AndreaBozzo/ceres-open-data-index huggingface dataset:
Contaminants-Mercury: biota stations v2019

This product displays the stations present in EMODnet validated dataset where mercury levels have been measured in biota.
EMODnet Chemistry has included the gathering of contaminants data since the beginning of the project in 2009. 
For the maps for EMODnet Chemistry Phase III, it was requested to plot data per matrix (water,sediment, biota), per biological entity and per chemical substance. 
The series of relevant map products have been developed according to the criteria D8C1 of the MSFD Directive, specifically focusing on the requirements under the new Commission Decision 2017/848 (17th May 2017). The Commission Decision points to relevant threshold values that are specified in the WFD, as well as relating how these contaminants should be expressed (units and matrix etc.) through the related Directives i.e. Priority substances for Water. EU EQS Directive does not fix any threshold values in sediments. On the contrary Regional Sea Conventions provide some of them, and these values have been taken into account for the development of the visualization products.
To produce the maps the following process has been followed:
    1. Data collection through SeaDataNet standards (CDI+ODV)
    2. Harvesting, harmonization, validation and P01 code decomposition of data
    3. SQL query on data sets from point 2 
    4. Production of map with each point representing at least one record that match the criteria
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols.
Preliminary processing were necessary to harmonize all the data :
    • For water: contaminants in the dissolved phase;
    • For sediment: data on total sediment (regardless of size class) or size class < 2000 μm
    • For biota: contaminant data will focus on molluscs, on fish (only in the muscle), and on crustaceans
    • Exclusion of data values equal to 0
Contaminants-Cadmium: sediment stations v2019

This product displays the stations present in EMODnet validated dataset where cadmium levels have been measured in sediment.
EMODnet Chemistry has included the gathering of contaminants data since the beginning of the project in 2009. 
For the maps for EMODnet Chemistry Phase III, it was requested to plot data per matrix (water,sediment, biota), per biological entity and per chemical substance. 
The series of relevant map products have been developed according to the criteria D8C1 of the MSFD Directive, specifically focusing on the requirements under the new Commission Decision 2017/848 (17th May 2017). The Commission Decision points to relevant threshold values that are specified in the WFD, as well as relating how these contaminants should be expressed (units and matrix etc.) through the related Directives i.e. Priority substances for Water. EU EQS Directive does not fix any threshold values in sediments. On the contrary Regional Sea Conventions provide some of them, and these values have been taken into account for the development of the visualization products.
To produce the maps the following process has been followed:
    1. Data collection through SeaDataNet standards (CDI+ODV)
    2. Harvesting, harmonization, validation and P01 code decomposition of data
    3. SQL query on data sets from point 2 
    4. Production of map with each point representing at least one record that match the criteria
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols.
Preliminary processing were necessary to harmonize all the data :
    • For water: contaminants in the dissolved phase;
    • For sediment: data on total sediment (regardless of size class) or size class < 2000 μm
    • For biota: contaminant data will focus on molluscs, on fish (only in the muscle), and on crustaceans
    • Exclusion of data values equal to 0
Contaminants-Mercury: stations above LOD/LOQ v2019

This product displays the stations where mercury has been measured and the values present in EMODnet Chemistry infrastructure are always above the limit of detection or quantification (LOD/LOQ), i.e quality value equal to 1.
It is necessary to take into account that LOD/LOQ can change with time. These products aggregate data by station, producing only one final value for each station (above, below or above/below).  
EMODnet Chemistry has included the gathering of contaminants data since the beginning of the project in 2009. 
For the maps for EMODnet Chemistry Phase III, it was requested to plot data per matrix (water,sediment, biota), per biological entity and per chemical substance. 
The series of relevant map products have been developed according to the criteria D8C1 of the MSFD Directive, specifically focusing on the requirements under the new Commission Decision 2017/848 (17th May 2017). The Commission Decision points to relevant threshold values that are specified in the WFD, as well as relating how these contaminants should be expressed (units and matrix etc.) through the related Directives i.e. Priority substances for Water. EU EQS Directive does not fix any threshold values in sediments. On the contrary Regional Sea Conventions provide some of them, and these values have been taken into account for the development of the visualization products.
To produce the maps the following process has been followed:
    1. Data collection through SeaDataNet standards (CDI+ODV)
    2. Harvesting, harmonization, validation and P01 code decomposition of data
    3. SQL query on data sets from point 2 
    4. Production of map with each point representing at least one record that match the criteria
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols.
Preliminary processing were necessary to harmonize all the data :
    • For water: contaminants in the dissolved phase;
    • For sediment: data on total sediment (regardless of size class) or size class < 2000 μm
    • For biota: contaminant data will focus on molluscs, on fish (only in the muscle), and on crustaceans
    • Exclusion of data values equal to 0
Contaminants-Lead: biota stations v2019

This product displays the stations present in EMODnet validated dataset where lead levels have been measured in biota.
EMODnet Chemistry has included the gathering of contaminants data since the beginning of the project in 2009. 
For the maps for EMODnet Chemistry Phase III, it was requested to plot data per matrix (water,sediment, biota), per biological entity and per chemical substance. 
The series of relevant map products have been developed according to the criteria D8C1 of the MSFD Directive, specifically focusing on the requirements under the new Commission Decision 2017/848 (17th May 2017). The Commission Decision points to relevant threshold values that are specified in the WFD, as well as relating how these contaminants should be expressed (units and matrix etc.) through the related Directives i.e. Priority substances for Water. EU EQS Directive does not fix any threshold values in sediments. On the contrary Regional Sea Conventions provide some of them, and these values have been taken into account for the development of the visualization products.
To produce the maps the following process has been followed:
    1. Data collection through SeaDataNet standards (CDI+ODV)
    2. Harvesting, harmonization, validation and P01 code decomposition of data
    3. SQL query on data sets from point 2 
    4. Production of map with each point representing at least one record that match the criteria
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols.
Preliminary processing were necessary to harmonize all the data :
    • For water: contaminants in the dissolved phase;
    • For sediment: data on total sediment (regardless of size class) or size class < 2000 μm
    • For biota: contaminant data will focus on molluscs, on fish (only in the muscle), and on crustaceans
    • Exclusion of data values equal to 0
Contaminants-Cadmium: stations above/below LOD/LOQ v2019

This product displays the stations where cadmium has been measured and the values present in EMODnet Chemistry infrastructure are either above or below the limit of detection or quantification (LOD/LOQ), i.e for the substance, in that station, quality values found in EMODnet validated dataset can be equal to 6, Q or 1.
It is necessary to take into account that LOD/LOQ can change with time. These products aggregate data by station, producing only one final value for each station (above, below or above/below).  
EMODnet Chemistry has included the gathering of contaminants data since the beginning of the project in 2009. 
For the maps for EMODnet Chemistry Phase III, it was requested to plot data per matrix (water,sediment, biota), per biological entity and per chemical substance. 
The series of relevant map products have been developed according to the criteria D8C1 of the MSFD Directive, specifically focusing on the requirements under the new Commission Decision 2017/848 (17th May 2017). The Commission Decision points to relevant threshold values that are specified in the WFD, as well as relating how these contaminants should be expressed (units and matrix etc.) through the related Directives i.e. Priority substances for Water. EU EQS Directive does not fix any threshold values in sediments. On the contrary Regional Sea Conventions provide some of them, and these values have been taken into account for the development of the visualization products.
To produce the maps the following process has been followed:
    1. Data collection through SeaDataNet standards (CDI+ODV)
    2. Harvesting, harmonization, validation and P01 code decomposition of data
    3. SQL query on data sets from point 2 
    4. Production of map with each point representing at least one record that match the criteria
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols.
Preliminary processing were necessary to harmonize all the data :
    • For water: contaminants in the dissolved phase;
    • For sediment: data on total sediment (regardless of size class) or size class < 2000 μm
    • For biota: contaminant data will focus on molluscs, on fish (only in the muscle), and on crustaceans
    • Exclusion of data values equal to 0
North East Atlantic Ocean - Seafloor litter aggregated datasets 2006/2023 v2024

EMODnet Chemistry aims to provide access to marine chemistry data sets and derived data products concerning eutrophication, ocean acidification, contaminants and litter. The chosen parameters are relevant for  the Marine Strategy Framework Directive (MSFD), in particular for descriptors 5, 8, 9 and 10. The datasets contain standardized, harmonized and validated data collections from seafloor litter. 
Datasets concerning seafloor litter data are loaded in a central database after a semi-automated validation phase. Once loaded, a data assessment is performed in order to check data consistency and potential errors are corrected thanks to a feedback loop with data originators.
EMODnet seafloor litter data and database are hosted and maintained by ‘Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Division of Oceanography (OGS/NODC)’ from Italy.
For seafloor litter, the harmonized datasets contain all unrestricted EMODnet Chemistry data on seafloor litter data.
Data are formatted following Guidelines and forms for gathering marine litter data, which can be found at: https://dx.doi.org/10.6092/15c0d34c-a01a-4091-91ac-7c4f561ab508
The updated vocabularies of admitted values are available at:
https://vocab.seadatanet.org/search
https://vocab.ices.dk/
The harmonized datasets can be downloaded as EMODnet Sea-floor litter data format version 1.0, which is a csv file, tab separated values.
Beach litter - Median number of plastic bags related items normalized per 100m & to 1 survey - Other sources 2001/2021 v2023

This visualization product displays the plastic bags abundance of marine macro-litter (> 2.5cm) per beach per year from non-MSFD monitoring surveys, research & cleaning operations.


EMODnet Chemistry included the collection of marine litter in its 3rd phase. Since the beginning of 2018, data of beach litter have been gathered and processed in the EMODnet Chemistry Marine Litter Database (MLDB).
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols and reference lists used on a European scale.


Preliminary processing were necessary to harmonize all the data:
		- Exclusion of OSPAR 1000 protocol: in order to follow the approach of OSPAR that it is not including these data anymore in the monitoring;
		- Selection of surveys from non-MSFD monitoring, cleaning and research operations;
		- Exclusion of beaches without coordinates;
		- Selection of plastic bags related items only. The list of selected items is attached to this metadata. This list was created using EU Marine Beach Litter Baselines and EU Threshold Value for Macro Litter on Coastlines from JRC (these two documents are attached to this metadata);
		- Exclusion of surveys without associated length;
		- Normalization of survey lengths to 100m & 1 survey / year: in some case, the survey length was not 100m, so in order to be able to compare the abundance of litter from different beaches a normalization is applied using this formula:
		Number of plastic bags related items of the survey (normalized by 100 m) = Number of plastic bags related items of the survey x (100 / survey length)
		Then, this normalized number of plastic bags related items is summed to obtain the total normalized number of plastic bags related items for each survey. Finally, the median abundance of plastic bags related items for each beach and year is calculated from these normalized abundances of plastic bags related items per survey.

Percentiles 50, 75, 95 & 99 have been calculated taking into account plastic bags related items from other sources data for all years.


More information is available in the attached documents.


Warning: the absence of data on the map doesn't necessarily mean that they don't exist, but that no information has been entered in the Marine Litter Database for this area.
Beach Litter - Median number of plastic bags related items normalized per 100m & to 1 survey - Other sources 2001/2020 v2021

This visualization product displays the plastic bags abundance of marine macro-litter (> 2.5cm) per beach per year from non-MSFD monitoring surveys, research & cleaning operations.


EMODnet Chemistry included the collection of marine litter in its 3rd phase. Since the beginning of 2018, data of beach litter have been gathered and processed in the EMODnet Chemistry Marine Litter Database (MLDB).
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols and reference lists used on a European scale.


Preliminary processing were necessary to harmonize all the data:
		- Exclusion of OSPAR 1000 protocol: in order to follow the approach of OSPAR that it is not including these data anymore in the monitoring;
		- Selection of surveys from non-MSFD monitoring, cleaning and research operations;
		- Exclusion of beaches without coordinates;
		- Selection of plastic bags related items only. The list of selected items is attached to this metadata. This list was created using EU Marine Beach Litter Baselines and EU Threshold Value for Macro Litter on Coastlines from JRC (these two documents are attached to this metadata);
		- Exclusion of surveys without associated length;
		- Normalization of survey lengths to 100m & 1 survey / year: in some case, the survey length was not 100m, so in order to be able to compare the abundance of litter from different beaches a normalization is applied using this formula:
		Number of plastic bags related items of the survey (normalized by 100 m) = Number of plastic bags related items of the survey x (100 / survey length)
		Then, this normalized number of plastic bags related items is summed to obtain the total normalized number of plastic bags related items for each survey. Finally, the median abundance of plastic bags related items for each beach and year is calculated from these normalized abundances of plastic bags related items per survey.

Percentiles 50, 75, 95 & 99 have been calculated taking into account plastic bags related items from other sources data for all years.


More information is available in the attached documents.


Warning: the absence of data on the map doesn't necessarily mean that they don't exist, but that no information has been entered in the Marine Litter Database for this area.
Micro litter - Size of litter per net - Other specific protocols 2011/2021 v2023

This visualization product displays the size of litter in percent per net per year from specific protocols different from research and monitoring protocols.
EMODnet Chemistry included the collection of marine litter in its 3rd phase. Before 2021, there was no coordinated effort at the regional or European scale for micro-litter. Given this situation, EMODnet Chemistry proposed to adopt the data gathering and data management approach as generally applied for marine data, i.e., populating metadata and data in the CDI Data Discovery and Access service using dedicated SeaDataNet data transport formats. EMODnet Chemistry is currently the official EU collector of micro-litter data from Marine Strategy Framework Directive (MSFD) National Monitoring activities (descriptor 10).
A series of specific standard vocabularies or standard terms related to micro-litter have been added to SeaDataNet NVS (NERC Vocabulary Server) Common Vocabularies to describe the micro-litter.
European micro-litter data are collected by the National Oceanographic Data Centres (NODCs). Micro-litter map products are generated from NODCs data after a test of the aggregated collection including data and data format checks and data harmonization.

A filter is applied to represent only micro-litter sampled according to a very specific protocol such as the Volvo Ocean Race (VOR) or Oceaneye.

To calculate percentages for each size, formula applied is:
Size (%) = (∑number of particles of each size)*100 / (∑number of particles of all size)
When the number of microlitters was not filled or zero, the percentage could not be calculated.

Standard vocabularies for microliter sizes are taken from Seadatanet's H03 library (https://vocab.seadatanet.org/v_bodc_vocab_v2/search.asp?lib=H03)

Warning: the absence of data on the map doesn't necessarily mean that they don't exist, but that no information has been entered in the National Oceanographic Data Centre (NODC) for this area.
Micro litter - Density per net normalized in grams per km² - Research and monitoring protocols 2011/2023 v2025

This visualization product displays the density of floating micro-litter per net normalized in grams per km² per year from research and monitoring protocols.
EMODnet Chemistry included the collection of marine litter in its 3rd phase. Before 2021, there was no coordinated effort at the regional or European scale for micro-litter. Given this situation, EMODnet Chemistry proposed to adopt the data gathering and data management approach as generally applied for marine data, i.e., populating metadata and data in the CDI Data Discovery and Access service using dedicated SeaDataNet data transport formats. EMODnet Chemistry is currently the official EU collector of micro-litter data from Marine Strategy Framework Directive (MSFD) National Monitoring activities (descriptor 10).
A series of specific standard vocabularies or standard terms related to micro-litter have been added to SeaDataNet NVS (NERC Vocabulary Server) Common Vocabularies to describe the micro-litter.
European micro-litter data are collected by the National Oceanographic Data Centres (NODCs). Micro-litter map products are generated from NODCs data after a test of the aggregated collection including data and data format checks and data harmonization.

A filter is applied to represent only micro-litter sampled according to research and monitoring protocols as MSFD monitoring.

Densities were calculated for each net using the following calculation:
Density (weight of particles per km²) = Micro-litter weight / (Sampling effort (km) * Net opening (cm) * 0.00001)

When information about the sampling effort (km) was lacking and point coordinates were known (start and end of the sampling), the sampling effort was calculated using the PostGIS ST_DistanceSpheroid function with a WGS84 measurement spheroid.
When the weight of microlitters or the net opening was not filled, it was not possible to calculate the density.

Percentiles 50, 75, 95 & 99 have been calculated taking into account data for all years.

Warning: the absence of data on the map does not necessarily mean that they do not exist, but that no information has been entered in the National Oceanographic Data Centre (NODC) for this area.
Beach litter - Median number of cigarette related items normalized per 100m & to 1 survey - without UNEP_MARLIN - EU-MSFD monitoring 2001/2022 v2023

This visualization product displays the cigarette related items abundance of marine macro-litter (> 2.5cm) per beach per year from Marine Strategy Framework Directive (MSFD) monitoring surveys without UNEP-MARLIN data.


EMODnet Chemistry included the collection of marine litter in its 3rd phase. Since the beginning of 2018, data of beach litter have been gathered and processed in the EMODnet Chemistry Marine Litter Database (MLDB).
The harmonization of all the data has been the most challenging task considering the heterogeneity of the data sources, sampling protocols and reference lists used on a European scale.


Preliminary processing were necessary to harmonize all the data:
		- Exclusion of OSPAR 1000 protocol: in order to follow the approach of OSPAR that it is not including these data anymore in the monitoring;
		- Selection of MSFD surveys only (exclusion of other monitoring, cleaning and research operations);
		- Exclusion of beaches without coordinates;
		- Selection of cigarette related items only. The list of selected items is attached to this metadata. This list was created using EU Marine Beach Litter Baselines and EU Threshold Value for Macro Litter on Coastlines from JRC (these two documents are attached to this metadata);
		- Exclusion of surveys referring to the UNEP-MARLIN list: the UNEP-MARLIN protocol differs from the other types of monitoring in that cigarette butts are surveyed in a 10m square. To avoid comparing abundances from very different protocols, the choice has been made to distinguish in two maps the cigarette related items results associated with the UNEP-MARLIN list from the others;
		- Normalization of survey lengths to 100m & 1 survey / year: in some case, the survey length was not exactly 100m, so in order to be able to compare the abundance of litter from different beaches a normalization is applied using this formula:
		Number of cigarette related items of the survey (normalized by 100 m) = Number of cigarette related items of the survey x (100 / survey length)
		Then, this normalized number of cigarette related items is summed to obtain the total normalized number of cigarette related items for each survey. Finally, the median abundance of cigarette related items for each beach and year is calculated from these normalized abundances of cigarette related items per survey.
		Sometimes the survey length was null or equal to 0. Assuming that the MSFD protocol has been applied, the length has been set at 100m in these cases.
		
Percentiles 50, 75, 95 & 99 have been calculated taking into account cigarette related items from MSFD monitoring data (excluding UNEP-MARLIN protocol) for all years.


More information is available in the attached documents.


Warning: the absence of data on the map doesn't necessarily mean that they don't exist, but that no information has been entered in the Marine Litter Database for this area.