WORLD REGISTER OF MARINE SPECIES AND THE CATALOGUE OF LIFE
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WORLD REGISTER OF MARINE SPECIES AND THE CATALOGUE OF LIFE

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WORLD REGISTER OF MARINE SPECIES AND THE CATALOGUE OF LIFE Presentation Transcript

  • 1. World Register of Marine Species (WoRMS), Click to edit Master title stylecontribution to the Catalogue of Life (CoL) Click to edit Master subtitle style Ward Appeltans, Bart Vanhoorne, Wim Decock Flanders Marine Institute (VLIZ) Oostende (Belgium)
  • 2. www.marinespecies.orgClick to edit Master title style Click to edit Master subtitle style
  • 3. WoRMS in a nutshell• Started in 2007. Grew out of ERMS through EU FP 6 MarBEF;• Expert-based, taxonomic database (not a Click index) Master title style name’s to edit • Species are classified in a taxonomic tree, and linked with synonyms and commonly used spelling mistakes; Click to edit Master subtitle style• Permanent host institute: VLIZ• Web-based, incl webservices• Follows international standards and serve permanent Global Unique IDs (LSIDs) http://www.tdwg.org/standards/150/download/
  • 4. WoRMS management• WoRMS is created by an editorial board of 250 taxonomists from 176 institutions in 33 countries. Click to edit Master title style• The editors are united under the umbrella of the Society for the Management of Electronic Biodiversity data (SMEBD), which main aim is to protect editors’ IPR and to represent the network internationally. Click to edit Master subtitle style• The WoRMS Steering Committee coordinates the network.• The Flanders Marine Institute (VLIZ) is publishing the database and provides data management support and IT tools.
  • 5. Statistics• 436,500 taxa;• 213,000 accepted marine species names;• 17,000 accepted non-marine species names;Click to edit Master title style• 139,000 synonyms (incl common misspellings);• 44,000 vernacular names (138 languages);• 150,000 key literature references;• 45,000 specimen details; Click to edit Master subtitle style• 328,000 published distributions;• 510,000 web links;• 20,000 images;• and many other species related information (biology, habitat, feeding type , e.g. 17,000 parasite-host relationships…).
  • 6. Status• If 230,000 valid marine species Clicknot yet expert-validated title style to edit Master – WoRMS = 92% (213K spp) complete, but 20K (9%) – Gaps are: Gastropoda (6,000spp), parasitic Nematoda (4,400spp), Digenea (4,200spp), Ostracodato edit Master subtitle style Click (3,500spp), Bacillariophyceae (2,000spp) en Cyanobacteria (500spp). – In 2011, >100 tax editors: • Added: +35,219 taxa (30,056 spp and subspp (incl synonyms); • Updated: 25,000 spp.
  • 7. WoRMS usersWoRMS is a standard taxonomic reference for many organizations and programmes (e.g. GBIF, OBIS, CoL, EoL, ICES, IODE, SeaDataNet, FAO …) Click to edit Master title style • >60 organisations requested download access.The website has • In 2011: 31M hits; 632.000 unique visitors; • ~3M hits/month; ~5,000 unique visitors per day (excl weekends); Click to edit Master subtitle style • >500 citations in Google Scholar (increasing @ 1/day).The Web Services and the Taxon Match tool are used extensively for quality control purposes. • 28 institutes are using the web service; • >5,142 species lists are matched (avg 14/day) .
  • 8. All names stored locally in Aphia database 71 GSDs 10 RSDs Click to edit Master title style Click to edit Master subtitle style 3 TSDs 9 ext. GSDsWoRMS integrates over 100 global, regional and thematic species databases intoa common IT platform, which means every speciesoccurs in the system only once.
  • 9. Click to edit Master title style Click to edit Master subtitle style
  • 10. www.marinespecies.org/carmsClick to edit Master title style Click to edit Master subtitle style
  • 11. www.marinespecies.org/copepoda Click to edit Master title style Click to edit Master subtitle style
  • 12. www.marinespecies.org/habClick to edit Master title style Click to edit Master subtitle style
  • 13. www.marinespecies.org/urmoClick to edit Master title style Click to edit Master subtitle style
  • 14. Main fields in WoRMS1. AphiaID;2. Click name; Master title style Taxon to edit3. Authority;4. Taxon Rank;5. Click to edit Master subtitle style Parent-child relationship (Classification);6. Accepted taxon relationship (synonymy);7. Vernaculars (common names);
  • 15. Main fields in WoRMS1. Environment (marine/brackish/fresh/terrestrial); Click to edit Master title style2. Sources (incl weblinks, DOI, PDFs);3. Published distributions (incl misidentifications), linked to gazetteer; Click to edit Master subtitle style4. Specimens (incl code, museum, links, identification history, ..);5. Ecological traits (e.g. feeding, associations etc);
  • 16. Main fields in WoRMS1. Deeplinks (GenBank, BOLD, ...), but also Click file cards, Master title style PDFs, to edit ...;2. Images;3. Page citation. Click to edit Master subtitle style
  • 17. Hard & software• MS SQL 2008 Click to edit Master title style – http://www.marinespecies.org/structure/index_files• PHP out/input webinterface• MS Access front end for administration: editClick toquality control (e.g. find rights, edit Master subtitle style duplicates)• Apache2 running on Windows Server 2008 (back-up daily)
  • 18. Web portalClick to edit Master title style Click to edit Master subtitle style
  • 19. Web portalClick to edit Master title style Click to edit Master subtitle style
  • 20. Web portal Scientific Name + Authority Parent /Child taxon Taxon/Name statusClick to edit Master title style Scrutiny/record status Taxon rank Invalid synonyms Literature sources Click to edit Master subtitle style
  • 21. Click to edit Master title style Click to edit Master subtitle style
  • 22. Vernaculars ‘138 languages’ Environment + fossil flags DistributionsClick to edit Master title style Click to edit Master subtitle style Ecological traits Deep links (incl webservices of GenBank, BOLD, BHL) Free notes
  • 23. Click to edit Master title style Click to edit Master subtitle style
  • 24. Click to edit Master title style Click to edit Master subtitle style
  • 25. Click to edit Master title style Click to edit Master subtitle style
  • 26. Type specimensClick to edit Master title style Click to edit Master subtitle style
  • 27. Click to edit Master title style Click to edit Master subtitle styleEdit LSIDsession Citation License
  • 28. Access Services• Match and extract information from WoRMS to edit Master title style Click using: – Taxon Match tool – Webservice – File transfer Click to edit Master subtitle style• E.g.: – Queries: classification, resolve spelling, synonyms, common names, ... – Sharing images, distribution layers, PDFs of original descriptions
  • 29. Name validation tool: Taxon MatchClick to edit Master title style This tool uses the following components: -TAXAMATCH fuzzy matching algorithm by Tony Rees -PHP/MySql port of TAXAMATCH by Michael Giddens -Scientific Names Parser by Dmitry Mozzherin Click to edit Master subtitle style
  • 30. TAXON MATCHClick to edit Master title style Click to edit Master subtitle style
  • 31. TAXON MATCHClick to edit Master title style Click to edit Master subtitle style
  • 32. TAXON MATCHClick to edit Master title style Click to edit Master subtitle style
  • 33. SOAP/WSDL/REST web serviceExamples Click to edit Master title style Click to edit Master subtitle style
  • 34. Web ServicesSystem Field Key MechanismWoRMS Taxon name AphiaID webservice Click to edit Master title styleWoRMS Parent taxon AphiaID webserviceWoRMS Child taxa AphiaID webserviceWoRMS Click to edit Master subtitle style Synonyms AphiaID webserviceWoRMS Common name AphiaID webserviceWoRMS References AphiaID webserviceWoRMS Attributes AphiaID Not yet
  • 35. Links with other systemsSystem Link-out System Link-in Mechanism Content applicationsWoRMS ID EoL AphiaID webservice taxonomy, distributions, sources, notes, citationsWoRMS / PESI AphiaID File transfer Taxonomy, distributions, sources, environmentWoRMS ID NCBI taxon AphiaID LinkOut taxon nameWoRMS IDWoRMS / Click to edit Master title style BoLD EMODnet / webservice taxon name AphiaID taxamatch taxon name, parent taxon, child taxa, synonyms, attributesWoRMS ID IUCN Red List AphiaID webservice taxon name, conservation statusWoRMS ID ITIS / file transferWoRMS / WikiSpecies NL AphiaID file transfer taxonomyWoRMS ID Click toAphiaID webservice Taxonomysubtitle style BIOTIC edit MasterWoRMS / Wikipedia AphiaID webservice taxonomyWoRMS name BHL / webservice bibliographic metrics, #papers, pagesWoRMS / OBIS AphiaID taxamatch taxonomyWoRMS / CoL AphiaID file transfer taxonomy, distributions, citationsWoRMS ID VLIMAR AphiaID regional checklists, hierarchical search, lat/lon of placenamesWoRMS ID Plankton-Net AphiaID taxamatch taxon name, picture sharingWoRMS ID IMIS AphiaID taxamatch metadata, Ref/person/instWoRMS ID BR Meise AphiaID taxamatch Specimen image, zoom
  • 36. WoRMS contribution to CoL• 2009: 6 GSDs + URMO• 2011: 21to edit Master title style Click GSDs + URMO (+15)• 2012: 28 GSDs + URMO (+7 & 22 updates) # species DB Click to edit Master subtitle style 59,500 WoRMS (28 GSDs) 12,500 URMO (31 GSDs) 72,000 33% of WoRMS
  • 37. WoRMS contribution to CoL• Adopted to a large extent the CoL management hierarchy; Click to edit Master title style• Mapped WoRMS to CoL schema;• Export to CoL: – (via script) Automated export generation Click to edit Master subtitle style (WoRMS) & automated harvest (CoL) – Tab-delimited file transfer (incl metadata) – Daily/weekly/montly updatableWoRMS is now also available in DwC-A
  • 38. Marine species (estimated valid): data sources• Bacteria & Archaea (2,500spp): MICROBIS edit Master title style Click to (BIOS in CoL)• Fungi (1,000spp): Index Fungorum• Plantae (7,500spp): AlgaeBase Click to edit Master subtitle style• Chromista (19,000spp): AlgaeBase• Protozoa (500spp): various• Animalia (200,000spp): various
  • 39. Marine species (estimated accepted): data sources• Animalia (200,000spp) Click to edit Master title style – Various sources (taxon groups): • WoRMS, URMO (58) • ITIS (31) • NZOR (8) edit Master Click to subtitle style • ETI (1) • FADA (1) • TIGR (1) • ZOBODAT (1)
  • 40. Marine species gaps in CoL 2012 Size (# spp) Taxon groups Click >30,000 Mollusca title style to edit Master >8,000 Nematoda >8,000 Platyhelminthes Click 5,000 Master subtitle style to edit Crustacea (2,000 decapods) 500 Echinodermata (crinoids) 200 Protozoa >51,500
  • 41. Conclusion• Animalia: – Taxa with exclusive marine spp mostly from WoRMS/URMO; Click to edit Master title style – Taxa with non-marine representatives (e.g. birds, fish, mammals, annelids, chelicerata, hexapods) mostly from other sources (ITIS Click to edit Master subtitle style the biggest);• Plants & Chromista: from AlgaeBase;• Fungi: from Species Fungorum;• Bacteria & Archaea: from BIOS (but no marine flags)
  • 42. Conclusion• Need to fill the latest gaps, >50,000 spp (22%) marine species;• Automated harvest routines title style Click to edit Master (what frequency?);• CoL will soon have close to 100 GSDs fromClick to edit Master subtitle style WoRMS: – Should we go for one WoRMS GSD minus x number of taxon groups? So “group by providers” instead of taxon group.