The Ocean

Biogeographic Information System

Ward Appeltans IOC-UNESCO/IODE

IODE-XXII Pre-conference Workshop, 8-9 March 2013, Ensenada, Mexico

“OBIS is world's largest online system for absorbing, integrating, and

accessing data about life in the ocean”

Census of Marine Life (2000-2010)

•  2,700 scientists •  80+ nations •  540 expeditions •  US$ 650 million •  2,600+ scientific publications •  6,000+ potential new species •  30 million distribution records and counting

Census of Marine Life (2000-2010)

Ocean Biogeographic Information System

OBIS is the world’s largest open access, online repository of spatially referenced marine life data that:

–  Nations can use to develop national and regional assessments, to discover trends, gaps and biodiversity hotspots and to meet their obligations to the Convention on Biological Diversity and other international commitments.

–  Stimulates research about our oceans to generate new hypotheses concerning evolutionary processes, species distributions, and roles of organisms in marine systems on a global scale.

–  Forms a baseline of marine life’s diversity, distribution, and abundance against which future change can be measured.

OBIS at IOC-UNESCO In June 2009, the 25th Session of the IOC Assembly decided through Resolution XXV-4 to adopt OBIS as part of IODE, because: 1. Knowledge of the oceans biodiversity is of such importance to national and global environmental issues that the responsibility for its continuing success should be assumed by governments. 2. IOC Member States have repeatedly identified the need to acquire ocean biogeographic data for national ocean and coastal resource management. 3. Without accurate, repeatable and timely biological data it is impossible to address adequately the global ocean environmental issues of pollution, climate impact and mitigation, ocean acidification, ecosystem management, biodiversity loss, and habitat destruction (Resolution of the UN General Assembly A/RES/63/111) 4. OBIS provided the opportunity to adopt an existing global network for biogeographic data and to attract the associated research community that can and should be a continuous part of the Commission’s ocean mandate.

10th Conference of the Parties to the Convention on Biological Diversity In Nagoya October 2010, the 10th Conference of the Parties to the Convention on Biological Diversity (Decision COP10/29 para 10 and 35;) requested Member States to further enhance globally networked scientific efforts, such as the Ocean Biogeographic Information System (OBIS), to continue to update a comprehensive and accessible global database of all forms of life in the sea, and further assess and map the distribution and abundance of species in the sea, and; Called upon IOC to facilitate availability and inter-operability of the best available marine and coastal biodiversity data sets and information across global, regional and national scales.

As a result OBIS is playing a crucial role in providing scientific guidance, data and information for the identification of Ecologically or Biologically Significant marine Areas, through a series of regional workshops in 2011, 2012 and 2013 convened by the CBD, as part of the UN Strategic Plan for Biodiversity 2011-2020, and in particular to contribute to Aichi Biodiversity Target 11 to conserve and sustainably manage at least 10 per cent of coastal and marine areas by 2020.

CBD-COP10 listed OBIS as a key source of information for the identification of Ecologically or Biologically Significant Areas (EBSAs) part of CBD"

Areas of high biodiversity

Areas of special importance for the life history of a

species

Areas of significant naturalness

Areas of uniqueness or rarity

OBIS contributions to the CBD process: "(1) national reporting and (2) open oceans & deep seas"

National EEZ data queries Open-ocean ABNJ data queries

Open-access data made available to all countries

and communities

International collaborative data and research in areas beyond national jurisdiction

North Pacific regional EBSA workshop, Moscow, 25 Feb – 1 March 2013

OBIS contributions to the CBD EBSA process"

OBIS contributions to the CBD EBSA process"

OBIS data are being used to support the identification of sites meeting the EBSA criteria at each regional workshop. OBIS data layers include: •  Species observations •  Biological Diversity indices •  IUCN Red List species Eastern Tropical & Temperate

Pacific EBSA workshop, Galapagos Ecuador, August 2012

OBIS contributions to the CBD EBSA process"

Marine Mammal Observations Eastern Tropical & Temperate Pacific

EBSA workshop, Galapagos Ecuador, August 2012

IUCN Red-List Species Wider Caribbean and Western Mid-Atlantic workshop, Recife,

Brazil, February 2012

examples

OBIS contributions to the CBD EBSA process"

Biological Diversity all taxa Wider Caribbean and Western Mid-Atlantic workshop, Recife,

Brazil, February 2012

Proposed site meeting EBSA criteria: Abrolhos Bank & Vitoria-Trindade Chain Described in-part due to high regional biodiversity

as depicted using OBIS data.

Species distribution modeling (aquamaps)

Flathead mullet (point data)

Species distribution modeling (aquamaps)

Flathead mullet (native range)

Species distribution modeling (aquamaps)

Flathead mullet (Year 2050 range)

Summary Stats

Summary Stats

Summary Stats

Summary stats (1950-2004)

species

records

Decline # species through the 1980s, but then an increase subsequently

# records increases steadily, until it begins to level off around 1990

# new species recorded in OBIS

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Data e-infrastructure Initiative for Fisheries Management and Conservation of Marine Living Resources (i-Marine)

•  Research Infrastructures CP & CSA funded by the European Commission under the FP7 Capacities Programme - eInfrastructure Unit DG CONNECT (1 Nov 2011 - 30 April 2014)

•  Launch an initiative aimed at establishing and operating an e-infrastructure supporting the principles of the Ecosystem Approach to Fisheries Management and Conservation of Marine Living Resources.

Trend Analysis and biodiversity assessments •  What are the most common species (10 - 25 or n)

reported in OBIS (per taxon, region, period) and is this changing over time?

•  Are we observing more or fewer species? •  Species Status:

–  Species with IUCN status per MPA –  Endemic species per MPA (Nr and occurrences) –  Species with IUCN status in < n MPA –  Edge effect; MPA near species distribution extension

The Unknown Ocean: A slice Red = many records, dark blue none

The vast midwaters, Earth�s largest habitat by volume, mostly unexplored (~95%)

Source: CoML OBIS Webb, O�Dor, Vanden Berghe

Coastal areas > open waters; Surface areas > the deep sea; Vertebrates and other large animals > smaller invertebrates; Northern hemisphere > southern.

World Ocean Assessment: First Global Integrated Marine Assessment of the Regular Process for Global Reporting and Assessment of the State of the Marine Environment, including Socioeconomic Aspects

Part VI Assessment of marine biological diversity and habitats •  Section A — Overview of marine biological diversity

–  Chapter 34 Scale of marine biological diversity –  Chapter 35 Extent of assessment of marine biological diversity –  Chapter 36 Overall status of major groups of species and habitats

•  Section B — Marine ecosystems, species and habitats scientifically identified as threatened, declining or otherwise in need of special attention or protection

–  Chapter 37 Coastal rock and biogenic habitats and related species –  Chapter 38 Coastal sediment habitats and related species –  Chapter 39 Shelf rock and biogenic reef habitats and related species –  Chapter 40 Shelf sediment habitats and related species –  Chapter 41 Deep sea habitats and related species –  Chapter 42 Water column habitats and related species

•  Section C — Environmental, economic and/or social aspects of the conservation of marine species and habitats and capacity-building needs

–  Chapter 43 Significant environmental, economic and/or social aspects in relation to the conservation of marine species and habitats

–  Chapter 44 Capacity-building needs •  Section D — Summary on marine biological diversity

–  Chapter 45 Summary on marine biological diversity

http://www.iobis.org/ Ocean Biogeographic Information System

Search data based on

Taxonomy Datasets

Geographical boundaries Time, season, depth

Oceanographic variables

Association of observation points with oceanography Observation data associated with

!  Bottom depth !  Temperature !  Salinity !  Nitrogen / Oxygen !  Phosphate / Silicate

Visualized through interactive graphs !  Time-series graphs !  Histograms

Environmental attributes from World Ocean Atlas

WOA09, http://www.nodc.noaa.gov/OC5/WOA09/pr_woa09.html

Example map #1 Cetacean species observations in LME region �Celtic-Biscay Shelf� (no environmental conditions set)

Example map #2 Cetacean species observations in LME region �Celtic-Biscay Shelf� filtered by a temperature range of 13 to 15 degrees

OBIS allows extraction of observations based on environmental conditions

User Statistics: 1 March 2011-2013 (Google Analytics)

•  Visits: 187,906 (av. ± 400 on a regular working day) •  Unique visitors: 124,587 •  Returning visitors: 35% •  Pages/visit: 2,34 •  Mobile devices/ipad: 2%

User Statistics Country(/(Territory(%(New(Visits(

1" Hong"Kong" 95,31%"2" Turkey" 86,77%"3" China" 76,04%"4" Philippines" 74,27%"5" (not"set)" 74,03%"6" India" 73,24%"7" ArgenGna" 71,15%"8" Italy" 70,52%"9" United"States" 68,14%"

10" Spain" 67,32%"11" Australia" 64,69%"12" United"Kingdom" 61,28%"13" Colombia" 61,00%"14" Brazil" 60,84%"15" Netherlands" 60,70%"16" Germany" 59,74%"17" Japan" 56,58%"18" Portugal" 54,96%"19" Canada" 54,20%"20" France" 53,49%"21" South"Korea" 53,16%"22" Mexico" 51,47%"23" Chile" 46,66%"24" Belgium" 45,73%"25" Russia" 44,22%"

Country(/(Territory( Visits( %(Visits(1" United"States" 47858" 25,5"2" Turkey" 12392" 6,6"3" Canada" 10412" 5,5"4" Germany" 9948" 5,3"5" United"Kingdom" 9301" 4,9"6" France" 7628" 4,1"7" Brazil" 7614" 4,1"8" Spain" 6808" 3,6"9" Australia" 5556" 3,0"10" Mexico" 5269" 2,8"11" Japan" 5226" 2,8"12" Belgium" 3890" 2,1"13" Italy" 3731" 2,0"14" India" 3330" 1,8"15" Portugal" 3155" 1,7"16" Russia" 2637" 1,4"17" Chile" 2413" 1,3"18" (not"set)" 2118" 1,1"19" Netherlands" 2005" 1,1"20" Colombia" 1659" 0,9"21" China" 1653" 0,9"22" Hong"Kong" 1622" 0,9"23" South"Korea" 1597" 0,8"24" Philippines" 1364" 0,7"25" ArgenGna" 1345" 0,7"

User Statistics City( Visits(

Aydin" 3854"(not"set)" 3113"

Sao"Paulo" 2272"Izmir" 2087"

Oberlin" 1695"London" 1647"Sydney" 1640"

Oostende" 1638"Hong"Kong" 1622"Dartmouth" 1605"

Paris" 1521"Yokohama" 1484"

Istanbul" 1459"Barcelona" 1458"

Mexico"City" 1334"New"York" 1219"

Rio"de"Janeiro" 1163"New"Brunswick" 1161"San"Francisco" 1143"

Halifax" 1074"Madrid" 1049"

Washington" 1026"Singapore" 1014"

Lisbon" 1012"Brisbane" 985"

Social Media

•  272 members –  88% senior level, 36% research

function

•  148 followers –  500–1,000 readers

•  74 followers

Outreach

•  PPT presentations –  100–200 views each

•  OBIS Public Library –  OBIS papers classified per year, per

node –  25 papers in 2012

•  Tracks OBIS publications –  >800 publications

Papers citing OBIS (Google Scholar)

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35 million geo-referenced species observations (+ 5 million since Jan 2011)

OBIS data growth: # datasets

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1,130 datasets (+ 219 since Jan 2011)

OBIS data growth:# records.k/dataset

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120,000 marine species (+ 5,000 since Jan 2011)

Very little historical data

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BIS

OBIS Network OBIS is a strategic alliance of hundreds of scientists and organisations who contribute data, information and expertise to OBIS.

OBIS PO

OBIS Steering Group

OBIS task teams

OBIS Group of Experts

OBIS Nodes

Data providers

Users policy makers,

managers, researchers,

public

Stakeholders Partnerships with CBD,

GBIF, EOL, GOBI, GOOS, FAO, UNEP-WCMC, ICES,

SMEBD/WoRMS, Species2000, GCMD, SCOR,

CBOL, …

Six (informal) task teams

1.  Technical task team (data system architecture, and data portal)

2.  Documentation/Training task team (QC, data validation, standards and best practices)

3.  Data task team (data and metadata schemes) 4.  Governance task team (sustainability plan,

governance model, vision, objectives, partnerships, funding)

5.  Taxonomy task team (name reconciliation) 6.  Outreach task team (communication strategy)

OBIS Data System Architecture

QC

indexing

classification

assembly

node node node

staging

production

portal

MarineRegions

WOD/ODP

GEBCO

Queries Mapping Extraction

-Excel, DiGIR, IPT -OBIS (extended DwC) schema

WoRMS ITIS, CoL,

IRMNG

EOL

GEO

iMarine

LifeWatch

GBIF

GCMD

Data flows in OBIS

Current

Future

Draft ToR OBIS nodes

•  Receiving or harvesting marine biodiversity data (and metadata) from national, regional and international programs, and the scientific community at large.

•  Perform data validation (using standards, tools and best practices), as described in the OBIS cookbook (OBIS tier II).

•  Reporting the results of quality control directly to data collectors/originator.

•  Making data (and metadata) available to OBIS using agreed upon standards and formats (OBIS cookbook).

•  Control data access, terms of use and sharing policies. •  Provide customer support (data queries, analyses, feedback). •  Increase visibility and reach out (Communication and Outreach

Strategy). •  Build customized portals (e.g., multiple languages). •  Comply with the IOC data policy for using and sharing OBIS data.

OBIS nodes (bold = NODC status, green = Candidate node)

1.  Antarctica/ AntOBIS 2.  Arctic/ ArcOD/AOOS 3.  Argentina/ArOBIS 4.  Australia/ OBIS-

Australia 5.  Black Sea/ BlackSea-

OBIS 6.  Canada/ OBIS-

Canada 7.  China/ OBIS-China 8.  Europe/ EurOBIS 9.  India/ IndOBIS 10. Japan/ OBIS-Japan 11. Korea/ KOBIS

12. Mediterranean/ MedOBIS

13. South-East Pacific/ ESPOBIS

14. South-West Atlantic/ WSAOBIS

15. South-West Pacific/ NZOBIS

16. Sub-Saharan/ AfrOBIS

17. USA/ OBIS-USA

18. Global/ MicrOBIS 19. Global/ OBIS-

SEAMAP 20. Global/ Hexacorals 21. Global/ FishBase 22. Global/ Seamounts 23. Gulf of Aden 24. South-East Asia 25. Caribbean

Establishment of new OBIS nodes (for consideration at IODE-XXII)

•  If the institute is an existing NODC: –  Send a letter of “expression of interest” to the OBIS project office, wishing to

join the OBIS network of nodes.

•  If the institute is not an existing NODC, but wishes to apply for an NODC status:

–  Follow the procedure for NODCs and include your wish to join the OBIS network of nodes.

•  If the institute is an existing SODC (if the SODC entity type is adopted by the 22nd session of the IODE Committee):

–  Send a letter of “expression of interest” to the OBIS project office, wishing to join the OBIS network.

•  If the institute is not an existing SODC, but wishes to apply for an SODC status:

–  Follow the procedure for SODCs and include your wish to join the OBIS network of nodes.

Establishment of new OBIS nodes (for consideration at IODE-XXII) The extra information required for OBIS to include in the application/expression of interest is the following:

–  Indicate the level of commitment to function as an OBIS tier II and/or tier III node;

–  Indicate the person who will act as the OBIS node manager (and deputy).

Applications will be reviewed by the IODE Steering Group for OBIS and a decision will be made within two weeks after confirmation of receipt. The results of the decision from the 22nd session of the IODE Committee will affect the final process developed by the SG-OBIS.

OBIS Standards and Best Practices •  Metadata, no single standard

–  ISO19115 compliancy (GCMD, FGCD, IMIS, EML..) •  Data

–  Geography: OBIS extension of Darwin Core –  Taxonomy: basis = World Register of Marine Species,

but also ITIS, CoL and IRMNG (when not in WoRMS). •  Data harvesting protocols

–  GBIFs Integrated Publishing Toolkit (IPT) (txt file + EML) –  DiGIR (XML) –  CSV

•  Data publishing services –  Maps using Open layers –  OGC/Open GIS web map/feature/coverage services

(OBIS GeoServer)

QC/data validation/quality flags

•  Principle OBIS never change records –  data cleaning needs to be done at the expert/data providers

level. •  OBIS can perform data integrity checks (completeness,

correctness), add precision and accuracy information (quality flags)

QC of metadata

•  Metadata"should"contain:"–  Title"(dataset"name,"comprehensive,"not"just"an"acronym)"–  CitaGon"(journal"style,"include"Gtle"of"dataset)"–  General"descripGon"(abstract)"–  Contact"informaGon"(name"–"insGtute"–"email)"–  User"restricGons"(most%cases:%�freely%available%if%cited�)"–  Sampling"design"(collaborate"with"GE]BICH"and"ODSBP)"

•  Metadata"can"also"contain:"–  Keywords,"habitat,"species"funcGonal"groups"–  Taxonomic"–"temporal"–"geographic"scope/boundaries"–  Links"(online%data,%metadata,%project%page,%DiGIR,%IPT%…)"–  Associated"documentaGon"(e.g.,%reports,%publica@ons%…)"

QC of data

•  Required"(mandatory)"fields"•  Taxonomy"•  Life"stage"(need"for"vocab"]>"GE]BICH/ODSBP)"•  Gender"(need"for"vocab"]>"GE]BICH/ODSBP)"•  Geographic"locaGons"(link"to"gazeheer)"•  Depth"•  Date"–"Gme"

–  Start"&"end"fields"•  Observed"individuals"•  Basis"of"record"(literature,"specimen,"observaGon)"

Taxonomic QC

•  Taxon Match tool to check if name is available in WoRMS, ITIS, IRMNG, CoL (if name not available in any of those -> more elaborate search in: PaleoDB, IPNI, Euro+Med Plantbase, Index Fungorum, Fishbase, BOLD, Web of Science

•  Avoid false matches (homonyms) by indicating higher taxonomic group •  Translate common names and cases of cf., sp., complexes etc to higher

taxonomic level:

Received taxon name Matching name

Mytiluus sp. Mytilus

Gadus cfr. morhua Gadus

Cladocera/Ostracoda Crustacea (= common subphylum)

Sponges Porifera

Bamboo sharks Galeomorphi (superorder)

•  Add taxon LSID to record (e.g. TSN, AphiaID)

Name validation tool: Taxon Match

This(tool(uses(the(following(components:(:TAXAMATCH(fuzzy(matching(algorithm(by(Tony(Rees(:PHP/MySql(port(of(TAXAMATCH(by(Michael(Giddens(:ScienHfic(Names(Parser(by(Dmitry(Mozzherin(

TAXON MATCH

TAXON MATCH

TAXON MATCH

SOAP/WSDL/REST web service

Examples

Web Services

System( Field( Key( Mechanism(

WoRMS" Taxon"name" AphiaID" webservice"

WoRMS" Parent"taxon" AphiaID" webservice"

WoRMS" Child"taxa" AphiaID" webservice"

WoRMS" Synonyms" AphiaID" webservice"

WoRMS" Common"name" AphiaID" webservice"

WoRMS" References" AphiaID" webservice"

WoRMS" Ahributes" AphiaID" Not"yet"

Taxonomic QC

•  Current"situaGon""""±"198,000"taxon"names"in"OBIS:"–  ±"153,500"matched"to"WoRMS""–  ±"80,000"matched"to"ITIS"–  ±"31,500"not"matched"to"any"standard"(WoRMS,"ITIS,"CoL,"IRMNG)"

•  Plan OBIS Taxonomic Task Team –  April 2013: Status report on numbers of errors (per

taxonomic groups and time) –  June 2013: Preliminary Cleaning Assessment –  Cleaning up residual errors – Ongoing

Overlap"of"±"72"000"taxa"

Geographic QC

•  Fields in OBIS 1.  LaHtude(2.  Longitude(3. Start"laGtude"4. End"laGtude"5. Start"longitude"6. End"longitude"7. Coordinate"precision"8. Start/end"coordinate"precision"9. Bounding"box"10. ConGnent"ocean"11. Country"12. State"province"13. County"14. Locality"

Geographic QC

•  Are"the""laGtude"and"the"longitude"completed"and"are"their"values"different"from"0?"

•  Are"the"laGtude"or"the"longitude"completed"and"are"their"decimal"values"between"]90"and"+90"(laGtude)"and"between"]180"and"+180"(longitude)"(WGS84)?"

•  Decimal"check"(X,aabb":"if"aa"<59"and"bb"<59"it"may"mean"the"coordinates"are"not"decimals,"but"degrees,"minutes"and"seconds)"""

•  Are"the"coordinates"situated"in"sea"or"coast"(buffer"20km)?"•  Are"the"coordinates"situated"in"the"right"geographical"area"(fields"9]14,"or""

e.g."AtlanGc"spohed"dolphins"should"not"be"found"in"the"Pacific)?"•  Is"the"observaGon"point"not"an"outlier"in"the"dataset?""

–  Is"the"observaGon"point"not"more"than"4"X"standard"deviaGon"from"the"centroid"of"the"dataset?"

•  Is"the"observaGon"point"not"an"outlier"in"the"observaGons"of"the"species?""–  Is"the"observaGon"point"not"more"than"4"X"standard"deviaGon"from"the"centroid"of"the"

observaGons"from"that"species?

Geographic QC

Example%dataset%“Marine%Turtles”:%sigh@ngs%and%strandings%of%marine%turtles%around%the%coast%of%UK%and%Ireland”"

Outliers%due%to%missing%of%minus%sign.%Correc@ons%made%aKer%consulta@on%data%provider."

Geographic QC

•  Related to depth: –  Is the minimum depth < maximum depth? –  Is the observation depth possible if compared with a depth

map (include margin)? –  Is the observation depth possible if compared with the given

depth range of the species

•  Related to environmental parameters: –  Is the observation possible if compared with the given (min-

max) salinity, temperature, oxygen, nutrient range of the species

QC Presence, abundance, biomass •  Is the field 'sample size' completed if the value of the

field 'Observed individual count’ or 'observed weight' >0?

Date QC •  Fields in OBIS

1.  YearCollected 2.  MonthCollected 3.  DayCollected

4.  StartYearCollected 5.  StartMonthCollected 6.  StartDayCollected 7.  EndYearCollected 8.  EndMonthCollected 9.  EndDayCollected

10.  StartTimeOfDay 11.  EndTimeOfDay 12.  TimeOfDay

13.  Timezone

Date QC

•  Is the collection date (year, month, day, end-start) completed and valid (i.e. between 1300 and now)?

•  Is the ‘collection date’ <= the ‘date identified’ and <= the ‘last modified date’

•  If the start date and the end date are completed, is the start date < the end date (taking into consideration the given time)?

•  Is the time/starttime/endtime >= 0 and <24 and is the timezone completed

Date QC

=>produce time graph for visual check.

Future plans

•  Expand on data types (marine extension of Darwin Core) –  Tracking data –  Acoustics –  Images (e.g. fin patterns)

•  Expand geographical coverage •  Capacity building

–  Biological data management –  Regional marine biological observatories

•  Close collaboration with IODE projects and IOC and UNESCO programmes