vessel Port Landings
At-Sea Observer records
1947-1999
1977-1999
Biological length/age samples for 37 species
Genetic
Population Genetics
1993-1999
Climate
SST
Hydrographic
Remote Sensing Data
1920-1999
ODI
Ocean Data Inventory
1965-1999
cDNA and microsatellite gene probe data
commercially harvested species NW Atlantic
temperature/salinity profiles
JPL 18 km MCSST (sea surface temperature)
SeaWifs Chlorophyll
Current meter and thermograph time series
BIOCHEM
National marine biological and
chemical database
1970-1999
GOM/NW Atlantic taxonomic data
1960-1999
1900-1999
Fisheries
ARC
DATA DESCRIPTION
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
Georeferenced egg/larval abundances
487 species
Georeferenced herring larval abundances
catch statistics for 151 species
catch statistics for 158 species
geo-referenced catch records for 158 species
BIO nutrient data
Approximately 100 chemical parameters
NW Atlantic Zooplankton samples
Continuous Plankton Recorder data (lines E and Z)
Ichthyoplankton
Deep sea epibenthos
Taxonomic reference collection
GMBIS Information System Design: Components & Information flow
BIS Information System Design: components & information flow
GMBIS Client PC
GMBIS Data Server & Web Portal
External-users
project collaborators
(developer tools eg. EASy, Matlab etc)
scientists, managers, public
(Web-Browser)
GMBIS Web Server
Web Site
http://netviewer.usc.edu/web
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EASy GIS
Protocols: FTP/DODS
Institutional Data Providers
DFO FTP/ DODS Servers
BIO
MS Access
HTTP
ODBC
DFO rDBMS
ARC rDBMS
ARC
Archive for high volume datasets
Satellite Imagery (AVHRR/SeaWifs)
Synthetic data products (Climatologies)
ODBC
ACON
Specify
rDBMS
Museums collections data
Oracle
rDBMS
server
node
OBIS Portal
BIO
St.Johns
ODBC
SQLnet
Field survey datasets
eg. Groundfish, BioChem, Climate
Rutgers
server
node
FishBase
CephBase
Fishnet
XML
Museum specimen data &
descriptive species information
Online Biogeographic
Information Sources
eg. FishBase
LarvalBase
GenBank
Environmental Analysis System (EASy GIS)
• PC/WinNT/XP/00/98 system
• 4D (lat/lon/depth/time) internal data representation
Time Series plots
Depth profile plots
Simulation control panel
Bubble Plots
Transect vertical contour
plots
Image Browse Toolbar
Contour plot False colour plot
Species richness relative to bathymetry, water density differentials & bottom temperature
AVHRR SST imagery for the Gulf(summer
of Maineclimatology)
EASy Netviewer – GIS Web Server
Remote Clients
• Web-enabled EASy GIS applications with Netviewer plug-in
• Deploy multiple GIS applications from single server
• Clients access with Web-browser (MS I.Explorer)
• Client-side Functionality:
- full data visualisation
- data export/download
- conferencing
• Netconsole:
- administration/monitoring tool
PC Server
MS IIS
EASy
Netviewer DLL
browser
W
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P
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Internet
Mean field Cod & Haddock abundance distributions - Summer
Diverse Imagery Supported
• Multiple types / formats (eg. HDF, NetCDF, Binary, DOQQ, Shp)
• Automated imagery ingestion/georeferencing – FTP , DODS sources
[CHL] SEAWIFS, Gulf of Maine
SAR Image, Santa Monica Bay
SST AVHRR, Gulf of Maine
Aerial photography, Malibu
Vector Imagery – LA
ESRI Shapefiles
NOAA Nautical Charts
Virtual Database Utility
Connectivity to any ODBC compliant data source (eg. Oracle, Excel, ASCII)
Maps variably structured relational DB to key fields required by EASy
Maps columnar, flat-file data to critical EASy fields
Save mapping configurations for reuse/automation
Import
EASy Project Database
EASy Project Database Structure
Internet
Table
Relationships
One-to-One (1:1)
One-to-Many (1:M)
Labels
Data Category
Link-Field name
Voyage
Table
Sources
Table
ge
ya
Vo #
Image Format
Measurement Type
Table
Station
Table
System
Table
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M e
p
Ty
n
io
at
St #
Se
n
T y so
pe r
Image Format
Meas Value
Image
Table
Sample
Table
le
Fi
r
te
in
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Po
ag
m
Im
pl
e
(Image #)
or
ns e
Se a m
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Format
Table
Image
Format
Table
Meas Value
(+1)
Measurement Table
Sensor
Table
Sa
Dialog Sequence
- Select a data source
- Choose data types to import
- Map the data fields
- Save the configuration
Generic relational database
Columnar ASCII/Excel flat-file
Re
c
Ty ord
pe
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Image Data
File
sample #
meas type #
time
depth
value/image #
Linking to Online Databases & Webpages
• Interactively browse web pages with either static or dynamic content
• Context sensitive querying of online biogeographic/species identification databases
(eg. OBIS portal, Fishbase, GenBank)
GoM Herring distributions and FishBase descriptive species information
Conclusions
GMBIS has produced a range of products of relevance to CoML/OBIS
• Generic approach for biogeographic/oceanographic information system
design & implementation
• Reusable software tools (EASy & ACON) for the assimilation, integration, visualization
& dissemination of the full range of likely CoML data types (biological & environmental)
• Assembled information system– precursor to a dynamic, electronic Atlas for the GoM
GMBIS – Methods for mapping species distribution patterns in the Gulf of Maine