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Energy, Climate change, Environment

Biology

Product published during Phase IV: Temporal Turnover in European Macrobenthos Communities (Webb, T.J. (2023)). View the map in the EMODnet map viewer.

EMODnet Biology provides open and free access to interoperable data and data products 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 Biology's taxonomic backbone is built upon the World Register of Marine Species (WoRMS ) and supported by the European Ocean Biodiversity Information System (EurOBIS ) data infrastructure, 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 1,200 thematic biological datasets. Due to being INSPIRE compliant these metadata records can also be found through the EU Open Data Portal. Our data and metadata follow the FAIR principles  and we continuously work on improving the Findability, Accessibility, Interoperability and Reusability for all records and data.

Objectives

EMODnet Biology aims to provide a single access point to European marine biodiversity data and products collected in the European regional seas, as defined by the EEA’s Europe’s seas dataset as well as the Caribbean Sea. 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:

  • Task 1: Maintain and improve a common method of access to data held in repositories;
  • Task 2: Construct products from one or more data sources that provide users with information about the distribution and quality of parameters in time and space;
  • Task 3: Develop procedures for machine-to-machine connections to data and data Products;
  • Task 4: Contribute data, data products and content to EMODnet Central Portal that allows users to find, view and download data and data products;
  • Task 5: Contributing static content to dedicated spaces in the Central Portal;
  • Task 6: Ensure the involvement of Regional Sea Conventions (RSC)
  • Task 7: Contribute to the implementation of the EU legislation and broader initiatives for open data;
  • Task 8: Monitor quality/performance and deal with user feedback.

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, in Phase IV (2021-2023), to better understand the linkages we have with key stakeholders and initiatives, we have created a map with the connections and touchpoints. This was done, following a targeted questionnaire to EMODnet Biology partners, we then used 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. In Phase V we plan to update this connectivity map with the current consortium and add other relevant connections to initiatives and/or programmes.

 
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)

Phase V started in May 2023 and will run until May 2025, the workplan is divided in five work packages, as follows:

  • WP1: Coordination (lead partner: VLIZ);
  • WP2: Data Management (lead partner: VLIZ);
  • WP3: Data Products (lead partner: INRAE);
  • WP4: Uptake and Outreach (lead partner: OGS);
  • WP5: Technical Infrastructure (lead partner: VLIZ).
EMODnet Biology Phase IV WP
EMODnet Biology Phase V: 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 the inclusion of new and historical datasets 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;
  • Citizen science;
  • 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 Timestamp, Position, Taxonomy, Provenance, Parameters, Units, among others.

The data infrastructure of EMODnet Biology is able to handle different data protocols and data standards for exchange of marine biodiversity data (e.g. specific data format enabling National Oceanographic Data Centres (NODC’s) to make biological data accessible using the SeaDataNet infrastructure) and adheres to:

  • Darwin Core standard used by the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS);
  • 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.
  • In-house developed web services where the available data are looked at in great detail and a mapping between the data and the Darwin Core Scheme is made allowing to capture as much data and information as possible.

While using controlled vocabularies like:

Submitted data undergo a series of quality control procedures before being made available online. These procedures focus on:

  • Metadata: the data management team checks 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 is missing, a request will be sent to the data provider asking for its completion.
  • Required data fields: if the required Darwin Core data fields are not properly filled, a notification will be sent to the data provider to complete them. 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. Taxon names provided by data originators 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', which 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 metadata information supplied. These errors can be due to accidental swapping of latitude and longitude or related to the use of the minus-sign. All instances found are communicated to the data provider, in order for the necessary corrections to 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, biomass data or other associated measurements or facts are supplied, the presence of the relevant units is checked. The absence of units, prevents data comparison between different datasets.

Data format

With the EMODnet centralisation several changes impacted the way EMODnet Biology exposes its data. One of the most relevant ones is the data access via the EMODnet Viewer. In Phase V we will continue to work on improving the data access and implementing various filters (e.g. Data source, Time period, Species Traits, Taxonomic grouping as per tender requirements, Parameter filters, etc.) allowing users with a better search capability of the data relevant for their work. The data will be made available as csv files where both the biological occurrences as well as associated parameters are included.

A description of the different fields contained in the output file is described below:

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