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Energy, Climate change, Environment

Biology

Over 670 biodiversity datasets are accessible, including large regional survey datasets, such as the North Sea Benthos Survey

EMODnet Biology provides free access to interoperable data on temporal and spatial distribution of marine species (angiosperms, benthos, birds, fish, macroalgae, mammals, phytoplankton, reptiles, zooplankton) and species traits from European regional seas, as defined by the EEA’s Europe’s seas’ dataset (Arctic Ocean, (North) Atlantic Ocean, Baltic Sea, Black Sea, Mediterranean Sea and North Sea).

EMODnet Biologyis built upon the World Register of Marine Species (WoRMS ) and the European Ocean Biodiversity Information System (EurOBIS ), with tools and services developed in collaboration with Lifewatch ERIC and Lifewatch Marine.

Because EMODnet Biology is OGC compliant, it enables access to metadata descriptions of more than 1200 thematic biological datasets.

Due to being INSPIRE compliant these metadata records can also be found through the EU Open Data Portal.

Objectives

EMODnet Biology aims to provide a single access point to European marine biodiversity data and products. Through our interoperable products, created by assembling individual datasets from various sources, we contribute to the environmental state of ecosystems and sea basins’ assessments.

The main objective is to contribute to EMODnet’s operational service by maintaining and enhancing services for the European biodiversity data and products.

EMODnet Biology’s specific objectives are defined in the following tasks:

  1. maintaining and improving a method of access to data held in repositories;
  2. constructing products from one or more data sources that provide users with information about the distribution and quality of parameters in time and space;
  3. maintaining and improving procedures for machine-to-machine connections for all data and data products;
  4. ensuring coherence with efforts of regional sea conventions and other relevant local actors;
  5. engaging with EU reporting mechanisms;
  6. exploiting opportunities for interoperability with data distributed by non-EU organisations;
  7. actively participating in the INSPIRE Directive28 and Digital Earth29 processes and ensuring compliance.

Background

Europe’s seas and oceans are home to a staggering abundance and diversity of life, from large charismatic species such as seals, whales and dolphins, to the microscopic marine algae that form the base of the marine food chain. More than 36,000 known species of marine plants and animals are found in Europe, and understanding their geographic distribution, abundance and seasonal, annual or decadal variation is key to detecting changes in the marine ecosystem and for assessing ecosystem health of maritime basins. Unfortunately, measuring or observing marine life on a large scale is difficult.

Marine biodiversity data are essential to measure and study the ecosystem health of maritime basins. These data are often collected with limited spatial and temporal scope and are scattered over different organisations in small datasets for a specific species group or habitat. In addition, as data are collected by multiple organisations, using different standards, technologies and conventions, it is challenging to combine them. Furthermore, a plethora of historical marine biodiversity datasets exist in the form of simple and unorganised printed documents or electronic files, on the hard disks or other media of electronic information storage of individual scientists and of marine institutes, research centres, academic departments, ministries, port authorities, public or private libraries. These types of data, which are not stored on a remote server (e.g. in the cloud or a research repository), are considered to be at permanent risk of being lost to future use. It is these datasets, however, which provide the historical context for present observations, facilitating the establishment of reference conditions for monitoring and management.

History of EMODnet Biology

The Maritime Policy Blue Book, welcomed by the European Council in 2007, announced that the European Commission would take steps to set up a European Marine Observation and Data Network to improve access to high quality marine data for private bodies, public authorities and researchers.

Partnership

The reach and breadth of the EMODnet Biology consortium represents a high-level of connectivity at the national, regional and global scales. An overview and details of the Phase IV partnership can be found in the Partnership page.

As part of an exercise to better understand the linkages we have with key stakeholders and initiatives, we have undertaken to map the connections and touchpoints.
Following a targeted questionnaire to EMODnet Biology partners, we undertook work to utilise the HighCharts application (see below) to provide a visualisation of the key linkages with UN Decade Programmes, Regional Sea Conventions, ICES Working Groups and the other EMODnet thematic lots. There exist a multitude of other connections, however these are excluded for the purposes of clarity. The intention is to periodically update and refine the network map to ensure the current connectivity is reflected.

 
EMODnet Biology's key linkages with the UN Decade Programmes, Regional Sea Conventions, ICES Working Groups and the other EMODnet thematic lots.

Work Packages (WP)

Currently Biology is in it's forth phase (2021-2023) and has divided their work in five workpackages, as follow:

  • WP1: Coordination (lead partner: VLIZ);
  • WP2: Access to marine biological data (lead partner: VLIZ & HCMR);
  • WP3: Data product creation (lead partner: U Sheffield);
  • WP4: Uptake, outreach and communication (lead partner: Marine Biological Association - MBA);
  • WP5: System architecture (lead partner: VLIZ).
EMODnet Biology Phase IV WP
EMODnet Biology - Phase 4 : WP diagram

Key services

EMODnet Biology provides key services and products which allow users to search and visualise data and related data products:

Data and Products

EMODnet Biology provides access to data from a wide range of sources and actively pursues inclusion of new and historical data sets to the inventory based on careful assessment of the ease of use and fitness for purpose of the data and associated databases.

The databases feeding into EMODnet Biology contain data from all regional and sub-regional seas of Europe, as specified by the Marine Strategy Framework Directive.

To ensure interoperability, EMODnet Biology implements (and if necessary adapts) common standards and vocabularies defined and used by SeaDataNet, WoRMS (World Register of Marine Species), OBIS (Ocean Biodiversity Information System), INSPIRE, GBIF (Global Biodiversity Information Facility), Marine Regions and the Lifewatch infrastructure.

Data sources

The main data contributors are:

  • International biogeographic datasets from EurOBIS (European Ocean Biogeographic data system);
  • National monitoring programmes;
  • International monitoring campaigns (databases storing data from multiples countries within the same regional European sea);
  • International data aggregators;
  • Data archaeology:
    • datasets recovered from scientists’ personal files;
    • excel spreadsheets;
    • paper documents;
    • other formats that would otherwise be lost or inaccessible.

Data product development

EMODnet Biology’s gridded map layers of species abundance for different time windows using geospatial modelling are made available to all users. In addition, we also create spatially distributed data products specifically relevant for Marine Strategy Framework Directive Descriptor 2 (non-indigenous species).

EMODnet Biology is currently working, on the development of the following data products:

  • Implementation of a methodology to produce statistically optimized gridded map layers based on Data-Interpolating Variational Analysis (DIVA, ULg);
  • Estimation of the accuracy of the gridding procedure by comparison with validated data;
  • Complementation of the gridded map of averages with indications of the precision of the result based on the distribution of the basic data used to calculate the products;
  • Production of spatial maps of quality indicators relevant for Marine Strategy Framework Directive.

Data infrastructure

EMODnet Biology’s data infrastructure and data flow is that of EurOBIS, submitted data undergo a series of quality control procedures before being made available online:

  • Metadata;
  • Required data fields, including Taxonomy, Position, Distance from land, Units;

The data infrastructure of EMODnet Biology is able to handle different data protocols and data standards for exchange of marine biodiversity data.

  • World Register of Marine Species (WoRMS ) as taxonomic backbone;
  • Darwin Core standard used by the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS);
  • Specific data format enabling National Oceanographic Data Centers (NODC’s) to make biological data accessible using the SeaDataNet infrastructure;
  • Several OGC Webservices making accessible geospatial data:
    • Catalogue Service of the Web (CSW) for metadata resources;
    • Web Feature Service (WFS) to allow requests for geographic features across the Web;
    • Web Coverage Service (WCS) to allow requests for gridded data across the web;
    • Web Map Service (WMS) to allow requests for maps across the web.
  • Using in house developed web services. In these cases, the available data are looked at in great detail and a mapping between the available data and the Darwin Core Scheme is made allowing to capture as much data and information as possible.
  • Data submitted undergo a series of quality control procedures before being made available online.
    • Metadata: the data management team will check whether the data and the supplied metadata match and that all necessary fields are filled in correctly and as completely as possible. If important information are missing, a notification will be sent to the data provider asking for its completion.
    • Required data fields: if the required data fields are not properly filled, a notification will be sent to the data provider. The data will not be published until all required fields are complete.
    • Taxonomy: all taxon names are linked to the World Register of Marine Species (WoRMS). Unmatched taxa are sent back to the data provider for a secondary check-up. Taxa with uncertain identifications are matched to the first suitable higher taxonomic level. Originally provided taxon names are stored in the database, as this allows the possibility to go back and revisit the information. When no taxon match can be made, the name is added to an 'annotation list': this list keeps track of the editors comments on why a taxon cannot be added to the World Register of Marine Species (see also the section on standards and quality control).
    • Geography: all supplied coordinates are converted to the WSG84 coordinate system and expressed as decimal degrees. Furthermore, these coordinates are checked for positioning errors which can include sampling locations on land or in different regions than those included in the supplied metadata information. These errors can be due to accidental swapping of latitude and longitude or related to the use of the minus-sign. Any instances are communicated to the data provider, so the necessary corrections can be made.
    • Depth: two checks are performed: (1) Is the documented depth-value possible, when compared with the General Bathymetric Chart of the Oceans (GEBCO) and (2) is the documented depth-value possible, when compared with the known depth range of the species?
    • Units: if abundance and/or biomass data are supplied, the presence of the relevant units is checked. The absence of units, prevents data comparison between different datasets.

Data format

Three format options are presented to you upon downloading data:

  • Basic Occurrence: provides the user with all data necessary to do temporal spatial analysis of the different taxa.
  • Full Occurrence: provides additional information which may help interpret the basic data.
  • Full Occurrence and Parameters: provides the user with all quantitative data and facts associated to the occurrence or the sample. These parameters include both abiotic measurements (e.g. temperature, grainsize), environmental facts (e.g. habitat), biotic measurements (e.g. abundance, length), biotic descriptors (e.g. lifestage, sex) and sampling descriptors (e.g. sampling instrument, surface area). The data are standardised: measurements have been recalculated to common units and facts and descriptors standardised using controlled vocabularies

For each of these options, several essential terms are delivered. The level of detail in each file depends on the chosen option.

The box 'Biology - Data format' below, contains a list of all terms that are delivered for each option.