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Marine Biodiversity data: an introduction on marine biodiversity data mangement @ VLIZ World Register of Marine Species Simon Claus Flanders Marine Institute (VLIZ) InnovOcean site VLIZ Project office IODE Flanders Marine Institute (VLIZ) Ostend, Belgium Since 1999 Supported by Flemish government Objective: Support and facilitate marine sciences Important focus on biodiversity data holdings ESF Marine Board Data management of biodiversity data Observations Documentation Registry & storage Use/Re-use Integration Discovery metadata Use/technical metadata Collating Structuring Standardizing IMIS MDA EUROBIS Quality Control Taxonomic WoRMS Geographic Gazetteer Web interfaces Web services EMODNET IMIS Integrated Marine Information System Modular Information system: scientific institutes, experts, projects, literature, datasets.... Module Datasets: ISO 19115 discovery metadata •Title •abstract •Temporal coverage •Spatial coverage •Taxonomic coverage •Institutes/experts involved •Related publications •Other details IMIS Integrated Marine Information System Module Datasets Module Module Institutes Persons IMIS Integrated Marine Information System Module Datasets link to Marine Data Archive MDA Marine Data Archive Online backup and storage system for data files http://mda.vliz.be Files stored together with their ‘use’ metadata General attributes: file name, date, contact, conditions of use, … Specific attributes for specific datatypes: biotic data, experiment data, geographic data, images and movies, … 3 access levels: Personal, Shared, Public Archival procedures in place EUROBIS EMODNET European Ocean Biogeographic Information System European Marine Observation and Data Network Uses OBIS Darwin Core2 scheme for integrating biogeographic species observation data Uses Digir protocol for data exchange with network of distributed data providers OGC compliant portal (makes use of Geoserver and incorporated web services) Developed within EU projects MarBEF and EMODNET biology pilot Linked with global systems: OBIS-IODE/IOC-GBIF http://www.eurobis.org http://bio.emodnet.eu http://bio.emodnet.eu/portal WoRMS View List Search by species group name (scientific, (cfr tender)common) Filter Download Metadata EMODnet 9 The portal functionalities → Taxonomic functionalities (WoRMS) Autocompletion taxonomic search queries Show map, include child taxa Show map, including synonyms EMODnet 10 April 12, 2012 The portal functionalities → Data visualization Records aggregated: increased performance, overview data density EMODnet 11 The portal functionalities → Data visualization Data distributions aggregated per grid EMODnet 12 The portal functionalities → Data visualization Overview data attributes from EurOBIS EMODnet 13 The portal functionalities → EMODnet Data visualization Plot modelled distribution maps from species 14 The portal functionalities → EMODnet Data visualization Layer and metadata served from FAO server through OGC 15 The portal functionalities → EMODnet Data visualization Combine observation data with modelled distribution maps: Data gaps / validation modelled distribution maps 16 The portal functionalities → Data visualization Visulaize other dataproducts from Emodnet habitats, geology, chemistry, physics to portal through OGC EMODnet 17 VLIMAR VLIZ Marine Gazetteer •Standard, relational list of geographic names •Linked with information and maps of the geographic location of these features •Over 21.000 geo-referenced localities •Including boundaries like Exclusive Economic Zones (EEZ), IHO Sea Areas, Intersect of IHO Sea Areas and Exclusive Economic Zones, FAO Fishing Areas, Large Marine Ecosystems of the World, Longhurst Biogeographical Provinces, ICES Ecoregions, Marine Ecoregions of the World, Continental margins between 140m and 3500m depth •Quality control and standardisation http://www.vliz.be/vmdcdata/vlimar VLIMAR VLIZ Marine Gazetteer VLIMAR VLIZ Marine Gazetteer WoRMS World Register of Marine Species www.marinespecies.org WoRMS in a nutshell • Started in 2007. Grew out of ERMS through EU FP 6 MarBEF; • Expert-based, taxonomic database (not a name’s index) • Species are classified in a taxonomic tree, and linked with synonyms and commonly used spelling mistakes; • 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/ WoRMS management 240 taxonomic editors, 176 institutions, 33 countries • WoRMS is created by an editorial board of 250 taxonomists from 176 institutions in 33 countries. • 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. • The WoRMS Steering Committee coordinates the network. • The Flanders Marine Institute (VLIZ) is publishing the database and provides data management support and IT tools. • • • • • • • • • • • Statistics 436,500 taxa; 213,000 accepted marine species names; 17,000 accepted non-marine species names; 139,000 synonyms (incl common misspellings); 44,000 vernacular names (138 languages); 150,000 key literature references; 45,000 specimen details; 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…). Status • If 230,000 valid marine species – WoRMS = 92% (213K spp) complete, but 20K (9%) not yet expert-validated – Gaps are: Gastropoda (6,000spp), parasitic Nematoda (4,400spp), Digenea (4,200spp), Ostracoda (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. WoRMS users WoRMS is a standard taxonomic reference for many organizations and programmes (e.g. GBIF, OBIS, CoL, EoL, ICES, IODE, SeaDataNet, FAO …) • >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); • >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) . All names stored locally in Aphia database 71 GSDs 3 TSDs 10 RSDs 9 ext. GSDs WoRMS integrates over 100 global, regional and thematic species databases into a common IT platform, which means every species occurs in the system only once. www.marinespecies.org/carms www.marinespecies.org/copepoda www.marinespecies.org/hab Web portal Web portal Scientific Name + Authority Taxon/Name status Scrutiny/record status Taxon rank Invalid synonyms Literature sources Parent /Child taxon Vernaculars ‘138 languages’ Environment + fossil flags Distributions Ecological traits Deep links (incl webservices of GenBank, BOLD, BHL) Free notes Web portal Type specimens Edit session LSID Citation License Access Services • Match and extract information from WoRMS using: – Taxon Match tool – Webservice – File transfer • E.g.: – Queries: classification, resolve spelling, synonyms, common names, ... – Sharing images, distribution layers, PDFs of original descriptions Name validation tool: Taxon Match 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 Attributes AphiaID Not yet Links with other systems System Link-out System Link-in Mechanism Content applications WoRMS ID EoL AphiaID webservice taxonomy, distributions, sources, notes, citations WoRMS / PESI AphiaID File transfer Taxonomy, distributions, sources, environment WoRMS ID NCBI taxon AphiaID LinkOut WoRMS ID BoLD / WoRMS / EMODnet AphiaID taxamatch WoRMS ID IUCN Red List AphiaID webservice taxon name, conservation status WoRMS ID ITIS / WoRMS / WikiSpecies NL AphiaID file transfer taxonomy WoRMS ID BIOTIC AphiaID webservice Taxonomy WoRMS / Wikipedia AphiaID webservice taxonomy WoRMS name BHL / WoRMS / OBIS AphiaID taxamatch WoRMS / CoL AphiaID file transfer taxonomy, distributions, citations WoRMS ID VLIMAR AphiaID regional checklists, hierarchical search, lat/lon of placenames WoRMS ID WoRMS ID Plankton-Net IMIS AphiaID taxamatch AphiaID taxamatch taxon name, picture sharing metadata, Ref/person/inst WoRMS ID BR Meise AphiaID taxamatch Specimen image, zoom taxon name webservice taxon name taxon name, parent taxon, child taxa, synonyms, attributes file transfer webservice bibliographic metrics, #papers, pages taxonomy Conclusions • Various steps in management of biodiversity data • Several systems and services operational at Flanders Marine Institute: MDA, IMIS, WoRMS, VLIMAR, EurOBIS, EMODNET biology • Taxonomic standard critical when integrating biodiversity data • WoRMS global standard, near completion for marine organisms, use it! Obregado!