Download Marine Biodiversity data: an introduction on marine

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.
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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!