Marine Biodiversity data: an introduction on marine biodiversity data VLIZ. World Register of Marine Species

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1 Marine Biodiversity data: an introduction on marine biodiversity data VLIZ World Register of Marine Species Simon Claus Flanders Marine Institute (VLIZ)

2 InnovOcean site VLIZ Project office IODE ESF Marine Board Flanders Marine Institute (VLIZ) Ostend, Belgium Since 1999 Supported by Flemish government Objective: Support and facilitate marine sciences Important focus on biodiversity data holdings

3 Data management of biodiversity data Observations Documentation Registry & storage Integration Use/Re-use Discovery metadata Use/technical metadata Collating Structuring Standardizing Web interfaces Web services IMIS MDA EUROBIS EMODNET Quality Control Taxonomic Geographic WoRMS Gazetteer

4 IMIS Integrated Marine Information System Modular Information system: scientific institutes, experts, projects, literature, datasets... Module Datasets: ISO discovery metadata Title abstract Temporal coverage Spatial coverage Taxonomic coverage Institutes/experts involved Related publications Other details

5 IMIS Integrated Marine Information System Module Datasets Module Institutes Module Persons

6 IMIS Integrated Marine Information System Module Datasets link to Marine Data Archive

7 MDA Marine Data Archive Online backup and storage system for data files 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

8 EUROBIS European Ocean Biogeographic Information System EMODNET 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

9 WoRMS View Search by species group name (scientific, (cfr tender) common) List Filter Download Metadata EMODnet 9

10 The portal functionalities Taxonomic functionalities (WoRMS) Autocompletion taxonomic search queries Show map, include child taxa EMODnet Show map, including synonyms 10 April 12, 2012

11 The portal functionalities Data visualization EMODnet Records aggregated: increased performance, overview data density 11

12 The portal functionalities Data visualization Data distributions aggregated per grid EMODnet 12

13 The portal functionalities Data visualization EMODnet Overview data attributes from EurOBIS 13

14 The portal functionalities Data visualization EMODnet Plot modelled distribution maps from species 14

15 The portal functionalities Data visualization EMODnet Layer and metadata served from FAO server through OGC 15

16 The portal functionalities Data visualization EMODnet Combine observation data with modelled distribution maps: Data gaps / validation modelled distribution maps 16

17 The portal functionalities Data visualization Visulaize other dataproducts from Emodnet habitats, geology, chemistry, physics to portal through OGC EMODnet 17

18 VLIMAR VLIZ Marine Gazetteer Standard, relational list of geographic names Linked with information and maps of the geographic location of these features Over 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

19 VLIMAR VLIZ Marine Gazetteer

20 VLIMAR VLIZ Marine Gazetteer

21 WoRMS World Register of Marine Species

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24 WoRMS in a nutshell Started in 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)

25 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.

26 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 ).

27 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.

28 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; unique visitors; ~3M hits/month; ~5,000 unique visitors per day (excl weekends); >500 citations in Google Scholar 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).

29 All names stored locally in Aphia database 71 GSDs 10 RSDs 3 TSDs 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.

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33 Web portal

34 Web portal Scientific Name + Authority Taxon/Name status Scrutiny/record status Taxon rank Parent /Child taxon Invalid synonyms Literature sources

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36 Vernaculars 138 languages Environment + fossil flags Distributions Ecological traits Deep links (incl webservices of GenBank, BOLD, BHL) Free notes

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38 Web portal

39 Type specimens

40 Edit session LSID Citation License

41 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

42 Name validation tool: Taxon Match

43 TAXON MATCH

44 TAXON MATCH

45 TAXON MATCH

46 Examples SOAP/WSDL/REST web service

47 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

48 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 taxon name WoRMS ID BoLD / webservice taxon name WoRMS / EMODnet AphiaID taxamatch taxon name, parent taxon, child taxa, synonyms, attributes WoRMS ID IUCN Red List AphiaID webservice taxon name, conservation status WoRMS ID ITIS / file transfer WoRMS / WikiSpecies NL AphiaID file transfer taxonomy WoRMS ID BIOTIC AphiaID webservice Taxonomy WoRMS / Wikipedia AphiaID webservice taxonomy WoRMS name BHL / webservice bibliographic metrics, #papers, pages WoRMS / OBIS AphiaID taxamatch taxonomy WoRMS / CoL AphiaID file transfer taxonomy, distributions, citations WoRMS ID VLIMAR AphiaID regional checklists, hierarchical search, lat/lon of placenames WoRMS ID Plankton-Net AphiaID taxamatch taxon name, picture sharing WoRMS ID IMIS AphiaID taxamatch metadata, Ref/person/inst WoRMS ID BR Meise AphiaID taxamatch Specimen image, zoom

49 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!

50 Obregado!