VLIZ • Flanders Marine Institute • Government funded • Scientific, non-profit organization • Since 2000. 1 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…. 2 EurOBIS European node for OBIS • Species observations and specimen collections • > 240 datasets > 8 M records • Started under Marbef & CoML, presently EMODNET 3 EurOBIS System overview WoRMS 4 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 5 WoRMS network 6 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 7 WoRMS governance Steering committee & responsibilities through present involvement in other organisations Mark J. Costello 1,2,3,5,8,16 European Register of Marine Species Edward Vanden Berghe 1,2,3,5,8 Ocean Biogeographic Information System Nicolas Bailly 1,3,5,6,12 Society for the Management of European Biodiversity Data Philippe Bouchet 1,3,4,1,13 International Code of Zoological Nomenclature Charles Griffiths 2,15 Species 2000 Michael D. Guiry 1,2,3,5,11 Catalogue of Life Ward Appeltans# 1,2,3 Echinodermata Maria (Deng) Palomares 10 Encyclopaedia of Life David (Paddy) J. Patterson 1,2,4,8,9 International Census of Marine Microbes Gary C. B. Poore 2,14 SeaLifeBase Tony Rees 2 AlgaeBase Gary Rosenberg 2,4,13 FishBase Sabine Stöhr 7 Mollusca Crustacea, Crustacea.net African species International Association for Biological Oceanography 8 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 9 10 Database download MS Access database Monthly archives Request forms are available online Password restricted 11 Webservices : taxonmatch tool Aphia taxon match tool 12 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 13 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 14 VLIMAR : Marine Gazetteer 15 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… 16 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 17 17 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 18 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 19 Lifewatch The infrastructure for biodiversity research • ESFRI • ERIC • Observatories • Data systems • Workflows • Service center 20 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 21 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 22 Taxonomic backbone 23 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 24 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() 25 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 26 .