AndreaBozzo/ceres-open-data-index huggingface dataset:
EUSeaMap (2023) Broad-Scale Predictive Habitat Map for the Caspian- Confidence in classification of MSFD Benthic Broad Habitat types and EUNIS 2022 habitat types

Confidence in the classification of:
- the Marine Strategy Framework Directive (MSFD) Benthic Broad Habitat Types (V. 2017)
- the EUNIS 2022 habitat types
in the EUSeaMap (2023) broad-scale predictive habitat map for the Caspian region.

Values are 1 to 3 (1=low confidence, 2=medium confidence, 3=high confidence).

The final habitat type is classified by overlaying several layers of information; these layers of information are collectively known as 'habitat descriptors'. Habitat descriptors differ per region but include:
Biological zone
Seabed substrate

The confidence in the classification of the habitat type is taken as the minimum of the confidence in all of the relevant habitat descriptors at that location. 

Confidence values are also available for each habitat descriptor and input data layer.

Detailed information on the modelling process is found in the EMODnet Seabed Habitats technical reports and appendices (links in Resources). 

Created by the EMODnet Seabed Habitats project consortium.
Credit: Licensed under CC-BY 4.0 from the European Marine Observation and Data Network (EMODnet) Seabed Habitats initiative (www.emodnet-seabedhabitats.eu), funded by the European Commission.

It is important to note that a habitat type confidence score is only relevant to that particular level of the classification system.
Contaminants-Tributyltin: stations below LOD/LOQ v2019

This product displays the stations where tributyltin has been measured and the values present in EMODnet Chemistry infrastructure are always below the limit of detection or quantification (LOD/LOQ), i.e quality values found in EMODnet validated dataset can be equal to 6 or Q.
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
MidMedPol: Polychaetes from midlittoral rocky shores in Greece and Italy (Mediterranean Sea)

This dataset contains records of polychaetes from intertidal rocky shores in the Mediterranean Sea.
Study area description:
Rocky intertidal zone (max depth 1.5m) in Alykes (Crete, Eastern Mediterranean), Elounda (Crete, Eastern Mediterranean), Evripos channel (Euboea, Eastern Mediterranean), Thermaikos Gulf (Eastern Mediterranean, Nea Roda (North Aegean Sea, Eastern Mediterranean), Porto Karas (North Aegean Sea, Eastern Mediterranean), Zingaro (Sicily, Italy), Capo Gallo (Sicily, Italy), Balestrate (Italy)

Sampling protocol:
Some samples were collected by scraping off the surface of a 20x20 cm square, stored in plastic bags, sieved through 0.4 mm mesh size in the lab and preserved in a 4% solution of formalin and sea water. Other samples were taken according to the sampling protocol described in "Iken, K., Konar, B. 2003. Natural Geography in Nearshore Areas (NaGISA): the nearshore component of the Census of Marine Life. Gayana 67: 53-160." And other samples were taken according to the sampling protocol described in "Kitsos M.S., 2003. Contribution to the study of the biodiversity of the midlittoral and supralittoral hard substratum assemblages. Aristotle University of Thessaloniki, Phd thesis, 1-299pp."

Preparation method:
For some samples, the whole animal was fixed and preserved in 96% ethanol. For other samples, the whole animal was fixed in formalin and sea water 4%.

Quality control:
Standardization against the World Register of Marine species and recent taxonomic reviews. Subjective synonyms are kept in the dataset with their original name and a reference to the currently accepted name.

The dataset is published under a Creative Commons CCZero license
Abundances of benthic infauna from grab sediment samples as part of the INIS Hyrdo project, Co. Down (Northern Ireland), 2011

This dataset contains information on the abundance of benthic infauna species from sediment grabs collected from the South East Mourne Coast off Co. Down (Northern Ireland). This survey is part of a large project called INIS Hydro which aims to provide high resolution seabed baseline data for the coast of Ireland, Northern Ireland and Scotland using multibeam echosounders and grab samples for ground truthing. This survey was carried out in February 2011 on the RV Corystes using a 0.1m2 day grab. There were 47 grab samples taken in which infaunal analysis, Particle Size Analysis (PSA) and and Carbon - Nitrogen (C-N) analysis were carried out. The most abundant species found was the brittle star Amphiura filiformis and the most frequently recorded was the polychaete Lumbrineris cingulata.
"This dataset contains information on the abundance of benthic infauna from sediment grabs collected from the South-east Mourne Coast off Co. Down (Northern Ireland). The main aim of this survey was to contribute to the INIS Hydro project. The main aims of the project are to provide a high resolution baseline dataset of the seabed off the coast of Ireland, Northern Ireland and Scotland using a multibeam echo sounder and ground truthing methods (grab samples). The areas surveyed in this project are important in many ways e.g. important navigation channels, environnmental/conservation significance or potential sites for renewable developments, but are poorly charted. Therefore, this project aims to create accurate, updated and concise seabed maps of these important areas. In this survey there were 47 samples taken for infaunal analysis and PSA and C - N analysis. The survey was carried out on board the RV Corystes using a 0.1m2 day grab on 2011-02-16 and 2011-02-17. The methodology for the day grab is detailed below.
• A 0.1m2 day grab was used to take a sample of the sediment - associated infaunal communities.
• When the sample reaches the deck, a 250ml sample is taken for PSA and a further 25ml is taken for C - N analysis. The rest of the sample is carefully sieved to reveal any infauna.
• Fixed Formalin (4% buffered formaldehyde) is added to the remains of the sample and these are placed in labelled buckets.
• The samples are sent to accredited taxonomic laboratories were they are identified to as high a level as possible and weighed.
"
Contaminants-Lead: stations below LOD/LOQ v2019

This product displays the stations where lead has been measured and the values present in EMODnet Chemistry infrastructure are always below the limit of detection or quantification (LOD/LOQ), i.e quality values found in EMODnet validated dataset can be equal to 6 or Q.
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
‘Proof of concept’ product: Fraction of mixoplankton (photo-phagotrophic) species in the Greater North Sea and Celtic Seas

Mixoplankton (sensu Flynn et al., 2019) is a newly introduced term  indicating plankton that is capabable of both photosynthesis and  phagotrophy. More details are found in Flynn et al., (2019). The potential trophic state can be seen as an inherent characteristic of  plankton species. A literature and expert-knowledge study has provided  the classification in either phototrophy or mixotrophy which is  submitted as traits data to WoRMS. This analysis makes use of this  classification to estimate the spatial and temporal distribution of the  fraction of mixoplanktonic species in the Greater North Sea including  the Celtic Seas.

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 766327.
BY_CelticExplorer_CelticSea_14m_WGS84

Description of measurements/samples, purpose for which they were collected, and the platforms/instrumentation and methods in collection RV Celtic Explorer 2019 Leg 1 Celtic Sea North Cork 14m Globe DTM WGS 1984 projection Lowest Astronomical Tide (LAT). The GSI has been permitted to utilise the UKHO VORF (Vertical Offshore Reference Frame) sea surface model. This model allows the use of ‘GPS tides’ and the GSI has gridded this model to a 1km resolution around Ireland to 15km offshore for reducing all soundings to Lowest Astronomical Tide - LAT (VORF). By utilising ‘GPS tides’ there is no requirement to adjust for draft or squat as the water level is modelled over the seabed as measured to the WGS84 ellipsoid.  This area was surveyed as part of the ongoing INFOMAR project (formerly Irish National Seabed Survey), a joint seabed mapping project between the Geological Survey Ireland and the Marine Institute.  Survey work was conducted to standards and recommendations set out by INFOMAR, the International Hydrographic Organisation (IHO), the United Kingdom Hydrographic Office (UKHO) and the UK’s Maritime and Coastguard Agency (MCA). Please note the following:  Data acquired prior to March 2011 were levelled to Lowest Astronomical Tide (LAT) using shifts derived from Proudman Oceanographic tidal model. Tidal height was derived using a network of offshore and onshore tide gauges. As such data are on average 0.54m deeper than the more recent UKHO Vertical Offshore Reference Frame (VORF) levelled data. We are currently updating the older datasets.  Statement on the level of data processed and quality control, limitations on reliability INFOMAR bathymetry products generated to meet International Hydrographic Organization (IHO) standards to ensure gridded data positional accuracy in the horizontal (XY) and vertical (Z) frame.  Arrangement of data  Data has been processed and arranged into a GLOBE DTM grid using XYZ data.  Spatial and temporal resolution of data within the dataset  Image resolution is a 14m DTM grid.  Length of time series  Image created from data collected between 2019-09-21 and 2019-10-08  Amount of data expressed in number of stations, sites, observations, cores, months of recordings, miles of track or other units as appropriate Bathymetry image meets GLOBE DTM standard.  Data provided under Creative Commons licence access and use conditions. Users of this data should provide the following attribution statement    “Contains Irish Public Sector Data (Geological Survey Ireland; Marine Institute) licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence”
Presenza di cetacei e tartarughe marine nel Golfo di Catania, Sicilia orientale, Mar Ionio (survey 2015-2019)

Data on population size, structure, behavior and distribution of cetaceans and sea turtles in eastern Sicily, Ionian Sea, collected by expert observers of the MareCamp association in the framework of the project "Dolphin watching and conservation in the Gulf of Catania" (years 2015-2019).
The ongoing Dolphin Watching and Conservation in the Gulf of Catania project started in 2014. It integrates research, eco-tourism and dissemination activities in order to inform the local community about the presence of cetaceans and the correct code of good conduct to follow during their observation.
Surveys at sea have been conducted onboard an inflatable boat with 150 Cv along random or preset fixed transects at low speed (£6 knots) and with good weather conditions (sea lower or equal to 3 Douglas scale). During sightings, the Ad libitum sampling and the Photo-Identification methods were applied.
Collected data during monitoring activities include: date, time and geographical coordinates of survey tracks and sightings, direction and speed of navigation, direction and general behavior of the animals, species sighted (indicating the total number of individuals, juveniles and calf), ID of adult bottlenose dolphins sighted and their social relationship (catalogue of 57 photo-identified individuals "recaptured" in the years). Data on the presence of marine traffic, marine litter and fisheries activities (position and number of the boats, type of fishing gears); presence of other species like birds, fish, jellyfish; information on bottlenose dolphin-fishing gears interaction cases, diving times of dolphins and whales; meteorological conditions (wind, sea, sky, precipitation, visibility) were collected too.
First results are helping scientists and policy makers to set up appropriate measure addressed to the protection of the most threatened species and habitats in Sicily. In this framework, many university internships are carried out.

"
SHARK - National zoobenthos monitoring in Sweden since 1971

Data collected within various monitoring programmes and surveys. Standard zoobenthos techniques using benthic grabbers and species analyses for counts and weights on species level.
Zoobenthos have been monitored in Sweden since 1971. The national monitoring program was initiated by the Swedish Environmental Protection Agency and is now financed by the Swedish Agency for Marine and Water Management.
Monitoring is performed by Stockholm University, Gothenburg University, Umeå University and Linnaeus University.
Data are stored in the Swedish Ocean Archive database (SHARK), by the Swedish Meteorological and Hydrological Institute.
The purpose of the monitoring program is to detect long term and short term changes in the soft bottom macrozoobenthos (>1mm) communities. Changes in the macrofauna community can indicate changes in environmental threats like eutrophication, environmental toxins and climate change.
Data are collected and analyzed according to Leonardsson K., 2004. (In Swedish) Metodbeskrivning för provtagning och analys av mjukbottenlevande makroevertebrater I marin miljö. Umeå universitet, Institutionen för ekologi och geovetenskap, 26 p (https://www.havochvatten.se/download/18.1690613b166605675de898f4/1539942622449/rapport-umu-metodbeskrivning-provtagning-analys-mjukbottenlevande-makroevertebrater-i-marin-miljo.pdf) or similar methods. Information about the program and the methods are available in Swedish at https://www.havochvatten.se/hav/vagledning--lagar/vagledningar/ovriga-vagledningar/undersokningstyper-for-miljoovervakning/undersokningstyper/mjukbottenlevande-makrofauna-trend--och-omradesovervakning.html and https://www.havochvatten.se/hav/vagledning--lagar/vagledningar/ovriga-vagledningar/undersokningstyper-for-miljoovervakning/undersokningstyper/sediment---basundersokning.html
Data are collected and analyzed according to Leonardsson K., 2004. (In Swedish) Metodbeskrivning för provtagning och analys av mjukbottenlevande makroevertebrater I marin miljö. Umeå universitet, Institutionen för ekologi och geovetenskap, 26 p (https://www.havochvatten.se/download/18.1690613b166605675de898f4/1539942622449/rapport-umu-metodbeskrivning-provtagning-analys-mjukbottenlevande-makroevertebrater-i-marin-miljo.pdf) or similar methods.
SHARK - National Ringed seal monitoring in Sweden since 1995

Data from Swedish environmental monitoring of abundance of Ringed seal. Swedish monitoring of Ringed seals started in 1995. The monitoring program was initiated by the Swedish Environmental Protection Agency and later the Swedish Agency for Marine and Water Management took over the responsibility and financing of the program. The monitoring is performed by the Swedish Museum of Natural History. Data is stored in the database SHARK, hosted and maintained by the Swedish Meteorological and Hydrological Institute. Monitoring of ringed seal is performed by counting seals in transects from airplane. More information is available in Swedish at https://www.havochvatten.se/hav/samordning--fakta/miljoovervakning/miljoovervakningens-programomrade-kust-och-hav/delprogram-sal-och-havsorn.html
EMODnet Digital Bathymetry (DTM 2020) - Tile C7

The "EMODnet Digital Bathymetry (DTM)- 2020" is a multilayer bathymetric product for Europe’s sea basins covering:
•  the Greater North Sea, including the Kattegat and stretches of water such as Fair Isle, Cromarty, Forth, Forties,Dover, Wight, and Portland 
•  the English Channel and Celtic Seas  
•  Western Mediterranean, the Ionian Sea and the Central Mediterranean Sea 
•  Iberian Coast and Bay of Biscay (Atlantic Ocean) 
•  Adriatic Sea (Mediterranean) 
•  Aegean - Levantine Sea (Mediterranean). 
•  Madeira and Azores (Macaronesia) 
•  Baltic Sea 
•  Black Sea 
•  Norwegian and Icelandic Seas 
•  Canary Islands (Macaronesia) 
•  Arctic region and Barentz Sea

The DTM is based upon more than 16360 bathymetric survey data sets and Composite DTMs that have been gathered from 49 data providers from 24 countries riparian to European seas. Also Satellite Derived Bathymetry data products have been included derived from Landsat 8 and Sentinel satellite images. Areas not covered by observations are completed by integrating GEBCO 2020 and IBCAO V4. 
The source reference layer in the portal viewing service gives metadata of the data sets used with their data providers; the metadata also acknowledges the data originators. The incorporated survey data sets itself can be discovered and requested for access through the Common Data Index (CDI) data discovery and access service that in December 2020 contained > 30.000 survey data sets from European data providers for global waters. This discovery service makes use of SeaDataNet standards and services and have been integrated in the EMODnet portal (https://emodnet.ec.europa.eu/en/bathymetry#bathymetry-services ). The Composite DTMs are described using the Sextant Catalogue Service that makes also use of SeaDataNet standards and services. Their metadata can be retrieved through interrogating the Source Reference map in the Central Map Viewing service (https://emodnet.ec.europa.eu/geoviewer/ ). 
In addition, the EMODnet Map Viewer gives users wide functionality for viewing and downloading the EMODnet digital bathymetry such as:
• water depth (refering to the Lowest Astronomical Tide Datum - LAT) in gridded form on a DTM grid of 1/16 * 1/16 arc minute of longitude and latitude (ca 115 * 115 meters).
• option to view depth parameters of individual DTM cells and references to source data
• option to download DTM in 58 tiles in different formats: ESRI ASCII, XYZ, EMODnet CSV, NetCDF (CF), GeoTiff and SD
• option to visualize the DTM in 3D in the browser without plug-in
• layer with a number of high resolution DTMs for coastal regions
• layer with wrecks from the UKHO Wrecks database.

The EMODnet DTM is also available by means of OGC web services (WMS, WFS, WCS, WMTS), which are specified at the EMODnet Bathymetry portal.  
The original datasets themselves are not distributed but described in the metadata services, giving clear information about the background survey data used for the DTM, their access restrictions, originators and distributors and facilitating requests by users to originator.
Baltic Sea - Eutrophication and Acidity aggregated datasets 1902/2022 v2023

EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on eutrophication and acidity, and covers the Baltic Sea. Data were aggregated and quality controlled by "Swedish Meteorological and Hydrological Institute (SMHI)" in Sweden.
ITS-90 water temperature and water body salinity variables have also been included ('as are') to complete the eutrophication and acidity data. If you use these variables for calculations, please refer to SeaDataNet for the quality flags: https://www.seadatanet.org/Products/Aggregated-datasets.
Regional datasets concerning eutrophication and acidity are automatically harvested, and the resulting collections are aggregated and quality controlled using ODV Software and following a common methodology for all sea regions ( https://doi.org/10.13120/8xm0-5m67). Parameter names are based on P35 vocabulary, which relates to EMODnet Chemistry aggregated parameter names and is available at: https://vocab.nerc.ac.uk/search_nvs/P35/.
When not present in original data, water body nitrate plus nitrite was calculated by summing all nitrate and nitrite parameters. The same procedure was applied for water body dissolved inorganic nitrogen (DIN), which was calculated by summing all nitrate, nitrite, and ammonium parameters. Concentrations per unit mass were converted to a unit volume using a constant density of 1.025 kg/L.
The aggregated dataset can also be downloaded as an ODV collection and spreadsheet, which is composed of a metadata header followed by tab separated values. This spreadsheet can be imported to ODV Software for visualisation (more information can be found at: https://www.seadatanet.org/Software/ODV).