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* * Chair OBIS International CommitteeChair OBIS International [email protected]@auckland.ac.nz
Ocean Biogeographic Information System
Evolution and challenges in Evolution and challenges in creating OBIScreating 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)
Today’s challengesToday’s challenges
Global scale impacts Global scale impacts • Over-fishingOver-fishing• Invasive speciesInvasive species• Climate changeClimate change• PollutionPollution
Do not know what, where Do not know what, where and when without the and when without the facts (the data)facts (the data)
How do we know anything? Knowledge from data !
• Empirical basis of scienceEmpirical basis of science• No knowledge without dataNo knowledge without data• More data leads to more knowledgeMore data leads to more knowledge• Facts remain despite changing theoriesFacts remain despite changing theories
• More irreplaceable with timeMore irreplaceable with time• Always increases in value Always increases in value • Future value may not be anticipated Future value may not be anticipated
New technologies enableNew technologies enable
• Data collectionData collection over large areas over large areas– Satellites, acoustic seabed mappingSatellites, acoustic seabed mapping– ROV video, telemetryROV video, telemetry
• Data managementData management and exchange and exchange– GISGIS– World wide webWorld wide web
New interdiscipinary New interdiscipinary science of Ocean science of Ocean Biodiversity informaticsBiodiversity informatics
Using information technologyUsing information technologyto better manage to better manage marine biodiversity and marine biodiversity and environmental environmental data and informationdata and information
Opportunities provided by Opportunities provided by informaticsinformatics
• Increase communication Increase communication
• Make data widely available to scientific Make data widely available to scientific communitycommunity
• Rapid publicationRapid publication
• Data mining and explorationData mining and exploration
• Low cost publication of maps and imagesLow cost publication of maps and images
• Interactive and/or user-defined readabilityInteractive and/or user-defined readability
• Data management tools widely available at little Data management tools widely available at little to no costto no cost
Are there other opportunities ?
Informatics helps Informatics helps managementmanagement
• Make Make metadatametadata more accessible more accessible
• Make Make datadata more accessible more accessible
• Enable better useEnable better use of existing data of existing data
• Identify gapsIdentify gaps in data that may need in data that may need fillingfilling
• Better communicationBetter communication for data and for data and environmental managementenvironmental management
Species informatics aids Species informatics aids research research
Globally accessible species registers:
Help minimise nomenclatural confusionFree up experts time to describe new speciesRepatriate data to developing countriesProvide a low cost rapid medium for the publication
of images, sounds, data and syntheses Rapid (automated) calculation statistics “how
many?”
Is biodiversity informatics Is biodiversity informatics launching a new era in marine launching a new era in marine biology?biology?
Always local scale, Always local scale, efforts of a fewefforts of a few
• 200 years of 200 years of “natural history”“natural history”
• 50 years of 50 years of “ecology”“ecology”
• 10 years of 10 years of “biodiversity”“biodiversity”
Recent top papers in Recent top papers in marine biologymarine biology
• address ocean scale address ocean scale impacts of fisheriesimpacts of fisheries
• Ability to combine Ability to combine large datasets large datasets collected by many is collected by many is transforming our view transforming our view of the oceansof the oceans
Shark declines (Pacific long-line Shark declines (Pacific long-line fishery)fishery)
From Baum, Myers, Kehler, Worm, Harley & Doherty. Science. Jan. 2003
Related biodiversityRelated biodiversity
• Global Biodiversity Information Facility (GBIF)
• Taxonomic Data Working Group (TDWG)
• Species 2000
• Integrated Taxonomic Information System (ITIS)
Species lists need Species lists need contextcontext
Distribution is the most important Distribution is the most important attribute of species, and can be used attribute of species, and can be used toto
• map resources (e.g. fisheries)map resources (e.g. fisheries)
• observe trends in timeobserve trends in time
• provide insights into provide insights into
- evolutionary history of faunas - evolutionary history of faunas
- factors contributing to - factors contributing to biodiversitybiodiversity
Photo-montage by Pal Mortensen
Reef
Transition zone
Coral debris
How important are deep-sea cold-water coral reefs as a habitat in the North Atlantic?
Deep sea coral reefs (Lophelia)
Ocean Biogeographic Ocean Biogeographic Information SystemInformation System
Mapping marine Mapping marine life life
over the internetover the internetwww.iobis.org
OBIS networkOBIS 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
FundingFunding
• Launched by the Alfred P. Sloan Foundation (New York) as the data management component of the global Census of Marine Life
• CoML is until 2010, but OBIS will continue
• International Committee members obtain funding from NSF, EU, national agencies
• US$30 million committed to 2006, funding proposals submitted on a project by project basis
2000 2005 2010
Online data served
Demo
Interoperable
Major data capture and rescue Modellin
g
Global census of fish
Global census of marine life
Currently on-line in OBISCurrently on-line in OBIS
Global Global • corals and anemones• squid and octopus• mammals, turtles, birds (SEAMAP)• plankton (NODC, ZooGene, • SAHFOS-CPR)• Fish (FishBase, FishNet)• Species from global seamounts
FisheriesFisheries Canadian fishery surveysCanadian fishery surveys Historical fish data back to 1600 Historical fish data back to 1600
(HMAP)(HMAP)
anemones
Indo-pacific snails and bivalves
Australian Antarctic sea mammals and birds
Bermuda Atlantic Time Series zooplankton (BATS)
Mid-water animals from Southampton Oceanography Centre databaseCentre database
BioMar benthos from IrelandBioMar benthos from Ireland Belgium North Sea dataBelgium North Sea data Ghent taxonomic dataGhent taxonomic data NOAA benthic inventoryNOAA benthic inventory USA EPA EMAP dataUSA EPA EMAP data
Regional data in OBISRegional data in OBIS
OBIS data sourcesOBIS data sources
Databases centered on Databases centered on
• Taxonomic group (literature Taxonomic group (literature sources)sources)
• Field surveys (benthos, plankton)Field surveys (benthos, plankton)
• Fishery surveysFishery surveys
• Museum collectionsMuseum 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 Where is OBIS data from?from?
November 2004
Seabed – benthosOpen water – pelagos, plankton
Names, species and records in OBIS Nov. 2004
Category Number marine names,
OBIS + CoL
Number of records
Number species with
point data
All categories 118709 4138297 36856
Vertebrates 17472 1411929 13318
Mammals 133 160977 70
Birds 385 218617 187
Reptiles 12 11760 7
Fishes 16942 1020575 13054
Invertebrates (any) 66673 1689979 20465
Some invertebratesSome 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, Cnidaria, plants, protists, microbesmicrobes
Anthozoans 4645 31165 2638
Sea anemones 2410 13771 2145
Stony corals 1547 15824 398
Hydrozoans 2274 49452 673
Sponges 1647 9986 297
Seagrasses 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
Cyanobacteria 33 7201 33
Distributed, cached, indexed Distributed, cached, indexed data systemdata system
Features Features seamless access of data from multiple seamless access of data from multiple
sources to the user sources to the user federated federated interoperable interoperable user-friendly user-friendly data portabilitydata portability low hardware and software dependancylow hardware and software dependancy
December 2004, OBIS serves:December 2004, OBIS serves:
In cacheIn cache• 5.6 million records 5.6 million records • 40,000 species40,000 species• 60,000 names60,000 names• 38 source 38 source
databasesdatabases
• March 2004March 2004 – 2.8 million – 2.8 million records records
• October 2003October 2003 – 1 million – 1 million recordsrecords
In Index (edited data)In Index (edited data)• 4.1 million records 4.1 million records
at genus levelat genus level• 37,000 species37,000 species• 119,000 names 119,000 names
(CoL)(CoL)
amongst largest data providers to the amongst largest data providers to the Global Biodiversity Information FacilityGlobal Biodiversity Information Facility www.gbif.orgwww.gbif.org
Present OBIS toolsPresent OBIS tools
Mapping over environment Mapping over environment featuresfeatures
• KGS Mapper (ARC-KGS Mapper (ARC-IMS)IMS)
• C-Squares C-Squares
System buildingSystem building• DiGIR DiGIR • XMLXML
Prediction /analysis KGS Mapper range finder WhyWhere
Species names Species name service (using Catalogue of Life)
Green or shore crab, Carcinus maenas
Invasive species in west North Atlantic
KGS Mapper – maps where similar environmental conditions occur
Major surveysMajor surveys
• British benthic British benthic marine life (MarLIN)marine life (MarLIN)
• New Zealand BryozoaNew Zealand Bryozoa
• East Mediterranean & East Mediterranean & Black Sea Black Sea
• Chemosynthetic Chemosynthetic Ecosystems (ChEss)Ecosystems (ChEss)
• Other CoML field Other CoML field projectsprojects
Global marine taxaGlobal marine taxa
• Aplacophora (primitive Aplacophora (primitive molluscs)molluscs)
• Nemertea (ribbon worms)Nemertea (ribbon worms)
• Trematode (flukes) Trematode (flukes) parasites of fishparasites of fish
• Turbellaria (flatworms)Turbellaria (flatworms)
• Porifera (SpongeBase)Porifera (SpongeBase)
• Seaweeds and other algaeSeaweeds and other algae
• Serpulidae (tube worms)Serpulidae (tube worms)
• Ostracoda (clam-like Ostracoda (clam-like crustaceans)crustaceans)
Data captureData capturecoming soon to OBIScoming soon to OBIS ! !
OBIS questionsOBIS questions
How to globalize OBIS?
• TaxonomicallyTaxonomically
• GeographicallyGeographically
• Institutionally Institutionally
• Foster expertiseFoster expertise
• Regional ‘nodes’Regional ‘nodes’
• PartnershipsPartnerships
OBIS priorities?• Data rescue• Data capture• On-line tools• Ocean data overlays• Species information (identification, genetic, images)
• Education & outreach• Other
Current OBIS activitiesCurrent 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
= Regional Nodes Managers
AustraliaCanadaChinaEuropeIndiaJapanNew ZealandSouth America Sub-Saharan Africa
Public Accessibility
IOBIS
Global Datasets e.g.FAO, HexacoralliaFishbase &Seamounts
Data Found ByIOBIS Not FromGlobal Databases
Online Providers
Regional Node With Local DatasetsAnd Online Providers
RegionalSubset
All data
Regional Node With Local Datasets Only
GBIF
Global NodeRegional NodeProviderGlobal DatabaseRegional DatabaseProductsAll DataSubset of Data
OBIS Regional Node Architecture
RMB - March 14, 2004
OBIS informatics challengesOBIS informatics challenges
NomenclaturesNomenclatures• Authoritative species names Authoritative species names
directoriesdirectories– ambiguous and unambiguous ambiguous and unambiguous
synonyms, misspellings, synonyms, misspellings, misapplications, taxon splitsmisapplications, taxon splits
• Geographic (gazetteers) Geographic (gazetteers) – georeferencing and mapping of georeferencing and mapping of
place names place names
• Habitat classifications and standards Habitat classifications and standards (ecoinformatics)(ecoinformatics)
• Merging dataMerging data– Automated cross-checking of Automated cross-checking of
nomenclaturesnomenclatures
MappingMapping• Polygons Polygons • Lines (large Lines (large
animal tracks)animal tracks)• Integration with Integration with
ocean data mapsocean data maps
• Interoperability and portal functionInteroperability and portal function– Exclusion duplicates and redundant dataExclusion duplicates and redundant data– Checking outliers and irregularitiesChecking outliers and irregularities– Middleware (wrappers, cross-mapping)Middleware (wrappers, cross-mapping)– Data exchange protocolsData exchange protocols– Expanding standard data fields (Darwin Core)Expanding standard data fields (Darwin Core)– Crediting sourcesCrediting sources– Metadata accessibilityMetadata accessibility– IndexingIndexing– Cache Cache
OBIS informatics challengesOBIS informatics challenges
Data availabilityData availability
• most paid for by tax-payermost paid for by tax-payer
• accessibility variableaccessibility variable
• No incentives to make freely availableNo incentives to make freely available
e.g. citation of source into citation e.g. citation of source into citation indices,indices,
data publication at same time as data publication at same time as syntheses and analysessyntheses and analyses
5 science culture 5 science culture challengeschallenges
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 usesOBIS – future usesRevelations from new data analysisRevelations from new data analysis• Effects of climate change Effects of climate change • Predicting spread of invasive species Predicting spread of invasive species • Biodiversity hotspots at species and phylum levelsBiodiversity hotspots at species and phylum levels• Interconnected-ness of ocean regions (seascape ecology)Interconnected-ness of ocean regions (seascape ecology)• Phylo- and macro- geography – evolution of fauna and Phylo- and macro- geography – evolution of fauna and
flora at population and species levelsflora at population and species levels
Expanded infrastructure ?Expanded infrastructure ?• Catalogue of all marine life (CaML)Catalogue of all marine life (CaML)• Species identification and informationSpecies identification and information• Habitat classification and mappingHabitat classification and mapping
Achievable visionAchievable vision
All valid marine species names on-line within 7 yearsAll valid marine species names on-line within 7 yearsAll known marine species listed in the Catalogue of LifeAll known marine species listed in the Catalogue of Life
Species guides (descriptions and images) on-lineSpecies guides (descriptions and images) on-lineSpecies distributions on-lineSpecies distributions on-line
Improved quality control in identification and taxonomyImproved quality control in identification and taxonomyIncreased rate of species being describedIncreased rate of species being described
New discoveries and understandings of role New discoveries and understandings of role of biodiversity in ecosystems based on dataof biodiversity in ecosystems based on data