EMODNET pilot biological lot - University of Auckland · 1 VLIZ • Flanders Marine Institute • Government funded • Scientific, non-profit organization • Since 2000.

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VLIZ

• Flanders Marine Institute • Government funded • Scientific, non-profit

organization • Since 2000.

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VMDC Vlaams marien datacentrum

• Flanders Marine Datacenter • Staff : 15 • National data centre in IODE

network • House EurOBIS & WoRMS • Networks: IODE, MARS, OBIS,

ICES, ASFA, SMEBD, GLOSS….

• International projects: Marbef, Lifewatch, Seadatanet, PESI, Emodnet….

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EurOBIS European node for OBIS

• Species observations and specimen collections • > 240 datasets > 8 M records • Started under Marbef & CoML, presently EMODNET

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EurOBIS System overview

WoRMS

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WoRMS World register of marine species

• Standard list of species names (&taxa) • 314,315 taxa / 253,071 species names • > 40 global or regional lists • Compiled, annotated and checked by >170

taxonomic experts • Accepted as a ‘standard’ by OBIS, IODE, ICES,

BODC, seadatanet? • Links to/from genbank, ITIS, CoL • Participates to PESI, CoL, EOL, 4D4life

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WoRMS network

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WoRMS links to international databases

Taxa linked To GenBank 31603

To FishBase 16887

To Barcode of Life 14022 (92678 sequences)

To Marine Species Identification Portal 7250

To CLEMAM 3886

To NeMys 3038

To AlgaeBase 2250

To Index Fungorum 1167

To Echinoid Directory 733

To FAO Species fact sheets 228

To The Sponge Guide 116

Others 8834

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WoRMS governance Steering committee & responsibilities through present involvement

in other organisations

Mark J. Costello 1,2,3,5,8,16 Edward Vanden Berghe 1,2,3,5,8 Nicolas Bailly 1,3,5,6,12

Philippe Bouchet 1,3,4,1,13 Charles Griffiths 2,15 Michael D. Guiry 1,2,3,5,11 Ward Appeltans# 1,2,3 Maria (Deng) Palomares 10 David (Paddy) J. Patterson 1,2,4,8,9 Gary C. B. Poore 2,14 Tony Rees 2 Gary Rosenberg 2,4,13 Sabine Stöhr 7

European Register of Marine Species Ocean Biogeographic Information System Society for the Management of European Biodiversity Data International Code of Zoological Nomenclature Species 2000 Catalogue of Life Echinodermata Encyclopaedia of Life International Census of Marine Microbes SeaLifeBase AlgaeBase FishBase Mollusca Crustacea, Crustacea.net African species International Association for Biological Oceanography

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End users Examples of end-users

Data systems • GBIF, OBIS, Species 2000, EoL, SeaLifeBase, ZooBank

Government science policy agencies that requested a copy of the database

• E.g. European Environment Agency, International Council for Exploration of the Sea, Rijkswaterstaat (Netherlands), Nature Protection Directorate (Italy), L'Inventaire national du Patrimoine naturel (France), IFREMER, Federal Environmental Agency (Germany), Akvaplan-NIVA (Norway), National Cancer Institute, Hellenic Centre for Marine Research (Greece), Stazione Zoologica Napoli (Italy), Joint Nature Conservation Committee (UK) [already users of European Register of Marine Species]

Individuals through website • scientists, students, naturalists, ecological consultants, environmental managers

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Database download

MS Access database Monthly archives Request forms are available online Password restricted

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Webservices : taxonmatch tool Aphia taxon match tool

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Webservices: SOAP requests

WoRMS web service

• get the AphiaID for your taxon • check the spelling of your taxa • get the authority for your taxa • get the full classification for your taxa • resolve all your invalid names to valid names • match your species list • resolve a common name to a scientific name

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Webservices: EOL

List of taxa updated since YYYY-MM-DD http://www.marinespecies.org/aphia.php?p=eol&

action=taxlist&startdate=YYYYMMDD

Taxon details for species with aphiaid=X http://www.marinespecies.org/aphia.php?

p=eol&action=taxdetails&id=X

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VLIMAR : Marine Gazetteer

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VLIMAR : Marine Gazetteer

• Dictionary for geographical names (28,000 names) • Hierarchy, the relationships (parent-child, adjacent to, streams

through, rises and flows out) • Place types: seas, islands, sandbanks, ridges, estuaries, bays,

seamount chains,… • Min-max lat/long, precision (radius of the circle) • Sources of information • Shapes • Different catalogues: EEZ, IHO Sea Areas, FAO Fishing Areas,

Large Marine Ecosystems of the World…

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EMODNET European Marine Observations and Data Network

An Integrated Maritime Policy for the European

Union Address whole chain “from observation to

information” Need to unlock access to existing data AND fill

existing gaps Complementary to other initiatives

• Data Management

– EMODNET as a system of systems – Organize a common data management

approach accepted by all actors to ensure that data are available to all

– Interoperability by adopting EU-INSPIRE principles

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EMODNET data portal

• Proof of concept (2009-2011): “Five portals for a number of maritime basins, providing

access to marine data of a standard format and known quality and identify gaps in coverage and identify the main challenges.”

– 1. hydrographic data – 2. marine geological data – 3. chemical data – 4. biological data – 5. habitat mapping

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EMODNET biology portal Plan

Build data system to provide biological data to EMODNET portal and other European initiatives

http://bio.emodnet.eu/portal/index.php

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Lifewatch The infrastructure for biodiversity research

• ESFRI • ERIC • Observatories • Data systems • Workflows • Service center

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LifeWatch workflow example

• Give me the maximum and minimum salinity where organisms with DNA seq homology above x% with this DNA seq. (=seqA) have been found.

• Step1: use seqA in blast / fasta against genbank – get list of genbank entries above cut-off

• Step2: feed list to WoRMS hierachy match – get list of taxa & specimens matching this seq.list

• Step3: feed list to EurOBIS mapping tool – get list of observations (positions, map, UW features)

• Step4: spatial query to environmental databases – select min/max salinity at these positions

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extending the workflow

• Where could we expect to find sequences with x% homology to seqA?

• And how would that change according to different global change scenario’s

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Taxonomic backbone

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Taxonomic backbone data

• Standardized taxon names : use a code from authoritative list – E.g. Terebella prudens Quatrefages, 1866 =

• Lanice conchilega Pallas, 1766 = • Lanice conchilega = • Schelpkokerworm = zandkokerworm = aphiaid:131495

• Hierarchy ,Common names, Synonyms, Status • Add. species information, attributes; traits

– Feeding types, size classes, habitats, life stages – Environmental data (salinity, temp,..) – Sensitivity, invasiveness – Genomic data

• Links to other databases

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Taxonomic backbone services

• TaxonMatch(‘name’,’author’,’year’) => list of matches

• GetID(‘name’), GetValidID(‘name’),GetName(ID) • GetTaxonInfo(ID) =>Hierarchy, Images, Attributes,

Common names, Synonyms

• GetChildrenof(), SelectTaxaWithFeatures() • GetBarcodeSequencesLinks(),

GetDNASequenceLinks()

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Use of standards • Quality control : existing name?

– taxon name => unique identifier • Combining data sets & data archaeology

– relation between id’s – status : valid, synonyms ,accepted

• Linking data systems – # links per id to other data systems – links to WoRMS

• Data mining & exploration – hierarchy, traits, attributes

• Derived data products • Taxonomic backbone

– flow controlled web services