Download Marine biodiversity informatics

Ocean Biogeographic Information System
Evolution and challenges in
creating OBIS
Mark J. Costello (Leigh Marine Laboratory, University of Auckland) *
Fred Grassle and Yunquing Zhang (Rutgers University)
Karen Stocks (University of California San Diego)
Tony Rees (CSIRO Hobart)
* Chair OBIS International Committee
[email protected]
Today’s challenges
Global scale impacts
• Over-fishing
• Invasive species
• Climate change
• Pollution
Do not know what, where and
when without the facts (the
data)
How do we know anything?
Knowledge from data !
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Empirical basis of science
No knowledge without data
More data leads to more knowledge
Facts remain despite changing theories
• More irreplaceable with time
• Always increases in value
• Future value may not be anticipated
New technologies enable
• Data collection over large areas
– Satellites, acoustic seabed mapping
– ROV video, telemetry
• Data management and exchange
– GIS
– World wide web
New interdiscipinary science of
Ocean Biodiversity informatics
Using information technology
to better manage
marine biodiversity and
environmental
data and information
Opportunities provided by
informatics
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Increase communication
Make data widely available to scientific community
Rapid publication
Data mining and exploration
Low cost publication of maps and images
Interactive and/or user-defined readability
Data management tools widely available at little to
no cost
Are there other opportunities ?
Informatics helps management
• Make metadata more accessible
• Make data more accessible
• Enable better use of existing data
• Identify gaps in data that may need filling
• Better communication for data and
environmental management
Species informatics aids
research
Globally accessible species registers:
Help minimise nomenclatural confusion
Free up experts time to describe new species
Repatriate data to developing countries
Provide a low cost rapid medium for the
publication of images, sounds, data and syntheses
Rapid (automated) calculation statistics “how
many?”
Is biodiversity informatics launching
a new era in marine biology?
Always local scale,
efforts of a few
• 200 years of “natural
history”
• 50 years of “ecology”
• 10 years of
“biodiversity”
Recent top papers in
marine biology
• address ocean scale
impacts of fisheries
• Ability to combine large
datasets collected by
many is transforming our
view of the oceans
Examples at large spatial scales
Shark declines (Pacific long-line fishery)
From Baum, Myers, Kehler, Worm, Harley & Doherty. Science. Jan. 2003
Related biodiversity
• Global Biodiversity Information Facility (GBIF)
• Taxonomic Data Working Group (TDWG)
• Species 2000
• Integrated Taxonomic Information System
(ITIS)
Species lists need context
Distribution is the most important attribute
of species, and can be used to
• map resources (e.g. fisheries)
• observe trends in time
• provide insights into
- evolutionary history of faunas
- factors contributing to biodiversity
How important are deep-sea cold-water coral
reefs as a habitat in the North Atlantic?
Reef
Deep sea coral
reefs (Lophelia)
Transition zone
Photo-montage by
Pal Mortensen
Coral debris
Records of Lophelia pertusa from Rogers (2001)
– a significant habitat
Reefs can be 40km long!
Ocean Biogeographic
Information System
Mapping marine life
over the internet
www.iobis.org
OBIS network
• Marine scientists and organizations
around over the world
collaborating
• Data from museums, fisheries,
universities and ecological surveys,
including CoML field projects
• Unique network for marine
biogeography at a global scale
• Associate Member of the Global
Biodiversity Information Facility
GBIF, IODE,
IOC
IOOS, Ocean.US
NODC
Species 2000,
ITIS, TDWG
IABO, SCOR
CSIRO, DFO,
NOAA, NMFS,
ICES, FAO
MARBEF
(EurOBIS),
EuroCAT,
BioCASE,
CORONA
Funding
• Launched by the Alfred P. Sloan
Global census of
marine life
Online
data
served
Global census of fish
Major data capture
and rescue
Modelling
Interoperable
2005
• CoML is until 2010, but OBIS
will continue
• International Committee
members obtain funding from
NSF, EU, national agencies
Demo
2000
Foundation (New York) as the
data management component of
the global Census of Marine Life
2010
• US$30 million committed to
2006, funding proposals
submitted on a project by
project basis
Currently on-line in OBIS
anemones
Global
• corals and anemones
• squid and octopus
• mammals, turtles, birds (SEAMAP)
• plankton (NODC, ZooGene,
• SAHFOS-CPR)
• Fish (FishBase, FishNet)
• Species from global seamounts
Fisheries
 Canadian fishery surveys
 Historical fish data back to 1600
(HMAP)
Regional data in OBIS
 Indo-pacific snails and bivalves
 Australian Antarctic sea
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mammals and birds
Bermuda Atlantic Time Series
zooplankton (BATS)
Mid-water animals from
Southampton Oceanography
Centre database
BioMar benthos from Ireland
Belgium North Sea data
Ghent taxonomic data
NOAA benthic inventory
USA EPA EMAP data
OBIS data sources
Databases centered on
• Taxonomic group (literature sources)
• Field surveys (benthos, plankton)
• Fishery surveys
• Museum collections
OBIS Data Sources (November 2004)
Total Records
SAHFOS_CPR_ZOOPLANKTON
1,467,694
NODC WOD01 Plankton
1,281,125
FishBase
793,318
SAHFOS_CPR_PHYTOPLANKTON
721,921
OBIS-SEAMAP
281,735
History of Marine Animals (HMAP)
242,384
NWAGSCOL (Canadian Regional Node)
228,519
Elephant Seal Sightings, Macquarie Island
199,499
NBI
154,458
Atlantic Reference Centre, Canada
127,876
AADC_seabirds
101,289
Southampton O.C. Discovery Collections
93,350
BIOMAR Project Ireland
92,959
DFO Scotian Summer Research Trawl
60,109
EPA EMAP DATABASE
41,703
Canadian Museum of Nature - Fish
39,920
Taxonomic Info. System Belgium
36,936
Hexacorals Database
27,438
Gwaii Haanas Invertebrates
24,311
OBIS Data Sources (November 2004)
Total Records
Ifremer BIOCEAN deep Sea Benthos
23,876
AADC_weddell_sightings
17,588
Indo-Pacific Mollusks
16,261
AADC_herbarium
10,204
Generic Taxonomical Database System
9,745
SeamountsOnline
7,394
AADC_whale_catch
7,122
Gwaii Haanas Marine Plants
6,353
Eastern Canada Benthic Macrofauna
5,650
AADC_weddell_census
4,603
Ichthyoplankton Scotian Shelf of N.America
4,169
CephBase
3,175
Bay of Fundy Species
2,381
AADC_ellie_sightings_heard
1,794
Atlantic Canada Conservation Data Centre
1,365
BATS Zooplankton
635
Nova Scotia Museum of Natural History
579
Marine Invertebrate Diversity Initiative
295
ZooGene
114
Where is OBIS data from?
Seabed – benthos
Open water – pelagos, plankton
November 2004
Most data in OBIS for fish
Fish
30,000 species
described
Invertebrates
200,000 species
described
Names, species and records in
OBIS Nov. 2004
Category
Number
marine names,
OBIS + CoL
Number of
records
Number
species with
point data
118709
4138297
36856
17472
1411929
13318
Mammals
133
160977
70
Birds
385
218617
187
12
11760
7
Fishes
16942
1020575
13054
Invertebrates (any)
66673
1689979
20465
All categories
Vertebrates
Reptiles
Some invertebrates
Tunicates
460
20787
166
Sea squirts (ascidians)
430
9107
147
Echinoderms
1302
15683
597
Bryozoans
1238
7510
455
Crustaceans
23433
1260502
4909
Chelicerates
1259
478
89
Annelids
5011
91973
2650
Polychaetes
4327
90735
2516
Molluscs
14551
134311
5307
Gastropods
10442
89792
3564
Bivalves
2749
27257
1145
Nematodes
4268
4126
1949
Cnidaria, plants, protists, microbes
Anthozoans
4645
31165
2638
Sea anemones
2410
13771
2145
Stony corals
1547
15824
398
Hydrozoans
2274
49452
673
Sponges
1647
9986
297
53
121
4
Macroalgae (seaweeds)
11946
25186
881
Microalgae
20206
993520
1957
Dinoflagellates
1542
341919
690
Diatoms
8964
609485
905
Unicellular green
microalgae
4167
4128
101
Protozoans
2036
10330
191
33
7201
33
Seagrasses
Cyanobacteria
Distributed, cached, indexed data
system
Features
 seamless access of data from multiple sources to
the user
 federated
 interoperable
 user-friendly
 data portability
 low hardware and software dependancy
December 2004, OBIS serves:
In cache
• 5.6 million records
• 40,000 species
• 60,000 names
• 38 source databases
In Index (edited data)
• 4.1 million records at
genus level
• 37,000 species
• 119,000 names (CoL)
• March 2004 – 2.8 million
records
• October 2003 – 1 million
records
amongst largest data providers to the
Global Biodiversity Information Facility www.gbif.org
Present OBIS tools
Mapping over environment
features
• KGS Mapper (ARCIMS)
Prediction /analysis
• C-Squares
 KGS Mapper range finder
 WhyWhere
System building
• DiGIR
Species names
• XML
 Species name service
(using Catalogue of Life)
KGS Mapper – maps where similar environmental conditions
occur
Green or shore crab, Carcinus maenas
Invasive species in west North Atlantic
Data capture
coming soon to OBIS
Major surveys
• British benthic marine
life (MarLIN)
• New Zealand Bryozoa
• East Mediterranean &
Black Sea
• Chemosynthetic
Ecosystems (ChEss)
• Other CoML field
projects
!
Global marine taxa
• Aplacophora (primitive
molluscs)
• Nemertea (ribbon worms)
• Trematode (flukes) parasites
of fish
• Turbellaria (flatworms)
• Porifera (SpongeBase)
• Seaweeds and other algae
• Serpulidae (tube worms)
• Ostracoda (clam-like
crustaceans)
OBIS questions
How to globalize
OBIS?
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Taxonomically
Geographically
Institutionally
Foster expertise
Regional ‘nodes’
Partnerships
OBIS priorities?
• Data rescue
• Data capture
• On-line tools
• Ocean data overlays
• Species information
(identification, genetic, images)
• Education & outreach
• Other
Current OBIS activities
Data capture
• More species distribution
data, e.g. EurOBIS
Technical development
• mapping, modeling,
species name services,
indexes, software tools
• standards for data sharing
• Time series data search
Management
• Regional nodes – global
network
• Hire Programme Manager
• Intellectual property
agreements
• User monitoring to guide
development
• Quality control system
• Educational modules
OBIS Management
Committee
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Regional Nodes Managers
Australia
Canada
China
Europe
India
Japan
New Zealand
South America
Sub-Saharan Africa
OBIS Regional Node Architecture
Global Node
Regional Node
Provider
Global Database
Regional Database
Products
All Data
Subset of Data
Public Accessibility
GBIF
IOBIS
Data Found By
IOBIS Not From
Global Databases
Regional
Subset
Regional Node
With Local Datasets
And Online Providers
All data
Global Datasets e.g.
FAO, Hexacorallia
Fishbase &
Seamounts
Online Providers
Regional Node
With Local Datasets Only
RMB - March 14, 2004
OBIS informatics challenges
Nomenclatures
• Authoritative species names directories
– ambiguous and unambiguous
synonyms, misspellings,
misapplications, taxon splits
• Geographic (gazetteers)
– georeferencing and mapping of place
names
• Habitat classifications and standards
(ecoinformatics)
• Merging data
– Automated cross-checking of
nomenclatures
Mapping
• Polygons
• Lines (large animal
tracks)
• Integration with
ocean data maps
OBIS informatics challenges
• Interoperability and portal function
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Exclusion duplicates and redundant data
Checking outliers and irregularities
Middleware (wrappers, cross-mapping)
Data exchange protocols
Expanding standard data fields (Darwin Core)
Crediting sources
Metadata accessibility
Indexing
Cache
Data availability
• most paid for by tax-payer
• accessibility variable
• No incentives to make freely available
e.g. citation of source into citation indices,
data publication at same time as
syntheses and analyses
5 science culture challenges
1. Data sharing part of scientific process in
marine biology
2. Data publication on-line becomes standard
practice
3. Quality control for scientific credibility
4. Recognition value on-line publication in
individual’s research performance
5. Citation rankings of on-line publications
OBIS – future uses
Revelations from new data analysis
• Effects of climate change
• Predicting spread of invasive species
• Biodiversity hotspots at species and phylum levels
• Interconnected-ness of ocean regions (seascape ecology)
• Phylo- and macro- geography – evolution of fauna and
flora at population and species levels
Expanded infrastructure ?
• Catalogue of all marine life (CaML)
• Species identification and information
• Habitat classification and mapping
Achievable vision
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All valid marine species names on-line within 7 years
All known marine species listed in the Catalogue of Life
Species guides (descriptions and images) on-line
Species distributions on-line
Improved quality control in identification and taxonomy
Increased rate of species being described
New discoveries and understandings of role of
biodiversity in ecosystems based on data