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CoMLCoML-USNC Briefing
Marine Geospatial Ecology Lab
&
OBISOBIS-SEAMAP
OBIS
- SEAMAP
Information & visualization system
Mapping systems and protocols
Briefing to CoMLCoML- USNC
Observation data (point locations)
Shore (time series)
Tracking data services (location series)
Pat Halpin
Center for Marine Conservation
Analysis systems & webservices
Future
Nicholas School of the Environment & Earth sciences
Duke University Marine Laboratory
OBIS-SEAMAP
The inverted pyramid of data dissemination …
data fusion & dissemination
Data fusion & dissemination
Objective: Create a searchable internet based
data warehouse for sharing and analyzing
marine biogeographic data.
Methods: standards based information systems
protocols, internet map serving technologies…
Information System
Project
Field Project
Read Lab Specialties:
Marine mammals, sea
turtle, seabird ecology
Conservation ecology
Forecasting
Project
data gathering
Data aggregation
Objective: Developing a biogeographic research data
commons for the conservation of marine mammals,
sea birds and sea turtles
Halpin Lab Specialties:
GIS
Spatial analysis
Modeling
Internet tool development
Method: Social interaction / datadata-provider meetings /
data processing tool development & support…
Marine Animal Data…
regional nodes
central
data portal
specialized nodes
Ocean Biogeographic Information System
Hierarchical Information networks….
“trophic”
trophic” information networks
CoML Field Projects
Portals
fisheries / mgmt
top predators
prey
producers
oceanography
OBIS-SEAMAP
“taxonomic”
portals?
Nodes
Regional
nodes?
1
Data Archive Growth
Thousands
Addition of Marine Animal Observation Records Over Time
600
1,000,000
?
500
525,000
400
320,000
300
265,000
200
37,000
100
0
12,000
0
2002
2003
2004
2005
2006
2007
Startup
Capacity
Tools & Analysis
Regional observation effort
Global observation effort
Effort tracks - 373,550 km
Species information
Data sources
358 Species Profiles
A million records of 517 species from 163 datasets
(as of Feb 1, 2006)
Country
US
datasets
150
government agency
Aves
Mammalia
Turtles
Total
570,217
180,502
29,750
780,469
(136)
NonNon-profit organization
(5)
University
(9)
UK
6
16,708
19,743
0
36,451
CA
3
201,465
4,732
0
206,197
2,476
6,832
International
Total
4
141
4,215
163
788,531
389,694
¾
¾
¾
¾
Natural history information
Taxonomic classification
Bibliography / Web Links
Links to “prey” profiles
32,226 1,029,949
2
Progress to date…
Data
Providers
Attribution
Overview - Mission
Shore (time series)
Future
OBIS – SEAMAP
Internet map service standards
General architecture
Website & Content Management: Plone
Mapping service: Mapserver
Emerging openopen-source, openopen-standards tools provide a
functional, open working environment for ocean biogeographic
information community.
community.
WMS - Web Mapping Standard
WFS - Web Feature Standard
WCS - Web Coverage Standard
Internet mapping standards:
Internet map service standards
IOOS / SEACOOS
Supporting Marine EcosystemEcosystem-Based Management
OBIS-SEAMAP
Data from OBIS-SEAMAP will be automatically
published via WMS (Web Map Service) to the South
Atlantic Fishery Management Council’s new South
Atlantic Habitat and Ecosystem Internet Mapping
Service.
physical oceanography
marine spatial ecology
Custom “widgets” can be easily exchanged between projects.
3
Mapping Software Alternatives
Mapserver (Open-Source)
Chameleon (chameleon.maptools.org) is server-side PHP scriptable interface with many ‘widgets’ available
for enhanced functionality. This is used by www.openioos.org and www.gomoos.org.
PrimaGIS (www.primagis.fi) is a new Python scriptable interface that works within a Plone environment.
uDig (udig.refractions.net) is a user-friendly Desktop Internet GIS client, which can render WMS and WFS
layers. uDig is a Java application, built within the Eclipse environment. Kepler (kepler-project.org) is a
scientific workflow tool, also built using Eclipse, that allows you to connect data and process steps, such as
fetching OBIS data and running multivariate analysis in the R statistical package.
Common Geodatabase design will
assist in the development of common
desktop tools…
ESRI (Commercial)
ArcIMS (www.esri.com/software/arcgis/arcims) is the internet map server by ESRI.
ArcGIS Server (www.esri.com/software/arcgis/arcims) provides functionality akin to the full ArcGIS Desktop,
through the web.
ArcGIS Desktop (www.esri.com/software/arcgis) as of version 9.1 has OGC rendering services. It also has a
Python scripting interface that allows us to create custom scripts for fetching OBIS data that can be dropped
into a scientific workflow using ModelBuilder.
ESRI Press Book (2006):
“Arc Marine: GIS for a blue planet”
3 CoML/OBIS
CoML/OBIS related chapters
Google (Shareware)
Google Maps (maps.google.com) offers an API for interactive mapping with minimal requirements. This
would be the simplest, most straightforward interactive mapping option for OBIS nodes with basic point data.
You can see an example of this in use at www.animalbehaviorarchive.org.
Google Earth (earth.google.com) is a 3D data application viewer. While not a scientific analysis platform, this
is an application that will probably increase in popularity over time. Allowing data feeds into Google Earth
could heighten the general visibility of OBIS and CoML. NASA WorldWind (worldwind.arc.nasa.gov) is a
similar product that also uses OGC services for dynamic data rendering.
Full featured online geodatabase
Integrated Google Mapper to browse
OBISOBIS-SEAMAP datasets
Comprehensive,
reliable data
Synergistic
Collaboration
Two way
data feeds
Dataset
Footprint
StateState-ofof-thethe-art
online map
CuttingCutting-edge
data viewing
MultiMulti-facet
search & extraction
Integrated Google Mapper to browse
OBISOBIS-SEAMAP datasets
Datasets
Original source
citation and
abstract
Original source contact link
4
MultiMulti-faceted search & extraction (1)
Combination
By dataset

Types of survey
Species observed
Geographic area
Any text keywords
By species
By dataset
By species
By time
By geographic area
Results can be seen
Scientific name
Common name
ITIS taxonomic serial number)
on online map
on Google Earth
Example of dataset search
Example of species search
Example of data extraction for humpback
whale between 2000 and 2005
Online mapping (1)
Rich information on
species
Support various types of
data
Distribution
Taxonomy
Physical Description
Boat/airplane with effort
lines
Telemetry with tracklines
Habitat based
Species data statistics

By year/season/month
Total effort time
Link to relevant datasets
Online mapping (2)
InIn-window panels
Data filter
Dataset information
Point identify
Online mapping (3)
Environmental data

Sea surface temperature
Chlorophyll
(Geostrophic Currents)
(Sea Surface Height)
(Sea Surface Winds)
(Habitat based)
In-window setting panel to select
environmental data layer
Overlay WMS layers
Do not need to enter long query
strings
Select from available layers list
Example of overlaying species
distribution layer from OBISSEAMAP WMS Service
5
Data viewing (1)
Data viewing (2)
Dataset locations on
Google Map
Data on Google Earth

Quick browsing
Easy navigation
Direct access to dataset
page
Data viewing (3)
Any types of data
Effort/telemetry lines
Informative popup
Link to OBISOBIS-SEAMAP
Data viewing (4)
Overlay environmental
data
Integration with OBISOBISSEAMAP application
Monthly sea surface
temperature over the
period of survey
Turtle nesting trends
Seabirds colonies
abundance time series
Example of turtle nesting trend
Example of seabirds colony abundance
Data viewing (5)
Two way data feed (1)
Time series animation
Telemetry data
Sea surface temperature
Create your own animation
Data download
Shapefile
CSV file
WMS Service
Google Earth
Example of animation
setting window
Partners
Data registration
WMS Service
6
OBISOBIS-SEAMAP
consumes partners’
partners’
WMS layers
Partner can consume
OBISOBIS-SEAMAP WMS
layers
ArcGIS 9
Any WMS clients
Example map on ArcGIS 9
displaying observation points
from NEFSC Survey 1998 1 and
its effort lines with the distribution
map of Tursiops (transparent
pink) fed by SERDP marine
mammal modeling project WMS
service.
Example map displaying two
layers from SEACOOS (MODIS
SST & etopo2 bathymetry relief)
overlayed by baleen whales
observation from OBISOBIS-SEAMAP
Satellite Tracking and Analysis Tool
Synergistic Collaboration
STAT
Satellite Tracking and Analysis Tool
(seaturtle.org)
Michael Coyne
Duke University
SEATURTLE.ORG
STAT
Data
Management
Interface
Public
Website
STAT
Data
Management
Interface
User
Website
Feeds data
every week
Custom
application
Provides
services
Example of turtle tracking data from
STAT on Google Earth
Phase Out
CoMLCoML-USNC Briefing
Phase In
Motivation:
To translate data on marine mammal distributions into
useful information for ocean scientists & managers…
Practical tools for marine mammal avoidance
OBIS
- SEAMAP
Reducing shipping lane interactions
Reducing sonar interactions
Shore (time series)
Future
NOAA Right Whale Surveys
7
Marine habitat modeling process
Two linked projects:
Data
Information
Modeling
&
Analysis
System
Observation
Data
Archive
Environmental variables
Available Data Sets
Survey Effort
Distance
to Shore
45 SEAMAP
data sets
1991 – 2002
Distance
to Shelf
Model:
individual species
guilds of species
SST
Atlantic
Depth
Distance
to Fronts
Data Providers:
NOAA/NMFS -- NEFSC
NOAA/NMFS – SEFSC
UNCUNC-W
Gulf
Habitat Modeling System
Environmental sampling through time
automated processing scripts
presence
T5…
SST
Chl
Depth
Shelf
Fronts
Time
T4
environmental sampling
absence
T3
Absences
T2
Example:
11 years @ 8 day time step
Diagnostic tools:
• Pair plots
• Histograms
T1
8
ROC evaluation
Receiver-Operator Characteristics
curves
0.32
~79% of the
observations are
correctly predicted
True positive
0.79
0.32
Probability of presence
0.32
Expected: Habitat
False positive
0.21
Phase 2:
Spatio - temporal habitat modeling
Habitat Modeling System
Marine animal
distribution
At large spatial scales:
East
Temporal lags
July
17 guilds
x 2 regions
x 4 seasons
x 3 methods (GLM, GAM, CART)
Phase 2: Spatio - temporal habitat modeling
Primary
productivity
Oceanography
(winds,currents)
At finer spatial scales:
Bathymetric and water
temperature gradients
Prey
availability
Marine mammal
distribution
Marine mammal habitat modeling system
Bayesian MCMC methods
Step 2: Communicate this information in a useful manner to
scientists and managers through webservices…
webservices…
Statistical modeling approach will allow
for “antecedent” oceanographic
conditions and behavioral information to
be used to more accurately predict
potential habitat.
Step 1: Create an automated spatiospatio-temporal
pelagic modeling environment…
9
Beaked Whale
observations & habitat
(July conditions)
10
GIS Web Services for Naval Planning
Remote - Duke
• Observations, Effort
• By Dataset
• By Species
• Range Maps
• Predictive Models
• ExpertExpert-Reviewed
• UpUp-toto-date
Area of elevated
Beaked Whale
encounter risk
Local – Navy
• Naval OPAREAs
• … (confidential)
(July 2004 conditions)
Remote - JPL
• Satellite Data
• SST, SSH, Wind…
• Near Real-time
Interactions with LMRIS
Navy user’s
PKI-enabled
(SSL)
computers
Web Link
Web Client
EIMS
Web Client
INTERNET
IIS 6
Web Server
Internet Map
Server (ArcIMS)
Navy-owned
server,
database,
and
associated
software
Modified by P. Halpin
Other Web
Content
“Web
Services”
ArcSDE
Gateway
Oracle Database
GIS Views
Relational
Tables
Spatial
Tables
Database
model
New info
update
Actions to promote biological data usage
Questions?
11