AndreaBozzo/ceres-open-data-index huggingface dataset:
Cymodocea nodosa in the slovenian coastal area

In the Mediterranean region Cymodocea nodosa is widely distributed throughout shallow sites. Therefore, a correct assessment of the status of its meadows is of great importance for the implementation of the Water Framework Directive (WFD), the Marine Strategy Framework Directive (MSFD), and the Habitat Directive (HD), especially for areas where Posidonia oceanica meadows (the most frequently used indicator in the Mediterranean Sea) are rare or not present. The previously proposed index for the evaluation of the status of C. nodosa meadows (CymoSkew) is based on ln-transformed relative frequencies of photosynthetic leaf lengths, which we believe is statistically questionable. Therefore, we further improved the methodology and developed a new index named MediSkew, where ln-transformation is applied to raw data of leaf lengths. More specifically, the index is a combination of two metrics, both based on C. nodosa leaf length: deviation from the reference median length (Medi-) and skewness of the length frequency distribution (-Skew), though greater importance was assigned to the first. To develop the classification criteria for the assessment of the status, also a Pressure Index for Seagrass Meadows (PISM), for the evaluation of pressure–impact relationships, was developed. The MediSkew is meant to be a rapid screening method for wide areas, therefore the index should be tested for the assessment of the status of C. nodosa meadows throughout Mediterranean coastal waters.

Martina Orlando-Bonaca, Janja Francé, Borut Mavric, Mateja Grego, Lovrenc Lipej, Vesna Flander-Putrle, Milijan Šiško, Annalisa Falace,
A new index (MediSkew) for the assessment of the Cymodocea nodosa (Ucria) Ascherson meadow's status, Marine Environmental Research, Volume 110, 2015, Pages 132-141, ISSN 0141-1136, 
https://doi.org/10.1016/j.marenvres.2015.08.009.
(http://www.sciencedirect.com/science/article/pii/S0141113615300374)
Phytoplankton dataset from the Lionceau and DYFAMED sediment traps

This dataset comprises results for the phytoplankton community structure and fluxes as recorded by two sediment trap series from the NW Mediterranean Sea between approximately 2010 and 2020. The sediment trap of the DYFAMED mooring site is located at 43.25°N, 7.52°E; it is a PPS-5 Technicap positioned at a depth of 1000m. The Lionceau sediment trap is located at 42.01°N, 4.8° E inside the winter deep convection zone of the NW Mediterranean. It is a Technicap PPS-3 sediment trap located at a depth of 2400m. Samples from the sediment trap series were imaged using automated microscopy methods. The image datasets were processed using a deep learning-based workflow, including a step for object detection and a second step for particle classification. This workflow yielded class counts for a total of thirteen morphospecies of coccoliths, seven morphospecies of diatoms, two dinoflagellates (one calcareous, the other siliceous) and two silicoflagellate morphospecies in the two sediment trap series. It also yielded estimates for major axis length for each particle. The results presented in this dataset include class-specific particle fluxes to the trap, class-specific contributions to the total assemblage, class-specific average major axis length, and, for the different coccolith classes, class-specific calcite fluxes to the trap.
Important Note: This submission has been initially submitted to SEA
scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI.
The metadata elements have been further processed (refined) in EMODnet
Ingestion Service in order to conform with the Data Submission Service
specifications.
EMODnet Physics - Platforms

In situ data as recorded by platforms (tide gauges, river stations, CTDs, and other platform types), including time-series, profiles and datasets. Each marker on the map represents a measuring platform interoperating with EMODnet Physics. The product integrates near real-time and delayed mode data from major marine and oceanographic initiatives and data repositories (EuroGOOS ROOS, Copernicus Marine Service INSTAC, SeaDataNet NODCs, ICES, PANGAEA).
Metadata are available for download via WFS in GeoJSON format.

Last data update: Continuously updated
Black Sea - DIVAnd 4D 6-year seasonal analysis of Water body dissolved inorganic nitrogen 1990/2021 v2023

Moving 6-year analysis of Water body dissolved inorganic nitrogen in Black Sea for each season: winter (December-February), spring (March-May), summer (June-August), autumn (September-November). Every year of the time dimension corresponds to the 6-year centered average of the season. 6-years periods span from 1990-1995 until 2016-2021.
Data Sources: observational data from SeaDataNet/EMODNet Chemistry Data Network.
Units: umol/l.
DIVA analysis: The computation was done with the DIVAnd (Data-Interpolating Variational Analysis in n dimensions), version 2.7.9, using GEBCO 30sec topography for the spatial connectivity of water masses.
The horizontal resolution of the produced DIVAnd maps grids is 0.05 degrees.
The vertical resolution is 12 depth levels: 0, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100m.
The horizontal correlation length: 80km.
The vertical correlation length (in meters):  twice the vertical resolution (10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20).
The error variance (epsilon2): 1 
An anamorphosis transformation was applied to the data: threshold value=200.
Background field: not used.
Quality control of the observations was applied using the interpolated field: QCMETHOD=3 and visual inspection (Observations with residuals outside the minimum and maximum values of the 99% quantile were discarded from the analysis after thoroughly visual inspection).
Plankton community in Régent (680µm) net, Point B, Villefranche-sur-Mer, France

This series is part of the long term planktonic monitoring of Villefranche-sur-mer, which is one of the oldest and richest in the world. It aims at describing the dynamics of the mesozooplankton community. The data collection and processing has been funded by several projects over its lifetime. It is currently supported directly by the Institut de la Mer de Villefranche (IMEV), as part of its long term monitoring effort. This dataset contains the planktonic organisms collected by a Régent net (680μm mesh) and therefore cover organisms from ~700µm to ~5cm.
"Régent net (680μm mesh) hauled vertically from the bottom (~80m) to the surface, in the morning.
Sample preserved in 4% buffered formalin and stored over the long term at the Centre de Collections Planctoniques de Villefranche (CCPv).
Sample scanned on a ZooScan, images processed with ZooProcess and sorted taxonomically on EcoTaxa, within the Plateforme d'Imagerie Quantitative de Villefranche (PIQv).
The PIQv and CCPv platforms are part of EMBRC-France, a national Research Infrastructure supported by ANR, under the reference ANR-10-INSB-02.
EMODnet Digital Bathymetry (DTM 2024) - Tile G7

The "EMODnet Digital Bathymetry (DTM)- 2024" 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 22032 bathymetric survey data sets and Composite DTMs that have been gathered from 66 data providers from 28 countries riparian to European seas and beyond. Also Satellite Derived Bathymetry data products have been included fro Landsat 8 and Sentinel satellite images. Areas not covered by observations are completed by integrating GEBCO 2024 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 contains > 41.000survey data sets from European data providers for global waters. The Composite DTMs can be discovered through the Sextant Catalogue service. Both discovery services make use of SeaDataNet standards and services and have been integrated in the EMODnet portal (https://emodnet.ec.europa.eu/en/bathymetry#bathymetry-services ).
In addition, the EMODnet Map Viewer (https://emodnet.ec.europa.eu/geoviewer/ ) 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 59 tiles in different formats: ESRI ASCII, XYZ, EMODnet CSV, NetCDF, 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.
2489_20241121-HRDTM-Alboran-60m

This composite Digital Terrain Model (cDTM) is a high resolution bathymetry dataset that covers STRENGTH, OASIS ans SEAQUAKE cruises. Multibeam data acquired in 2022 and 2023 on board the R/V Sarmiento de Gamboa, RV Pelagia and R/V Belgica.
OceanCare cetacean sightings in Sicily, Italy 2016-2019

This dataset comprises the work carried out by OceanCare in the waters east and north of Sicily, Italy between 2016-2019. The project was dedicated to survey cetacean populations in these waters. Cetacean spatial and temporal distribution is studied using boat-based surveys.
Original provider: OceanCare Dataset credits: Silvia Frey, OceanCare Purpose: OceanCare is a non-profit and non-governmental organization founded in 1989 in Switzerland. The organization is dedicated to the protection of marine mammals and the conservation of the marine environment. The association works at national and international level in the areas of whaling, industrial fishing, environmental changes, seal hunting, dolphin captivity, and cetacean research. OceanCare has the Special Consultative Status with the Economic and Social Council of the United Nations and is a partner of the UNEP/CMS Agreement on the Conservation of Cetaceans in the Black Sea, Mediterranean Sea and Contiguous Atlantic Area (ACCOBAMS). With this cetacean monitoring project OceanCare provides long-term data on cetacean abundance in the Mediterranean Sea.
Zoological Museum Amsterdam, University of Amsterdam (NL) - Mollusca_Pectinoidea

Currently the molluscan collection of ZMA consists of over 12.000 samples (ca. 50.000 specimens) of Pectinoidea (ca. 10.800 Pectinidae and ca. 1450 Propeamussiidae samples) of which 143 type samples (69 type lots of Pectinidae and 74 type lots of Propeamussiidae), all (re)identified and digitilized by Henk H. Dijkstra (The Netherlands). The major part (8345 samples) of this collection is donated by Dijkstra to ZMA. The remaining part is from different sources, i.e. from private donations, exchanges, scientific cruises and expeditions. Nearly all the recent species of Pectinidae (ca. 300 species) and Propeamussiidae (ca. 100 species) are represented. Most of the Pectinidae species are collected by private collectors or by fishermen from the tidal zone to upper bathyal depths, whereas Propeamussiidae are mostly sampled from bathyal depths by the Siboga expedition and the recent French expeditions to the tropical Indo-Pacific.
The molluscs collection (IM) of the Muséum national d'Histoire naturelle (MNHN - Paris)

The collection of marine, terrestrial and freshwater molluscs is primarily a scientific but also a historical and museological collection. It includes about 800 000 lots, totaling approximately 5 million specimens from around the world. These specimens are preserved as either dry specimens (dried animals, shells) or in alcohol. The type collection contains 11 000 types of nominal species. The collection dates back to Michel Adanson (shells of Senegal, 1757) and Jean-Baptiste Lamarck.
The collection increased through donations of amateur collectors, institutional legacies and purchases, and the activity of scientists from both the Museum and other institutions. This diversity of sources continues today, but large expeditions have been very important from the late eighteenth century through to the colonial era, a role they continue to play to this day. The "Tropical Deep-Sea benthos" oceanographic expeditions (formerly MUSORSTOM), launched in the early 1980s to sample the benthos of the tropical South and West-Pacific, have resulted in the collection becoming the best in the world for deep-sea faunas (100-1.500 m bathymetric zone). It is particularly rich in micromolluscs. Historical sections of the collection contain representatives of terrestrial and freshwater molluscs that are now extinct.
Seafloor pressure data from two SBE53 pressure gauges on EMSO-Azores observatory, 2018-2019

This dataset contains seafloor pressure data acquired in the framework of EMSO-Azores observatory between August 2018 and June 2019 using a SBE53 pressure gauges deployed on two sites. West site : The sensor was deployed on an existing benchmark installed with the submersible Nautile in August 2006 during the GRAVILUCK cruise (https://doi.org/10.17600/6010110). The benchmark sits on hard substratum with light hydrothermal sedimentation, on the North-West border of the Lucky Strike lava lake, next to a hydrothermal site. East site : The sensor was deployed on an existing benchmark installed by freefall in July 2007 during the MOMARDREAM cruise (https://doi.org/10.17600/7030060). The benchmark sits in the axial valley, East of the LuckyStrike volcano in a lightly sedimented area, with apparent pillow lavas. Instrument location bathymetric map Image Reference: https://www.seanoe.org/data/00654/76598/illustrations/illustration-96.gif.  
Important Note: This submission has been initially submitted to SEA
scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI.
The metadata elements have been further processed (refined) in EMODnet
Ingestion Service in order to conform with the Data Submission Service
specifications.
North Cyprus 2015 - Green Turtles (aggregated per 1-degree cell)

The MTCP have placed 22 satellite trackers on green turtles since 1998 which have revealed several major foraging areas within the Mediterranean. However, recent research using stable isotope analysis suggest that an important foraging area may have been missed due to chance. Therefore, MTCP have taken the opportunity to attach satellite trackers to 5 turtles which the stable isotopes suggest forage in the area of interest.
Original provider: Marine Turtle Research Group Dataset credits: Data provider Marine Turtle Research Group Originating data center Satellite Tracking and Analysis Tool (STAT) Project partner Society for Protection of Turtles (SPOT) was founded in the late 1980s by British expatriates Ian and Celia Bell who came together with local conservationist Kutlay Keço. In 1988 a preliminary field study was carried out by Brian Groombridge and Claire Whitmore and SPOT later made further surveys of the North Cyprus coast and found numbers of nesting green and loggerhead turtles sufficient to merit further investigation. In the early 1990s SPOT contacted Glasgow University and in 1992 the first pioneering team of students were sent to make a thorough survey. On the basis of this expedition, Kutlay agreed to provide accommodation on his land at Alagadi, and this became the Alagadi Goat Shed and Sleeping House, which twenty years on are still used by the Marine Turtle Conservation Project (MTCP) as the hub of research and conservation of turtles in North Cyprus. MTCP is a collaboration between the University of Exeter's Marine Turtle Research Group, SPOT and the North Cyprus Department for Environmental Protection. Supplemental information: Visit STAT's project page for additional information. This dataset is a summarized representation of the telemetry locations aggregated per species per 1-degree cell.
3288_Mineplat_HR_C - Alentejo shelf - folded structures & sorted bedforms- 4m res.

High resolution (1/512 minute ~ 3.6m) bathymetry dataset from the Mineplat 4 cruise onboard IPMA RV Noruega. Portugal southern continental shelf, off Alentejo coast,  24 March to 4 April 2019. Depths between 60 and 110m.
Seabed sediments sampling was performed during daytime and multibeam mapping during the night, with a Reson T50-P multibeam echosounder. Depths are referenced to the Portuguese Chart Datum (2m below MSL) and  WGS84 horizontal reference frame. Position and attitude data (GNSS+Inertial via Applanix OceanMaster POSMV) was post-processed with POSPAC.
Contaminants-Naphthalene: sediment stations v2019

This product displays the stations present in EMODnet validated dataset where naphthalene 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
EMODnet Digital Bathymetry (DTM 2022) - Tile G6

The "EMODnet Digital Bathymetry (DTM)- 2022" 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 21937 bathymetric survey data sets and Composite DTMs that have been gathered from 64 data providers from 28 countries riparian to European seas and beyond. Also Satellite Derived Bathymetry data products have been included fro Landsat 8 and Sentinel satellite images. Areas not covered by observations are completed by integrating GEBCO 2022 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 2022 contained > 41.000survey data sets from European data providers for global waters. The Composite DTMs can be discovered through the Sextant Catalogue service. Both discovery services make use of SeaDataNet standards and services and have been integrated in the EMODnet portal (https://emodnet.ec.europa.eu/en/bathymetry#bathymetry-services ).
In addition, the EMODnet Map Viewer (https://emodnet.ec.europa.eu/geoviewer/ ) 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 - DIVAnd 6-year seasonal analysis of Water body dissolved inorganic nitrogen (DIN) 1980/2018 v2021

Moving 6-year analysis of Water body dissolved inorganic nitrogen (DIN) in the Baltic Sea. Four seasons (March-May, June-August, September-November, December-February). Every year of the time dimension corresponds to a 6-year centred average. Periods span between 1980-1985 and 2013-2018. Analyses for depths (m) (HELCOM standard depths): 0, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275, 300.

Data Sources: observational data from SeaDataNet/EMODnet Chemistry Data Network. Description of DIVA analysis: Geostatistical data analysis by DIVA (Data-Interpolating Variational Analysis) tool. GEBCO Grid (30 arc-seconds) topography is used for the contouring preparation. Files contain analysed fields, error fields and combined field with the deepest value for each grid point selected. Also pre-masked fields using relative error threshold 0.3 and 0.5 are included. In the analyses the Correlation length in the horizontal direction were fixed to 80 km and in the vertical direction to 25 m. Signal to noise ratio were fixed to 1.0. Background fields were created using data for the given time period and season. Log transformation was used in the analyses. No detrending, advection constraints or weighting are applied. Unit is umol/l.